Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T02703 Target Info
Target Name Nitric-oxide synthase inducible (NOS2)
Synonyms iNOS; Peptidyl-cysteine S-nitrosylase NOS2; Nitric oxide synthase, inducible; NOS2A; NOS type II; Inducible NOS; Inducible NO synthase; Hepatocyte NOS; HEP-NOS
Target Type Clinical trial Target
Gene Name NOS2
Biochemical Class Paired donor oxygen oxidoreductase
UniProt ID
NOS2_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Arginine Ligand Info
Structure Description HUMAN INDUCIBLE NITRIC OXIDE SYNTHASE, ZN-BOUND, L-ARG COMPLEX PDB:1NSI
Method X-ray diffraction Resolution 2.55 Å Mutation No [1]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEFTQLCID
292
LGWKPKYGRF
302
DVVPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
LHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
Loading data...
Dynamically generated for selected residues.
Nodes can be dragged or clicked.
    
Label:

Selection: Name:   

Defined Sets:
Set Operations:

Select:
Name:
   
Specification Tips:

Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.

PDB ID:
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.

Option 1, search with your selection (all residues are selected by default) in the loaded structures:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

Option 2, search with PDB ID and chain name:
PDB ID:   Chain Name:


Option 3, search with a PDB file:
PDB File:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

1. your selection (all residues are selected by default) in the loaded structures to Foldseek web server.

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:
Note: AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100:
  Very high (pLDDT > 90)
  Confident (90 > pLDDT > 70)
  Low (70 > pLDDT > 50)
  Very low (pLDDT < 50)

AlphaFold Uniprot ID:



PAE Map:
NCBI Protein Accession:
Orientations of Proteins in Membranes(OPM) PDB ID:
Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.

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,20C
1TUP_A,100,101,,,132,,,,
1TUP_B,110,111,,141,142,,,,
1TUP_C,,,,,,,200,201,230
The 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:

Enter the PDB IDs or MMDB IDs of the structures:

ID1:       ID2:

VAST+ based on VAST:    

VAST+ based on TM-align:

Enter two AlphaFold Uniprot IDs:

ID1:       ID2:

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:
AlphaFold PAE File:

File type:
URL in the same host:
Multiple mmCIF Files:
mmCIF ID:
MMDB or PDB ID:




Note: The "biological unit" is the biochemically active form of a biomolecule,
List of PDB, MMDB, or AlphaFold UniProt structures:



or


Note: The "biological unit" is the biochemically active form of a biomolecule,
Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the 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.

Protein Sequence ID(NCBI protein accession of a sequence):
or FASTA sequence:


Aligned Protein Accession (or a chain of a PDB):
The sequence to structure prediction is done via ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here.

FASTA sequence:


Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".


Protein/Gene name:
PubChem CID/Name/InchI:
Chemical SMILES:
Multiple iCn3D PNG images:
State file:
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.

Share Link URL:


Selection file:
Collection File:

You can load a collection of structures via a file. Here are some example files

Collection file:


Structures:





Preference file:
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ




fofc contour at default threshold or at: σ





Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


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:




Click in the input box to use the color picker:

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)

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


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.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

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:


1. Choose interaction types and their thresholds:
Hydrogen Bonds    
Å   
Salt Bridge/Ionic    
Å   
Contacts/Interactions    
Å   
Halogen Bonds    
Å   
π-Cation    
Å   
π-Stacking    
Å   
2. Select the first set:
3. Select the second set:
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:
Helix or Sheet: Coil or Nucleotide: Disulfide Bonds:
Hydrogen Bonds: Salt Bridge/Ionic: Contacts:
Halogen Bonds: π-Cation: π-Stacking:
(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:

051015202530
Expected position error (Angstroms)

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
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

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

1. Text:
2. Size:
3. Color:
4. Pick TWO atoms while holding "Alt" key
5.
1. Text:
2. Size:
3. Color:
4.
Color for all labels:

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
First set:
Second set:
2. Color:

3.
1. Select two sets
First set:
Second set:
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
First sets:
Second sets:
2.
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
First sets:
Second sets:
2.
1. Pick TWO atoms while holding "Alt" key
2.
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)
   
Note: The following parameters will be saved in cache. You just need to set them once.

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)

   
Note: The following parameters will be saved in cache. You just need to set them once.





Note: Show exons for all isoforms of the protein in the same gene as specified below.

NCBI Gene ID:    

Position of the first residue in Sequences & Annotations window:

Name:



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: 
All  Conserved Domains  ClinVar  Functional Sites  
Custom  3D Domains  SNPs  PTM (UniProt)  
Disulfide Bonds  Interactions  Cross-Linkages  Transmembrane  
Ig Domains  



Zoom: mouse wheel;     Move: left button;     Select Multiple Nodes: Ctrl Key and drag an Area   
       
Force on Nodes:
   Label Size:    
Internal Edges:
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm:
(0-20% out is considered "in". 50-100% out is considered "out".)

Toal: Å2

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 1, X: Y: Z:
Vector 2, X: Y: Z:



The angle is: degree.

0: 4: 8: 12:
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:



Residue
Distance (Å)
GLN263
2.870
ARG266
4.830
TRP346
4.670
TYR347
3.426
PRO350
3.546
VAL352
3.924
ASN370
4.677
Residue
Distance (Å)
GLY371
3.851
TRP372
3.034
TYR373
2.901
MET374
4.700
GLU377
2.869
ILE378
4.843
ASP382
2.714
Ligand Name: Ethylisothiourea Ligand Info
Structure Description HUMAN INDUCIBLE NITRIC OXIDE SYNTHASE WITH INHIBITOR PDB:4NOS
Method X-ray diffraction Resolution 2.25 Å Mutation No [2]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEFTQLCID
292
LGWKPKYGRF
302
DVVPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
IHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
D
Loading data...
Dynamically generated for selected residues.
Nodes can be dragged or clicked.
    
Label:

Selection: Name:   

Defined Sets:
Set Operations:

Select:
Name:
   
Specification Tips:

Note: VAST+ finds other macromolecular structures that have a similar biological unit. To do this, VAST+ takes into consideration the complete set of 3D domains that VAST identified within a query structure, throughout all of its component protein molecules, and finds other macromolecular structures that have a similar set of proteins/3D domains.

PDB ID:
Note: VAST identifies 3D domains (substructures) within each protein structure in the Molecular Modeling Database (MMDB), and then finds other protein structures that have one or more similar 3D domains, using purely geometric criteria. You have two ways to do a VAST search.

Option 1, search with your selection (all residues are selected by default) in the loaded structures:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

Option 2, search with PDB ID and chain name:
PDB ID:   Chain Name:


Option 3, search with a PDB file:
PDB File:
Searching against: Medium-redundancy Subset of PDB ? All of PDB

1. your selection (all residues are selected by default) in the loaded structures to Foldseek web server.

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:
Note: AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100:
  Very high (pLDDT > 90)
  Confident (90 > pLDDT > 70)
  Low (70 > pLDDT > 50)
  Very low (pLDDT < 50)

AlphaFold Uniprot ID:



PAE Map:
NCBI Protein Accession:
Orientations of Proteins in Membranes(OPM) PDB ID:
Note: Several PDB files could be concatenated into a single PDB file. Use the line "ENDMDL" to separate PDB files.

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,20C
1TUP_A,100,101,,,132,,,,
1TUP_B,110,111,,141,142,,,,
1TUP_C,,,,,,,200,201,230
The 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:

Enter the PDB IDs or MMDB IDs of the structures:

ID1:       ID2:

VAST+ based on VAST:    

VAST+ based on TM-align:

Enter two AlphaFold Uniprot IDs:

ID1:       ID2:

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:
AlphaFold PAE File:

File type:
URL in the same host:
Multiple mmCIF Files:
mmCIF ID:
MMDB or PDB ID:




Note: The "biological unit" is the biochemically active form of a biomolecule,
List of PDB, MMDB, or AlphaFold UniProt structures:



or


Note: The "biological unit" is the biochemically active form of a biomolecule,
Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the 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.

Protein Sequence ID(NCBI protein accession of a sequence):
or FASTA sequence:


Aligned Protein Accession (or a chain of a PDB):
The sequence to structure prediction is done via ESM Metagenomic Atlas. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion here.

FASTA sequence:


Your note will be saved in the HTML file when you click "File > Save File > iCn3D PNG Image".


Protein/Gene name:
PubChem CID/Name/InchI:
Chemical SMILES:
Multiple iCn3D PNG images:
State file:
Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click "Show Originial View". Note the version in the parameter "v" was used to replace "full.html" with "full_[v].html" in the URL.

Share Link URL:


Selection file:
Collection File:

You can load a collection of structures via a file. Here are some example files

Collection file:


Structures:





Preference file:
Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


2fofc contour at default threshold or at: σ




fofc contour at default threshold or at: σ





Note: Always load a PDB file before loading map files. If you don't specify the threshold below, a default one will be chosen.


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:




Click in the input box to use the color picker:

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)

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


Note: Always load a PDB file before loading a PQR or DelPhi potential file.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

Grid Size: Salt Concentration: M

PQR File:

Phi File:

Cube File:


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.

Surface with max potential at: kT/e(25.6mV at 298K)

Surface: Opacity: Wireframe:

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:


1. Choose interaction types and their thresholds:
Hydrogen Bonds    
Å   
Salt Bridge/Ionic    
Å   
Contacts/Interactions    
Å   
Halogen Bonds    
Å   
π-Cation    
Å   
π-Stacking    
Å   
2. Select the first set:
3. Select the second set:
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:
Helix or Sheet: Coil or Nucleotide: Disulfide Bonds:
Hydrogen Bonds: Salt Bridge/Ionic: Contacts:
Halogen Bonds: π-Cation: π-Stacking:
(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:

051015202530
Expected position error (Angstroms)

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
Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

1. Extracellular membrane Z-axis position: Å

2. intracellular membrane Z-axis position: Å

3. the adjusted membranes

Note: The membranes are parallel to the X-Y plane. The center of the membranes is at Z = 0.

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

1. Text:
2. Size:
3. Color:
4. Pick TWO atoms while holding "Alt" key
5.
1. Text:
2. Size:
3. Color:
4.
Color for all labels:

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
First set:
Second set:
2. Color:

3.
1. Select two sets
First set:
Second set:
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
First sets:
Second sets:
2.
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
First sets:
Second sets:
2.
1. Pick TWO atoms while holding "Alt" key
2.
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)
   
Note: The following parameters will be saved in cache. You just need to set them once.

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)

   
Note: The following parameters will be saved in cache. You just need to set them once.





Note: Show exons for all isoforms of the protein in the same gene as specified below.

NCBI Gene ID:    

Position of the first residue in Sequences & Annotations window:

Name:



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: 
All  Conserved Domains  ClinVar  Functional Sites  
Custom  3D Domains  SNPs  PTM (UniProt)  
Disulfide Bonds  Interactions  Cross-Linkages  Transmembrane  
Ig Domains  



Zoom: mouse wheel;     Move: left button;     Select Multiple Nodes: Ctrl Key and drag an Area   
       
Force on Nodes:
   Label Size:    
Internal Edges:
Solvent Accessible Surface Area(SASA) calculated using the EDTSurf algorithm:
(0-20% out is considered "in". 50-100% out is considered "out".)

Toal: Å2

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 1, X: Y: Z:
Vector 2, X: Y: Z:



The angle is: degree.

0: 4: 8: 12:
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:



Residue
Distance (Å)
PRO350
3.750
ALA351
4.911
VAL352
3.889
PHE369
3.101
ASN370
3.952
Residue
Distance (Å)
GLY371
3.759
TRP372
3.252
TYR373
4.130
MET374
4.577
GLU377
2.760
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: BH4 Ligand Info
Structure Description Structure of human INOSOX with inhibitor AR-C95791 PDB:3E7G
Method X-ray diffraction Resolution 2.20 Å Mutation No [3]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEFTQLCID
292
LGWKPKYGRF
302
DVVPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
LHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H4B or .H4B2 or .H4B3 or :3H4B;style chemicals stick;color identity;select .A:118 or .A:119 or .A:120 or .A:381 or .A:462 or .A:463; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER118
3.139
ILE119
4.478
MET120
3.373
Residue
Distance (Å)
ARG381
3.519
ILE462
3.122
TRP463
3.192
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: flavin mononucleotide Ligand Info
Structure Description Human iNOS Reductase and Calmodulin Complex PDB:3HR4
Method X-ray diffraction Resolution 2.50 Å Mutation No [4]
PDB Sequence
REIPLKVLVK
520
AVLFACMLMR
530
KTMASRVRVT
540
ILFATETGKS
550
EALAWDLGAL
560

FSCAFNPKVV
570
CMDKYRLSCL
580
EEERLLLVVT
590
STFGNGDCPG
600
NGEKLKKSLF
610

MLKELNNKFR
620
YAVFGLGSSM
630
YPRFCAFAHD
640
IDQKLSHLGA
650
SQLTPMGEGD
660

ELSGQEDAFR
670
SWAVQTFKAA
680
CETFDVRGKQ
690
HIQIPKLYT
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FMN or .FMN2 or .FMN3 or :3FMN;style chemicals stick;color identity;select .A:544 or .A:545 or .A:546 or .A:547 or .A:548 or .A:549 or .A:550 or .A:591 or .A:592 or .A:593 or .A:594 or .A:595 or .A:596 or .A:626 or .A:627 or .A:628 or .A:631 or .A:633 or .A:634 or .A:635 or .A:636 or .A:661 or .A:665; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA544
4.436
THR545
2.428
GLU546
2.581
THR547
2.363
GLY548
3.054
LYS549
2.674
SER550
2.744
SER591
2.850
THR592
2.865
PHE593
3.479
GLY594
3.203
ASN595
4.322
Residue
Distance (Å)
GLY596
3.925
LEU626
3.497
GLY627
3.151
SER628
3.222
TYR631
3.444
ARG633
2.836
PHE634
3.286
CYS635
2.725
ALA636
4.747
GLU661
2.943
GLN665
3.370
Ligand Name: (R)-6-(3-Amino-2-(5-(2-(6-Amino-4-Methylpyridin-2-Yl)ethyl)pyridin-3-Yl)propyl)-4-Methylpyridin-2-Amine Ligand Info
Structure Description Structure of human iNOS heme domain in complex with (R)-6-(3-AMINO-2-(5-(2-(6-AMINO-4- METHYLPYRIDIN-2-YL)ETHYL)PYRIDIN-3-YL)PROPYL)-4- METHYLPYRIDIN-2-AMINE PDB:4CX7
Method X-ray diffraction Resolution 3.16 Å Mutation No [5]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGICLGSI
119
MTPKSLTRGP
129
RDKPTPPDEL
139

LPQAIEFVNQ
149
YYGSFKEAKI
159
EEHLARVEAV
169
TKEIETTGTY
179
QLTGDELIFA
189

TKQAWRNAPR
199
CIGRIQWSNL
209
QVFDARSCST
219
AREMFEHICR
229
HVRYSTNNGN
239

IRSAITVFPQ
249
RSDGKHDFRV
259
WNAQLIRYAG
269
YQMPDGSIRG
279
DPANVEFTQL
289

CIDLGWKPKY
299
GRFDVVPLVL
309
QANGRDPELF
319
EIPPDLVLEV
329
AMEHPKYEWF
339

RELELKWYAL
349
PAVANMLLEV
359
GGLEFPGCPF
369
NGWYMGTEIG
379
VRDFCDVQRY
389

NILEEVGRRM
399
GLETHKLASL
409
WKDQAVVEIN
419
IAVLHSFQKQ
429
NVTIMDHHSA
439

AESFMKYMQN
449
EYRSRGGCPA
459
DWIWLVPPMS
469
GSITPVFHQE
479
MLNYVLSPFY
489

YYQVEAWKTH
499
VWQD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .S71 or .S712 or .S713 or :3S71;style chemicals stick;color identity;select .A:120 or .A:121 or .A:199 or .A:263 or .A:266 or .A:350 or .A:352 or .A:369 or .A:370 or .A:371 or .A:372 or .A:373 or .A:374 or .A:377 or .A:463 or .A:491; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
MET120
3.189
THR121
3.667
ARG199
3.850
GLN263
3.258
ARG266
4.497
PRO350
3.695
VAL352
3.820
PHE369
4.191
Residue
Distance (Å)
ASN370
4.084
GLY371
3.839
TRP372
2.692
TYR373
3.826
MET374
4.106
GLU377
2.637
TRP463
3.823
TYR491
3.649
Ligand Name: 4a-Carbinolamine tetrahydrobiopterin Ligand Info
Structure Description HUMAN INDUCIBLE NITRIC OXIDE SYNTHASE WITH INHIBITOR PDB:4NOS
Method X-ray diffraction Resolution 2.25 Å Mutation No [2]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEFTQLCID
292
LGWKPKYGRF
302
DVVPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
IHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H2B or .H2B2 or .H2B3 or :3H2B;style chemicals stick;color identity;select .A:118 or .A:119 or .A:120 or .A:381 or .A:462 or .A:463; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER118
2.600
ILE119
4.583
MET120
3.842
Residue
Distance (Å)
ARG381
3.215
ILE462
3.075
TRP463
3.062
Ligand Name: Ethyl 4-[(4-methylpyridin-2-yl)amino]piperidine-1-carboxylate Ligand Info
Structure Description Structure of human INOSOX with inhibitor AR-C95791 PDB:3E7G
Method X-ray diffraction Resolution 2.20 Å Mutation No [3]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEFTQLCID
292
LGWKPKYGRF
302
DVVPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
LHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AT2 or .AT22 or .AT23 or :3AT2;style chemicals stick;color identity;select .A:263 or .A:265 or .A:266 or .A:280 or .A:346 or .A:347 or .A:350 or .A:351 or .A:352 or .A:369 or .A:370 or .A:371 or .A:372 or .A:373 or .A:377 or .A:382 or .A:388; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN263
3.198
ILE265
4.176
ARG266
3.399
ASP280
4.652
TRP346
4.884
TYR347
2.862
PRO350
3.628
ALA351
4.189
VAL352
3.854
Residue
Distance (Å)
PHE369
3.696
ASN370
4.024
GLY371
3.672
TRP372
3.284
TYR373
3.619
GLU377
2.614
ASP382
3.615
ARG388
3.251
Ligand Name: Ferroheme c(2-) Ligand Info
Structure Description Structure of double mutant of human iNOS oxygenase domain with bound immidazole PDB:3EJ8
Method X-ray diffraction Resolution 2.55 Å Mutation Yes [3]
PDB Sequence
RHVRIKNWGS
92
GMTFQDTLHH
102
KAKGILTCRS
112
KSCLGSIMTP
122
KSLTRGPRDK
132

PTPPDELLPQ
142
AIEFVNQYYG
152
SFKEAKIEEH
162
LARVEAVTKE
172
IETTGTYQLT
182

GDELIFATKQ
192
AWRNAPRCIG
202
RIQWSNLQVF
212
DARSCSTARE
222
MFEHICRHVR
232

YSTNNGNIRS
242
AITVFPQRSD
252
GKHDFRVWNA
262
QLIRYAGYQM
272
PDGSIRGDPA
282

NVEITQLCID
292
LGWKPKYGRF
302
DVLPLVLQAN
312
GRDPELFEIP
322
PDLVLEVAME
332

HPKYEWFREL
342
ELKWYALPAV
352
ANMLLEVGGL
362
EFPGCPFNGW
372
YMGTEIGVRD
382

FCDVQRYNIL
392
EEVGRRMGLE
402
THKLASLWKD
412
QAVVEINIAV
422
LHSFQKQNVT
432

IMDHHSAAES
442
FMKYMQNEYR
452
SRGGCPADWI
462
WLVPPMSGSI
472
TPVFHQEMLN
482

YVLSPFYYYQ
492
VEAWKTHVWQ
502
D
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HEC or .HEC2 or .HEC3 or :3HEC;style chemicals stick;color identity;select .A:190 or .A:194 or .A:197 or .A:199 or .A:200 or .A:201 or .A:202 or .A:205 or .A:209 or .A:242 or .A:355 or .A:369 or .A:370 or .A:371 or .A:372 or .A:373 or .A:374 or .A:377 or .A:381 or .A:463 or .A:489 or .A:491; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
THR190
4.221
TRP194
3.220
ALA197
4.254
ARG199
3.670
CYS200
2.532
ILE201
4.098
GLY202
3.942
GLN205
3.342
LEU209
3.724
SER242
3.446
MET355
3.855
Residue
Distance (Å)
PHE369
3.350
ASN370
3.605
GLY371
3.500
TRP372
3.290
TYR373
4.829
MET374
4.286
GLU377
3.573
ARG381
4.979
TRP463
3.530
TYR489
3.559
TYR491
2.379
References  Top
REF 1 Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase. J Biol Chem. 1999 Jul 23;274(30):21276-84.
REF 2 Structural characterization of nitric oxide synthase isoforms reveals striking active-site conservation. Nat Struct Biol. 1999 Mar;6(3):233-42.
REF 3 Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase. Nat Chem Biol. 2008 Nov;4(11):700-7.
REF 4 Regulation of Interdomain Interactions by CaM in Inducible Nitric Oxide Synthase
REF 5 The mobility of a conserved tyrosine residue controls isoform-dependent enzyme-inhibitor interactions in nitric oxide synthases. Biochemistry. 2014 Aug 19;53(32):5272-9.

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