Binding Site Information of Target
Target General Information | Top | ||||
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Target ID | T77594 | Target Info | |||
Target Name | Endoplasmic reticulum chaperone BiP (HSPA5) | ||||
Synonyms | Immunoglobulin heavy chainbinding protein; Immunoglobulin heavy chain-binding protein; Heat shock protein family A member 5; Heat shock protein 70 family protein 5; Heat shock 70 kDa protein 5; HSP70 family protein 5; GRP78; GRP-78; Endoplasmic reticulum lumenal Ca(2+)binding protein grp78; Binding-immunoglobulin protein; BiP; 78 kDa glucose-regulated protein | ||||
Target Type | Clinical trial Target | ||||
Gene Name | HSPA5 | ||||
Biochemical Class | Acid anhydride hydrolase | ||||
UniProt ID |
Drug Binding Sites of Target | Top | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Ligand Name: Adenosine triphosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | BiP-ATP2 | PDB:6ASY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [1] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
SEDVGTVVGI
33 DLGTTYSCVG43 VFKNGRVEII53 ANDQGNRITP63 SYVAFTPEGE73 RLIGDAAKNQ 83 LTSNPENTVF93 DAKRLIGRTW103 NDPSVQQDIK113 FLPFKVVEKK123 TKPYIQVDIG 133 GGQTKTFAPE143 EISAMVLTKM153 KETAEAYLGK163 KVTHAVVTVP173 AYFNDAQRQA 183 TKDAGTIAGL193 NVMRIINEPT203 AAAIAYGLDK213 REGEKNILVF223 DLGGGTFDVS 233 LLTIDNGVFE243 VVATNGDTHL253 GGEDFDQRVM263 EHFIKLYKKK273 TGKDVRKDNR 283 AVQKLRREVE293 KAKRALSSQH303 QARIEIESFY313 EGEDFSETLT323 RAKFEELNMD 333 LFRSTMKPVQ343 KVLEDSDLKK353 SDIDEIVLVG363 GSTRIPKIQQ373 LVKEFFNGKE 383 PSRGINPDEA393 VAYGAAVQAG403 VLSGDQDTGD413 LVLLDVCPLT423 LGIETVGGVM 433 TKLIPRNTVV443 PTKKSQIFSV453 GGTVTIKVYE463 GERPLTKDNH473 LLGTFDLTGI 483 PPAPRGVPQI493 EVTFEIDVNG503 ILRVTAEDKG513 TGNKNKITIT523 NDQNRLTPEE 533 IERMVNDAEK543 FAEEDKKLKE553 RIDTRNELES563 YAYSLKNQIG573 DKEKLGGKLS 583 SEDKETMEKA593 VEEKIEWLES603 HQDADIEDFK613 AKKKELEEIV623 QPIISK |
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☰Loading data... Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
ASP34
3.915
LEU35
4.540
GLY36
3.326
THR37
2.660
THR38
3.028
TYR39
3.242
LYS96
2.736
GLU201
2.871
ASP224
4.765
GLY226
3.366
GLY227
2.734
GLY228
3.040
THR229
2.803
GLY255
3.388
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: Adenosine monophosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | A novel and unique ATP hydrolysis to AMP by a human Hsp70 BiP | PDB:7N1R | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | No | [2] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
SEDVGTVVGI
33 DLGTTYSCVG43 VFKNGRVEII53 ANDQGNRITP63 SYVAFTPEGE73 RLIGDAAKNQ 83 LTSNPENTVF93 DAKRLIGRTW103 NDPSVQQDIK113 FLPFKVVEKK123 TKPYIQVDIG 133 GGQTKTFAPE143 EISAMVLTKM153 KETAEAYLGK163 KVTHAVVTVP173 AYFNDAQRQA 183 TKDAGTIAGL193 NVMRIINEPT203 AAAIAYGLDK213 REGEKNILVF223 DLGGGTFDVS 233 LLTIDNGVFE243 VVATNGDTHL253 GGEDFDQRVM263 EHFIKLYKKK273 TGKDVRKDNR 283 AVQKLRREVE293 KAKRALSSQH303 QARIEIESFY313 EGEDFSETLT323 RAKFEELNMD 333 LFRSTMKPVQ343 KVLEDSDLKK353 SDIDEIVLVG363 GSTRIPKIQQ373 LVKEFFNGKE 383 PSRGINPDEA393 VAYGAAVQAG403 VLSGDQDTGD413 LVLLDVCPLT423 LGIETVGGVM 433 TKLIPRNTVV443 PTKKSQIFSV453 GGTVTIKVYE463 GERPLTKDNH473 LLGTFDLTGI 483 PPAPRGVPQI493 EVTFEIDVNG503 ILRVTAEDKG513 TGNKNKITIT523 NDQNRLTPEE 533 IERMVNDAEK543 FAEEDKKLKE553 RIDTRNELES563 YAYSLKNQIG573 DKEKLGGKLS 583 SEDKETMEKA593 VEEKIEWLES603 HQDADIEDFK613 AKKKELEEIV623 QPIISK |
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☰Loading data... Dynamically generated for selected residues. Nodes can be dragged or clicked. Label: Selection: Name:
PDB ID: Option 1, search with your selection (all residues are selected by default) in the loaded structures: Option 2, search with PDB ID and chain name: PDB ID: Chain Name: Option 3, search with a PDB file: Foldseek web server. 1. your selection (all residues are selected by default) in the loaded structures to 2 (Optional). Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. The PDB chain IDs are the same as the record names such as "1HHO_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v4" is "P69905". Chain ID List: BCIF/MMTF ID: PDB ID: Very high (pLDDT > 90) Confident (90 > pLDDT > 70) Low (70 > pLDDT > 50) Very low (pLDDT < 50) AlphaFold Uniprot ID: PAE Map: NCBI Protein Accession: PDB File: Multiple PDB Files: The custom JSON file on residue colors has the following format for proteins("ALA" and "ARG") and nucleotides("G" and "A"): {"ALA":"#C8C8C8", "ARG":"#145AFF", ..., "G":"#008000", "A":"#6080FF", ...} Residue Color File: The custom file for the structure has two columns separated by space or tab: residue number, and score in the range of 0-100. If you click "Apply Custom Color" button, the scores 0, 50 and 100 correspond to the three colors specified below. If you click "Apply Custom Tube", the selected residues will be displayed in a style similar to "B-factor Tube". Custom File: 1. Score to Color: 0: 50: 100: or 2. You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas. refnum,11,12,,21,22,,10C,11C,20CThe first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure. To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the Specification. For example, "%12" selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A. Custom File: ID1: ID2: VAST+ based on VAST: VAST+ based on TM-align: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: The sequence alignment (followed by structure alignment) is based on residue numbers in the First/Master chain: (Note: To align chains in custom PDB files, you could load them in "File > Open File > PDB Files (appendable)" and click "Analysis > Defined Sets". Finally select multiple chains in Defined Sets and click "File > Realign Selection".) All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Option 1: Option 2: All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures). Chain IDs: Each alignment is defined as " | "-separated residue lists in one line. "10-50" means a range of residues from 10 to 50. Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[uppercase PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A". If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page". Mutations: ID Type: PDB IDAlphaFold UniProt ID Show Mutation in: Current PageNew Page Mol2 File: SDF File: XYZ File: URL in the same host: Multiple mmCIF Files: mmCIF ID: Note: The "biological unit" is the biochemically active form of a biomolecule, or Note: The "biological unit" is the biochemically active form of a biomolecule, BLAST search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used. Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the Protein Sequence ID(NCBI protein accession of a sequence): or FASTA sequence: Aligned Protein Accession (or a chain of a PDB): ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here. The sequence to structure prediction is done via FASTA sequence: Protein/Gene name: PubChem CID/Name/InchI: Chemical SMILES: Share Link URL: Collection File: Structures: 2fofc contour at default threshold or at: σ fofc contour at default threshold or at: σ 2fofc contour at default threshold or at: σ URL in the same host: fofc contour at default threshold or at: σ URL in the same host: Custom Color: Grid Size: Salt Concentration: M Potential contour at: kT/e(25.6mV at 298K) Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Grid Size: Salt Concentration: M Surface with max potential at: kT/e(25.6mV at 298K) Surface: Opacity: Wireframe: Note: Only the selected residues are used for DelPhi potential calculation by solving linear Poisson-Boltzmann equation. Potential contour at: kT/e(25.6mV at 298K) Note: Always load a PDB file before loading a PQR or DelPhi potential file. Potential contour at: kT/e(25.6mV at 298K) Grid Size: Salt Concentration: M PQR URL in the same host: Phi URL in the same host: Cube URL in the same host: Note: Always load a PDB file before loading a PQR or DelPhi potential file. Symmetry: Distance: Contact Type:
4. Sort Interactions on: to show two lines of residue nodes to show map with atom details to show interactions with strength parameters in 0-200:
(Note: you can also adjust thresholds at #1 to add/remove interactions.) 5. and select new sets 1. Select sets below or use your current selection: 2. 1. Select sets below or use your current selection. 2. 1. Select sets below or use your current selection: 2. Overall maximum RMSD: Å 3. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. 1. Select sets below: 2. Hold Ctrl key to select multiple nodes/lines. Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Note: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. Color legend for interactions (dashed lines): Green: H-Bonds; Cyan: Salt Bridge/Ionic; Grey: Contacts Magenta: Halogen Bonds; Red: π-Cation; Blue: π-Stacking Scale: Hold Ctrl key to select multiple nodes. Scale: Hold Ctrl key to select multiple nodes. Scale:
Contour at: σ Contour at: σ Contour at: % of maximum EM values 1. Select the first set: 2. Sphere with a radius: Å 3. Select the second set to apply the sphere: 4. the sphere around the first set of atoms interacting/contacting residue pairs in a file 1. Extracellular membrane Z-axis position: Å 2. intracellular membrane Z-axis position: Å 3. the adjusted membranes 1. Z-axis position of the first X-Y plane: Å 2. Z-axis position of the second X-Y plane: Å 3. the region between the planes to Defined Sets 2. Size: 3. Color: 4. Pick TWO atoms while holding "Alt" key 5. 2. Size: 3. Color: 4. 1. Pick TWO atoms while holding "Alt" key 2. Line Color: 3. 1. Pick TWO atoms while holding "Alt" key 2. Color: 3. 1. Select two sets
3. 1. Select two sets
2. Line style: 3. Line radius: 4. Color: 5. Opacity: 6. 1. Select a set: 2. Shape: 3. Radius: 4. Color: 5. Opacity: 6. 1. Select sets for pairwise distances
Note: Each set is represented by a vector, which is the X-axis of the principle axes. The angles between the vectors are then calculated. 1. Select sets for pairwise angles
1. Pick TWO atoms while holding "Alt" key 2. Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 1. Shininess: (for the shininess of the 3D objects, default 40) 2. Three directional lights: Key Light: (for the light strength of the key light, default 0.8) Fill Light: (for the light strength of the fill light, default 0.4) Back Light: (for the light strength of the back light, default 0.2) 3. Thickness: Line Radius: (for stabilizers, hydrogen bonds, distance lines, default 0.1) Coil Radius: (for coils, default 0.3) Stick Radius: (for sticks, default 0.4) Cross-Linkage Radius: (for cross-linkages, default 0.4) Trace Radius: (for C alpha trace, O3' trace, default 0.4) Ribbon Thickness: (for helix and sheet ribbons, nucleotide ribbons, default 0.2) Protein Ribbon Width: (for helix and sheet ribbons, default 1.3) Nucleotide Ribbon Width: (for nucleotide ribbons, default 0.8) Ball Scale: (for styles 'Ball and Stick' and 'Dot', default 0.3) 4. Show Glycan Cartoon: (0: hide, 1: show, default 0) 5. Show Membrane: (0: hide, 1: show, default 1) 6. Enlarge Command Window: (0: Regular, 1: Large, default 0) 1. URLs Used in Browsers Please copy one of the URLs below. They show the same result. (To add a title to share link, click "Windows > Your Note" and click "File > Share Link" again.) Original URL with commands: Lifelong Short URL:(To replace this URL, send a pull request to update share.html at iCn3D GitHub) Lifelong Short URL + Window Title:(To update the window title, click "Analysis > Your Note/Window Title".) 2. Commands Used in Jupyter Noteboook Please copy the following commands into a cell in Jupyter Notebook to show the same result. More details are at https://github.com/ncbi/icn3d/tree/master/jupyternotebook. Annotations:
Zoom: mouse wheel; Move: left button; Select Multiple Nodes: Ctrl Key and drag an Area Force on Nodes: Label Size: Internal Edges: Color each residue based on the percentage of solvent accessilbe surface area. The color ranges from blue, to white, to red for a percentage of 0, 35(variable), and 100, respectively. Middle Percentage(White): % Select residue based on the percentage of solvent accessilbe surface area. The values are in the range of 0-100. Min Percentage: % Max Percentage: % Select residue based on B-factor/pLDDT. The values are in the range of 0-100. Min B-factor/pLDDT: % Max B-factor/pLDDT: % X: Y: Z: Vector 2, X: Y: Z: The angle is: degree. 1: 5: 9: 13: 2: 6: 10: 14: 3: 7: 11: 15: Choose an Ig template for selected residues: Choose an Ig template to align with selected residues: |
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Ligand Name: VER-155008 | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of ATPase domain of Human GRP78 bound to Ver155008 | PDB:6CZ1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.68 Å | Mutation | No | [3] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3FD or .3FD2 or .3FD3 or :33FD;style chemicals stick;color identity;select .A:39 or .A:59 or .A:61 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: dATP | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 2'-deoxy-ADP and inorganic phosphate | PDB:5F0X | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DTP or .DTP2 or .DTP3 or :3DTP;style chemicals stick;color identity;select .A:60 or .A:296 or .A:297 or .A:300 or .A:301 or .A:364 or .A:365 or .A:367 or .A:368 or .A:389 or .A:391; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: adenosine diphosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ADP and inorganic phosphate | PDB:5EVZ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ADP or .ADP2 or .ADP3 or :3ADP;style chemicals stick;color identity;select .A:34 or .A:36 or .A:37 or .A:38 or .A:39 or .A:61 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP34
4.544
GLY36
4.146
THR37
3.677
THR38
2.593
TYR39
2.784
ILE61
4.334
ASP224
4.734
LEU225
4.699
GLY226
3.176
GLY227
2.803
GLY228
4.348
THR229
3.845
GLY255
3.413
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: L-betagamma-meATP | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with AMP-PCP | PDB:5F2R | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
VGTVVGIDLG
36 TTYSCVGVFK46 NGRVEIIAND56 QGNRITPSYV66 AFTPEGERLI76 GDAAKNQLTS 86 NPENTVFDAK96 RLIGRTWNDP106 SVQQDIKFLP116 FKVVEKKTKP126 YIQVDIGGGQ 136 TKTFAPEEIS146 AMVLTKMKET156 AEAYLGKKVT166 HAVVTVPAYF176 NDAQRQATKD 186 AGTIAGLNVM196 RIINEPTAAA206 IAYGLDKREG216 EKNILVFDLG226 GGTFDVSLLT 236 IDNGVFEVVA246 TNGDTHLGGE256 DFDQRVMEHF266 IKLYKKKTGK276 DVRKDNRAVQ 286 KLRREVEKAK296 RALSSQHQAR306 IEIESFYEGE316 DFSETLTRAK326 FEELNMDLFR 336 STMKPVQKVL346 EDSDLKKSDI356 DEIVLVGGST366 RIPKIQQLVK376 EFFNGKEPSR 386 GINPDEAVAY396 GAAVQAGVLS406 G
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ACP or .ACP2 or .ACP3 or :3ACP;style chemicals stick;color identity;select .A:34 or .A:35 or .A:36 or .A:37 or .A:38 or .A:39 or .A:61 or .A:96 or .A:201 or .A:224 or .A:225 or .A:226 or .A:227 or .A:229 or .A:231 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP34
4.261
LEU35
4.536
GLY36
3.405
THR37
2.871
THR38
2.807
TYR39
2.863
ILE61
4.780
LYS96
2.762
GLU201
3.618
ASP224
3.488
LEU225
4.577
GLY226
3.348
GLY227
3.158
THR229
2.514
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Ligand Name: AMP-PNP | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with AMPPNP | PDB:3LDO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [5] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .ANP or .ANP2 or .ANP3 or :3ANP;style chemicals stick;color identity;select .A:34 or .A:36 or .A:37 or .A:38 or .A:39 or .A:61 or .A:96 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ASP34
3.660
GLY36
3.269
THR37
2.570
THR38
2.704
TYR39
2.893
ILE61
4.848
LYS96
4.640
LEU225
4.885
GLY226
3.465
GLY227
2.958
GLY228
2.715
THR229
2.639
GLY255
3.402
|
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Click to View More Binding Site Information of This Target and Ligand Pair | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ligand Name: [(2R,3S,4R,5R)-5-[4-(2-acetamidoethyl)triazol-1-yl]-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of HYPE covalently tethered to BiP bound to AMP-PNP | PDB:6ZMD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.64 Å | Mutation | Yes | [6] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
GSGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGAFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SGDQDTGDLV415 LLDVCPLTLG425 IETVGGVMTK 435 LIPRNTVVPT445 KKSQIFSTAS455 DNQPTVTIKV465 YEGERPLTKD475 NHLLGTFDLT 485 GIPPAPRGVP495 QIEVTFEIDV505 NGILRVTAED515 KGTGNKNKIT525 ITNDQNRLTP 535 EEIERMVNDA545 EKF
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QMK or .QMK2 or .QMK3 or :3QMK;style chemicals stick;color identity;select .A:516 or .A:518 or .A:519; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 7-Deazaadenosine-5'-Diphosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ADP and inorganic phosphate | PDB:5EX5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7DD or .7DD2 or .7DD3 or :37DD;style chemicals stick;color identity;select .A:34 or .A:36 or .A:37 or .A:38 or .A:39 or .A:61 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP34
4.484
GLY36
4.088
THR37
3.654
THR38
2.577
TYR39
2.832
ILE61
4.264
ASP224
4.746
LEU225
4.767
GLY226
3.175
GLY227
2.958
GLY228
4.430
THR229
4.050
GLY255
3.435
|
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Ligand Name: 7-Deazaadenosine-5'-Triphosphate | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ATP | PDB:5EXW | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [4] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
VGTVVGIDLG
36 TTYSCVGVFK46 NGRVEIIAND56 QGNRITPSYV66 AFTPEGERLI76 GDAAKNQLTS 86 NPENTVFDAK96 RLIGRTWNDP106 SVQQDIKFLP116 FKVVEKKTKP126 YIQVDIGGGQ 136 TKTFAPEEIS146 AMVLTKMKET156 AEAYLGKKVT166 HAVVTVPAYF176 NDAQRQATKD 186 AGTIAGLNVM196 RIINEPTAAA206 IAYGLDKREG216 EKNILVFDLG226 GGTFDVSLLT 236 IDNGVFEVVA246 TNGDTHLGGE256 DFDQRVMEHF266 IKLYKKKTGK276 DVRKDNRAVQ 286 KLRREVEKAK296 RALSSQHQAR306 IEIESFYEGE316 DFSETLTRAK326 FEELNMDLFR 336 STMKPVQKVL346 EDSDLKKSDI356 DEIVLVGGST366 RIPKIQQLVK376 EFFNGKEPSR 386 GINPDEAVAY396 GAAVQAGVLS406 G
|
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7DT or .7DT2 or .7DT3 or :37DT;style chemicals stick;color identity;select .A:34 or .A:36 or .A:37 or .A:38 or .A:39 or .A:61 or .A:96 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:230 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASP34
3.932
GLY36
3.478
THR37
2.935
THR38
2.787
TYR39
2.762
ILE61
4.463
LYS96
4.697
LEU225
4.852
GLY226
3.407
GLY227
3.256
GLY228
2.852
THR229
2.421
PHE230
4.835
|
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Ligand Name: 8-[(Quinolin-2-Ylmethyl)amino]adenosine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with small molecule inhibitor | PDB:3LDP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [5] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 S
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3P1 or .3P12 or .3P13 or :33P1;style chemicals stick;color identity;select .A:38 or .A:39 or .A:61 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:294 or .A:296 or .A:297 or .A:300 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 7-Deaza-2'-C-methyladenosine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine | PDB:6DO2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [7] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H5V or .H5V2 or .H5V3 or :3H5V;style chemicals stick;color identity;select .A:38 or .A:39 or .A:61 or .A:225 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 8-{[(2-Chlorophenyl)methyl]amino}adenosine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol | PDB:6DWS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [8] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HFY or .HFY2 or .HFY3 or :3HFY;style chemicals stick;color identity;select .A:38 or .A:39 or .A:61 or .A:225 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:298 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 8-Aminoadenosine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 in complex with 8-aminoadenosine | PDB:6DFM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.14 Å | Mutation | No | [9] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 SNPENTVFDA95 KRLIGRTWND105 PSVQQDIKFL115 PFKVVEKKTK125 PYIQVDIGGG 135 QTKTFAPEEI145 SAMVLTKMKE155 TAEAYLGKKV165 THAVVTVPAY175 FNDAQRQATK 185 DAGTIAGLNV195 MRIINEPTAA205 AIAYGLDKRE215 GEKNILVFDL225 GGGTFDVSLL 235 TIDNGVFEVV245 ATNGDTHLGG255 EDFDQRVMEH265 FIKLYKKKTG275 KDVRKDNRAV 285 QKLRREVEKA295 KRALSSQHQA305 RIEIESFYEG315 EDFSETLTRA325 KFEELNMDLF 335 RSTMKPVQKV345 LEDSDLKKSD355 IDEIVLVGGS365 TRIPKIQQLV375 KEFFNGKEPS 385 RGINPDEAVA395 YGAAVQAGVL405 SG
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3BH or .3BH2 or .3BH3 or :33BH;style chemicals stick;color identity;select .A:38 or .A:39 or .A:61 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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Ligand Name: 8-Bromoadenosine | Ligand Info | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure Description | Crystal structure of human GRP78 in complex with 8-bromoadenosine | PDB:6DFO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-ray diffraction | Resolution | 2.54 Å | Mutation | No | [10] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PDB Sequence |
DVGTVVGIDL
35 GTTYSCVGVF45 KNGRVEIIAN55 DQGNRITPSY65 VAFTPEGERL75 IGDAAKNQLT 85 PENTVFDAKR97 LIGRTWNDPS107 VQQDIKFLPF117 KVVEKKTKPY127 IQVDIGGGQT 137 KTFAPEEISA147 MVLTKMKETA157 EAYLGKKVTH167 AVVTVPAYFN177 DAQRQATKDA 187 GTIAGLNVMR197 IINEPTAAAI207 AYGLDKREGE217 KNILVFDLGG227 GTFDVSLLTI 237 DNGVFEVVAT247 NGDTHLGGED257 FDQRVMEHFI267 KLYKKKTGKD277 VRKDNRAVQK 287 LRREVEKAKR297 ALSSQHQARI307 EIESFYEGED317 FSETLTRAKF327 EELNMDLFRS 337 TMKPVQKVLE347 DSDLKKSDID357 EIVLVGGSTR367 IPKIQQLVKE377 FFNGKEPSRG 387 INPDEAVAYG397 AAVQAGVLSG407
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GBA or .GBA2 or .GBA3 or :3GBA;style chemicals stick;color identity;select .A:38 or .A:39 or .A:61 or .A:225 or .A:226 or .A:227 or .A:255 or .A:256 or .A:259 or .A:293 or .A:296 or .A:297 or .A:300 or .A:363 or .A:364 or .A:365 or .A:367 or .A:368 or .A:391; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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References | Top | ||||
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REF 1 | Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s. Nat Commun. 2017 Oct 31;8(1):1201. | ||||
REF 2 | A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP). Protein Sci. 2022 Apr;31(4):797-810. | ||||
REF 3 | Crystallographic selection of adenosine analogs that fit the mold of the active site of human GRP78 and beyond | ||||
REF 4 | Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs. PLoS One. 2016 May 4;11(5):e0154862. | ||||
REF 5 | Adenosine-derived inhibitors of 78 kDa glucose regulated protein (Grp78) ATPase: insights into isoform selectivity. J Med Chem. 2011 Jun 23;54(12):4034-41. | ||||
REF 6 | Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD. Nat Commun. 2021 Apr 23;12(1):2426. | ||||
REF 7 | Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine | ||||
REF 8 | Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol | ||||
REF 9 | Crystal structure of human GRP78 in complex with 8-aminoadenosine | ||||
REF 10 | Crystal structure of human GRP78 in complex with 8-bromoadenosine |
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