Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T87374 | Target Info | |||
| Target Name | COVID-19 spike glycoprotein (S) | ||||
| Synonyms | COVID-19 S glycoprotein; COVID-19 E2; COVID-19 Peplomer protein | ||||
| Gene Name | COVID-19 S | ||||
| Biochemical Class | Betacoronaviruses spike protein family | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Linoleic acid | Ligand Info | |||
| Canonical SMILES | CCCCCC=CCC=CCCCCCCCC(=O)O | ||||
| InChI | 1S/C18H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h6-7,9-10H,2-5,8,11-17H2,1H3,(H,19,20)/b7-6-,10-9- | ||||
| InChIKey | OYHQOLUKZRVURQ-HZJYTTRNSA-N | ||||
| PubChem Compound ID | 5280450 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7JJI Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry) | ||||||
| Method | Electron microscopy | Resolution | 3.60 Å | Mutation | Yes | [1] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 QSQSIIAYTM 697 SLGAENSVAY707 SNNSIAIPTN717 FTISVTTEIL727 PVSMTKTSVD737 CTMYICGDST 747 ECSNLLLQYG757 SFCTQLNRAL767 TGIAVEQDKN777 TQEVFAQVKQ787 IYKTPPIKDF 797 GGFNFSQILP807 DPSKPSKRSF817 IEDLLFNKVT827 LADAGFIKQY837 GDCLGDIAAR 847 DLICAQKFNG857 LTVLPPLLTD867 EMIAQYTSAL877 LAGTITSGWT887 FGAGAALQIP 897 FAMQMAYRFN907 GIGVTQNVLY917 ENQKLIANQF927 NSAIGKIQDS937 LSSTASALGK 947 LQDVVNQNAQ957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDPP987 EAEVQIDRLI 997 TGRLQSLQTY1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS1037 KRVDFCGKGY 1047 HLMSFPQSAP1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA1087 HFPREGVFVS 1097 NGTHWFVTQR1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV1137 YDPLQPELD |
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| PDB ID: 7OD3 SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry | ||||||
| Method | Electron microscopy | Resolution | 2.80 Å | Mutation | No | [2] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 ANPVLPFNDG89 VYFASTEKSN 99 IIRGWIFGTT109 LDSKTQSLLI119 VNNNVVIKVC131 EFQFCNDPFL141 FRVYSSANNC 166 TFEYVSNLRE191 FVFKNIDGYF201 KIYSKHTPID215 LPQGFSALEP225 LVDLPIGINI 235 TRFQTLLAAA263 AYYVGYLQPR273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL 303 KSFTVEKGIY313 QTSNFRVQPT323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW 353 NRKRISNCVA363 DYSVLYNSAS373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR 403 GDEVRQIAPG413 QTGKIADYNY423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY 453 RLFRKSNLKP463 FERDISTEIY473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV 503 GYQPYRVVVL513 SFELLHAPAT523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT 553 ESNKKFLPFQ563 QFGRDIADTT573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN 603 TSNQVAVLYQ613 DVNCTTWRVY636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI 666 GAGICASYQS689 QSIIAYTMSL699 GAENSVAYSN709 NSIAIPTNFT719 ISVTTEILPV 729 SMTKTSVDCT739 MYICGDSTEC749 SNLLLQYGSF759 CTQLNRALTG769 IAVEQDKNTQ 779 EVFAQVKQIY789 KTPPIKDFGG799 FNFSQILPDP809 SKPSKRSFIE819 DLLFNKVTLG 832 FIKQYGDCLG842 DIAARDLICA852 QKFNGLTVLP862 PLLTDEMIAQ872 YTSALLAGTI 882 TSGWTFGAGA892 ALQIPFAMQM902 AYRFNGIGVT912 QNVLYENQKL922 IANQFNSAIG 932 KIQDSLSLGK947 LQDVVNQNAQ957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDKV 987 EAEVQIDRLI997 TGRLQSLQTY1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS 1037 KRVDFCGKGY1047 HLMSFPQSAP1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA 1087 HFPREGVFVS1097 NGTHWFVTQR1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV 1137 YD
|
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CYS336
4.213
PRO337
3.814
PHE338
3.861
VAL341
3.835
PHE342
4.433
ILE358
3.762
ALA363
3.808
TYR365
3.335
LEU368
4.057
TYR369
3.293
|
|||||
| PDB ID: 7ODL SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry | ||||||
| Method | Electron microscopy | Resolution | 3.03 Å | Mutation | No | [2] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 ANPVLPFNDG89 VYFASTEKSN 99 IIRGWIFGTT109 LDSKTQSLLI119 VNNATNVVIK129 VCEFQFCNDP139 FLFRVYSSAN 164 NCTFEYVSQP174 NLREFVFKNI197 DGYFKIYSKH207 TPIDLPQGFS221 ALEPLVDLPI 231 GINITRFQTL241 LAAAAYYVGY269 LQPRTFLLKY279 NENGTITDAV289 DCALDPLSET 299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF329 PNITNLCPFG339 EVFNATRFAS 349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC379 YGVSPTKLND389 LCFTNVYADS 399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPDDF429 TGCVIAWNSN439 NLDSKVGGNY 449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP479 CNGVEGFNCY489 FPLQSYGFQP 499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK529 STNLVKNKCV539 NFNFNGLTGT 549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP579 QTLEILDITP589 CSFGGVSVIT 599 PGTNTSNQVA609 VLYQDVNCTT632 WRVYSTGSNV642 FQTRAGCLIG652 AEHVNNSYEC 662 DIPIGAGICA672 SYQTQTIASQ690 SIIAYTMSLG700 AENSVAYSNN710 SIAIPTNFTI 720 SVTTEILPVS730 MTKTSVDCTM740 YICGDSTECS750 NLLLQYGSFC760 TQLNRALTGI 770 AVEQDKNTQE780 VFAQVKQIYK790 TPPIKDFGGF800 NFSQILPDPS810 KPSKRSFIED 820 LLFNKVTLGF833 IKQYGDCLGD843 IAARDLICAQ853 KFNGLTVLPP863 LLTDEMIAQY 873 TSALLAGTIT883 SGWTFGAGAA893 LQIPFAMQMA903 YRFNGIGVTQ913 NVLYENQKLI 923 ANQFNSAIGK933 IQDSLSSLGK947 LQDVVNQNAQ957 ALNTLVKQLS967 SNFGAISSVL 977 NDILSRLDKV987 EAEVQIDRLI997 TGRLQSLQTY1007 VTQQLIRAAE1017 IRASANLAAT 1027 KMSECVLGQS1037 KRVDFCGKGY1047 HLMSFPQSAP1057 HGVVFLHVTY1067 VPAQEKNFTT 1077 APAICHDGKA1087 HFPREGVFVS1097 NGTHWFVTQR1107 NFYEPQIITT1117 DNTFVSGNCD 1127 VVIGIVNNTV1137 YD
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CYS336
4.170
PRO337
4.011
PHE338
3.845
VAL341
3.715
PHE342
4.383
ILE358
4.028
ALA363
3.522
TYR365
3.494
LEU368
4.371
TYR369
3.578
|
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| PDB ID: 7DWY S protein of SARS-CoV-2 in the locked conformation | ||||||
| Method | Electron microscopy | Resolution | 2.70 Å | Mutation | Yes | [3] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPDD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 WRVYSTGSNV 642 FQTRAGCLIG652 AEHVNNSYEC662 DIPIGAGICA672 SYQTQSIIAY695 TMSLGAENSV 705 AYSNNSIAIP715 TNFTISVTTE725 ILPVSMTKTS735 VDCTMYICGD745 STECSNLLLQ 755 YGSFCTQLNR765 ALTGIAVEQD775 KNTQEVFAQV785 KQIYKTPPIK795 DFGGFNFSQI 805 LPDPSKPSKR815 SFIEDLLFNK825 VTLADAGFIK835 QYGDCLGDIA845 ARDLICAQKF 855 NGLTVLPPLL865 TDEMIAQYTS875 ALLAGTITSG885 WTFGAGAALQ895 IPFAMQMAYR 905 FNGIGVTQNV915 LYENQKLIAN925 QFNSAIGKIQ935 DSLSSTALGK947 LQDVVNQNAQ 957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDPP987 EAEVQIDRLI997 TGRLQSLQTY 1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS1037 KRVDFCGKGY1047 HLMSFPQSAP 1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA1087 HFPREGVFVS1097 NGTHWFVTQR 1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV1137 YDPLQPELD
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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 .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:336 or .A:337 or .A:338 or .A:341 or .A:342 or .A:358 or .A:363 or .A:365 or .A:368 or .A:369 or .A:374 or .A:377 or .A:387 or .A:392 or .A:395 or .A:432 or .A:434 or .A:513 or .A:515 or .A:524; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS336
3.694
PRO337
3.880
PHE338
3.815
VAL341
4.320
PHE342
4.156
ILE358
3.409
ALA363
3.784
TYR365
3.830
LEU368
3.842
TYR369
3.655
|
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| PDB ID: 7X08 S protein of SARS-CoV-2 in complex with 2G1 | ||||||
| Method | Electron microscopy | Resolution | 2.70 Å | Mutation | Yes | [4] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPDD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 WRVYSTGSNV 642 FQTRAGCLIG652 AEHVNNSYEC662 DIPIGAGICA672 SYQTQSIIAY695 TMSLGAENSV 705 AYSNNSIAIP715 TNFTISVTTE725 ILPVSMTKTS735 VDCTMYICGD745 STECSNLLLQ 755 YGSFCTQLNR765 ALTGIAVEQD775 KNTQEVFAQV785 KQIYKTPPIK795 DFGGFNFSQI 805 LPDPSKPSKR815 SPIEDLLFNK825 VTLADAGFIK835 QYGDCLGDIA845 ARDLICAQKF 855 NGLTVLPPLL865 TDEMIAQYTS875 ALLAGTITSG885 WTFGAGPALQ895 IPFPMQMAYR 905 FNGIGVTQNV915 LYENQKLIAN925 QFNSAIGKIQ935 DSLSSTALGK947 LQDVVNQNAQ 957 ALNTLVKQLS967 SNFGAISSVL977 NDILSRLDPP987 EAEVQIDRLI997 TGRLQSLQTY 1007 VTQQLIRAAE1017 IRASANLAAT1027 KMSECVLGQS1037 KRVDFCGKGY1047 HLMSFPQSAP 1057 HGVVFLHVTY1067 VPAQEKNFTT1077 APAICHDGKA1087 HFPREGVFVS1097 NGTHWFVTQR 1107 NFYEPQIITT1117 DNTFVSGNCD1127 VVIGIVNNTV1137 YDPLQPELD
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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 .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:336 or .A:337 or .A:338 or .A:341 or .A:342 or .A:358 or .A:363 or .A:365 or .A:368 or .A:369 or .A:374 or .A:377 or .A:387 or .A:392 or .A:395 or .A:408 or .A:409 or .A:415 or .A:416 or .A:417 or .A:432 or .A:513 or .A:515 or .A:524; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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CYS336
3.693
PRO337
3.880
PHE338
3.815
VAL341
4.201
PHE342
3.567
ILE358
4.052
ALA363
4.032
TYR365
3.612
LEU368
3.939
TYR369
3.796
PHE374
3.667
PHE377
3.207
|
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| PDB ID: 7QUR SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry | ||||||
| Method | Electron microscopy | Resolution | 2.27 Å | Mutation | Yes | [5] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS 698 LGAENSVAYS708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE 748 CSNLLLQYGS758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG 798 GFNFSQILPD808 PSKPSKRSFI818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD 848 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKVE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 D |
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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 .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:408 or .A:409 or .A:415 or .A:416 or .A:417; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 7QUS SARS-CoV-2 Spike, C3 symmetry | ||||||
| Method | Electron microscopy | Resolution | 2.39 Å | Mutation | Yes | [5] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVSGT 73 NGTKRFDNPV83 LPFNDGVYFA93 STEKSNIIRG103 WIFGTTLDSK113 TQSLLIVNNA 123 TNVVIKVCEF133 QFCNDPFLGV143 YYHKNNKSWM153 ESEFRVYSSA163 NNCTFEYVSQ 173 PFLMDLEGKQ183 GNFKNLREFV193 FKNIDGYFKI203 YSKHTPINLV213 RDLPQGFSAL 223 EPLVDLPIGI233 NITRFQTLLA243 LHRSYLTPGD253 SSSGWTAGAA263 AYYVGYLQPR 273 TFLLKYNENG283 TITDAVDCAL293 DPLSETKCTL303 KSFTVEKGIY313 QTSNFRVQPT 323 ESIVRFPNIT333 NLCPFGEVFN343 ATRFASVYAW353 NRKRISNCVA363 DYSVLYNSAS 373 FSTFKCYGVS383 PTKLNDLCFT393 NVYADSFVIR403 GDEVRQIAPG413 QTGKIADYNY 423 KLPDDFTGCV433 IAWNSNNLDS443 KVGGNYNYLY453 RLFRKSNLKP463 FERDISTEIY 473 QAGSTPCNGV483 EGFNCYFPLQ493 SYGFQPTNGV503 GYQPYRVVVL513 SFELLHAPAT 523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT553 ESNKKFLPFQ563 QFGRDIADTT 573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN603 TSNQVAVLYQ613 DVNCTTWRVY 636 STGSNVFQTR646 AGCLIGAEHV656 NNSYECDIPI666 GAGICASYQT676 SQSIIAYTMS 698 LGAENSVAYS708 NNSIAIPTNF718 TISVTTEILP728 VSMTKTSVDC738 TMYICGDSTE 748 CSNLLLQYGS758 FCTQLNRALT768 GIAVEQDKNT778 QEVFAQVKQI788 YKTPPIKDFG 798 GFNFSQILPD808 PSKPSKRSFI818 EDLLFNKVTL828 ADAGFIKQYG838 DCLGDIAARD 848 LICAQKFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKVE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 D |
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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 .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:408 or .A:409 or .A:415 or .A:416 or .A:417; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 6ZB5 SARS CoV-2 Spike protein, Closed conformation, C3 symmetry | ||||||
| Method | Electron microscopy | Resolution | 2.85 Å | Mutation | No | [6] |
| PDB Sequence |
CVNLPPAYTN
30 SFTRGVYYPD40 KVFRSSVLHS50 TQDLFLPFFS60 NVTWFHAKRF79 DNPVLPFNDG 89 VYFASTEKSN99 IIRGWIFGTT109 LDSKTQSLLI119 VNNATNVVIK129 VCEFQFCNDP 139 FLGVEFRVYS161 SANNCTFEYV171 SKNLREFVFK195 NIDGYFKIYS205 KHTPILPQGF 220 SALEPLVDLP230 IGINITRFQT240 LLALHRGWTA260 GAAAYYVGYL270 QPRTFLLKYN 280 ENGTITDAVD290 CALDPLSETK300 CTLKSFTVEK310 GIYQTSNFRV320 QPTESIVRFP 330 NITNLCPFGE340 VFNATRFASV350 YAWNRKRISN360 CVADYSVLYN370 SASFSTFKCY 380 GVSPTKLNDL390 CFTNVYADSF400 VIRGDEVRQI410 APGQTGKIAD420 YNYKLPDDFT 430 GCVIAWNSNN440 LDSKVGGNYN450 YLYRLFRKSN460 LKPFERDIST470 EIYQAGSTPC 480 NGVEGFNCYF490 PLQSYGFQPT500 NGVGYQPYRV510 VVLSFELLHA520 PATVCGPKKS 530 TNLVKNKCVN540 FNFNGLTGTG550 VLTESNKKFL560 PFQQFGRDIA570 DTTDAVRDPQ 580 TLEILDITPC590 SFGGVSVITP600 GTNTSNQVAV610 LYQDVNCTTW633 RVYSTGSNVF 643 QTRAGCLIGA653 EHVNNSYECD663 IPIGAGICAS673 YQQSIIAYTM694 SLGAENSVAY 704 SNNSIAIPTN714 FTISVTTEIL724 PVSMTKTSVD734 CTMYICGDST744 ECSNLLLQYG 754 SFCTQLNRAL764 TGIAVEQDKN774 TQEVFAQVKQ784 IYKTPPIKDF794 GGFNFSQILP 804 DPSKPSKRSF814 IEDLLFNKVT824 LGFIKQYGDC837 LGDDLICAQK851 FNGLTVLPPL 861 LTDEMIAQYT871 SALLAGTITS881 GWTFGAGAAL891 QIPFAMQMAY901 RFNGIGVTQN 911 VLYENQKLIA921 NQFNSAIGKI931 QDSLSSALGK944 LQDVVNQNAQ954 ALNTLVKQLS 964 SNFGAISSVL974 NDILSRLDKV984 EAEVQIDRLI994 TGRLQSLQTY1004 VTQQLIRAAE 1014 IRASANLAAT1024 KMSECVLGQS1034 KRVDFCGKGY1044 HLMSFPQSAP1054 HGVVFLHVTY 1064 VPAQEKNFTT1074 APAICHDGKA1084 HFPREGVFVS1094 NGTHWFVTQR1104 NFYEPQIITT 1114 DNTFVSGNCD1124 VVIGIVNNTV1134 YD
|
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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 .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .C:408 or .C:415 or .C:416; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6ZB4 SARS CoV-2 Spike protein, Closed conformation, C1 symmetry | ||||||
| Method | Electron microscopy | Resolution | 3.03 Å | Mutation | No | [6] |
| PDB Sequence |
CVNLLPPAYT
29 NSFTRGVYYP39 DKVFRSSVLH49 STQDLFLPFF59 SNVTWFHAKR78 FDNPVLPFND 88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI128 KVCEFQFCND 138 PFLGVEFRVY160 SSANNCTFEY170 VSKNLREFVF194 KNIDGYFKIY204 SKHTPILPQG 219 FSALEPLVDL229 PIGINITRFQ239 TLLALHRSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPDD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 TWRVYSTGSN 641 VFQTRAGCLI651 GAEHVNNSYE661 CDIPIGAGIC671 ASYQSQSIIA691 YTMSLGAENS 701 VAYSNNSIAI711 PTNFTISVTT721 EILPVSMTKT731 SVDCTMYICG741 DSTECSNLLL 751 QYGSFCTQLN761 RALTGIAVEQ771 DKNTQEVFAQ781 VKQIYKTPPI791 KDFGGFNFSQ 801 ILPDPSKPSK811 RSFIEDLLFN821 KVTLGFIKQY834 GDCLGDDLIC848 AQKFNGLTVL 858 PPLLTDEMIA868 QYTSALLAGT878 ITSGWTFGAG888 AALQIPFAMQ898 MAYRFNGIGV 908 TQNVLYENQK918 LIANQFNSAI928 GKIQDSLSSA941 LGKLQDVVNQ951 NAQALNTLVK 961 QLSSNFGAIS971 SVLNDILSRL981 DKVEAEVQID991 RLITGRLQSL1001 QTYVTQQLIR 1011 AAEIRASANL1021 AATKMSECVL1031 GQSKRVDFCG1041 KGYHLMSFPQ1051 SAPHGVVFLH 1061 VTYVPAQEKN1071 FTTAPAICHD1081 GKAHFPREGV1091 FVSNGTHWFV1101 TQRNFYEPQI 1111 ITTDNTFVSG1121 NCDVVIGIVN1131 NTVYD
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .C:336 or .C:337 or .C:338 or .C:342 or .C:358 or .C:363 or .C:365 or .C:368 or .C:369 or .C:374 or .C:377 or .C:387 or .C:392 or .C:395 or .C:432 or .C:434 or .C:513 or .C:515 or .C:524; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7XU1 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-122 Conformation | ||||||
| Method | Electron microscopy | Resolution | 3.00 Å | Mutation | Yes | [7] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPCD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 EVPVAIHADQ 628 LTPTWRVYST638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ 690 SIIAYTMSLG700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM 740 YICGDSTECS750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK 790 TPPIKDFGGF800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLAD830 AGFIKQYGDC 840 LGDIAARDLI850 CAQKFNGLTV860 LPPLLTDEMI870 AQYTSALLAG880 TITSGWTFGA 890 GAALQIPFAM900 QMAYRFNGIG910 VTQNVLYENQ920 KLIANQFNSA930 IGKIQDSLSS 940 TASALGKLQD950 VVNQNAQALN960 TLVKQLSSNF970 GAISSVLNDI980 LSRLDKCEAE 990 VQIDRLITGR1000 LQSLQTYVTQ1010 QLIRAAEIRA1020 SANLAATKMS1030 ECVLGQSKRV 1040 DFCGKGYHLM1050 SFPQSAPHGV1060 VFLHVTYVPA1070 QEKNFTTAPA1080 ICHDGKAHFP 1090 REGVFVSNGT1100 HWFVTQRNFY1110 EPQIITTDNT1120 FVSGNCDVVI1130 GIVNNTVYDP 1140
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .C:408 or .C:409 or .C:415 or .C:416 or .C:417; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 6ZP2 Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | Yes | [8] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVKRF 79 DNPVLPFNDG89 VYFASTEKSN99 IIRGWIFGTT109 LDSKTQSLLI119 VNNATNVVIK 129 VCEFQFCNDP139 FLGVYYHKNN149 KSWMESEFRV159 YSSANNCTFE169 YVSQPFLMDL 179 EGKQGNFKNL189 REFVFKNIDG199 YFKIYSKHTP209 INLVRDLPQG219 FSALEPLVDL 229 PIGINITRFQ239 TLLALHRSYL249 TPGDSSSGWT259 AGAAAYYVGY269 LQPRTFLLKY 279 NENGTITDAV289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF 329 PNITNLCPFG339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC 379 YGVSPTKLND389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPDDF 429 TGCVIAWNSN439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP 479 CNGVEGFNCY489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK 529 STNLVKNKCV539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP 579 QTLEILDITP589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTT632 WRVYSTGSNV 642 FQTRAGCLIG652 AEHVNNSYEC662 DIPIGAGICA672 SYQTSQSIIA694 YTMSLGAENS 704 VAYSNNSIAI714 PTNFTISVTT724 EILPVSMTKT734 SVDCTMYICG744 DSTECSNLLL 754 QYGSFCTQLN764 RALTGIAVEQ774 DKNTQEVFAQ784 VKQIYKTPPI794 KDFGGFNFSQ 804 ILPDPSKPSK814 RSFIEDLLFN824 KVTLADAGFI834 KQYGDCLGDI844 AARDLICAQK 854 FNGLTVLPPL864 LTDEMIAQYT874 SALLAGTITS884 GWTFGAGAAL894 QIPFAMQMAY 904 RFNGIGVTQN914 VLYENQKLIA924 NQFNSAIGKI934 QDSLSSTASA944 LGKLQDVVNQ 954 NAQALNTLVK964 QLSSNFGAIS974 SVLNDILSRL984 DPPEAEVQID994 RLITGRLQSL 1004 QTYVTQQLIR1014 AAEIRASANL1024 AATKMSECVL1034 GQSKRVDFCG1044 KGYHLMSFPQ 1054 SAPHGVVFLH1064 VTYVPAQEKN1074 FTTAPAICHD1084 GKAHFPREGV1094 FVSNGTHWFV 1104 TQRNFYEPQI1114 ITTDNTFVSG1124 NCDVVIGIVN1134 NTVYDPL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:336 or .A:337 or .A:338 or .A:341 or .A:342 or .A:358 or .A:363 or .A:365 or .A:368 or .A:369 or .A:374 or .A:377 or .A:387 or .A:392 or .A:395 or .A:408 or .A:409 or .A:415 or .A:416 or .A:417 or .A:434 or .A:513 or .A:515 or .A:524; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS336
4.181
PRO337
3.685
PHE338
3.664
VAL341
3.990
PHE342
4.347
ILE358
3.858
ALA363
4.006
TYR365
3.541
LEU368
3.520
TYR369
3.697
PHE374
3.819
PHE377
3.731
|
|||||
| PDB ID: 7XTZ Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-1 Conformation | ||||||
| Method | Electron microscopy | Resolution | 2.80 Å | Mutation | Yes | [7] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVKRF 79 DNPVLPFNDG89 VYFASTEKSN99 IIRGWIFGTT109 LDSKTQSLLI119 VNNATNVVIK 129 VCEFQFCNDP139 FLGVYYHKNN149 KSWMESEFRV159 YSSANNCTFE169 YVSQPFLMDL 179 EGKQGNFKNL189 REFVFKNIDG199 YFKIYSKHTP209 INLVRDLPQG219 FSALEPLVDL 229 PIGINITRFQ239 TLLALHRSYL249 TPGDSSSGWT259 AGAAAYYVGY269 LQPRTFLLKY 279 NENGTITDAV289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF 329 PNITNLCPFG339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC 379 YGVSPTKLND389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPCDF 429 TGCVIAWNSN439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP 479 CNGVEGFNCY489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK 529 STNLVKNKCV539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP 579 QTLEILDITP589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTT632 WRVYSTGSNV 642 FQTRAGCLIG652 AEHVNNSYEC662 DIPIGAGICA672 SYQTSQSIIA694 YTMSLGAENS 704 VAYSNNSIAI714 PTNFTISVTT724 EILPVSMTKT734 SVDCTMYICG744 DSTECSNLLL 754 QYGSFCTQLN764 RALTGIAVEQ774 DKNTQEVFAQ784 VKQIYKTPPI794 KDFGGFNFSQ 804 ILPDPSKPSK814 RSFIEDLLFN824 KVTLADAGFI834 KQYGDCLGDI844 AARDLICAQK 854 FNGLTVLPPL864 LTDEMIAQYT874 SALLAGTITS884 GWTFGAGAAL894 QIPFAMQMAY 904 RFNGIGVTQN914 VLYENQKLIA924 NQFNSAIGKI934 QDSLSSTASA944 LGKLQDVVNQ 954 NAQALNTLVK964 QLSSNFGAIS974 SVLNDILSRL984 DKCEAEVQID994 RLITGRLQSL 1004 QTYVTQQLIR1014 AAEIRASANL1024 AATKMSECVL1034 GQSKRVDFCG1044 KGYHLMSFPQ 1054 SAPHGVVFLH1064 VTYVPAQEKN1074 FTTAPAICHD1084 GKAHFPREGV1094 FVSNGTHWFV 1104 TQRNFYEPQI1114 ITTDNTFVSG1124 NCDVVIGIVN1134 NTVYDPL
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:408 or .A:409 or .A:415 or .A:416 or .A:417; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7XU0 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-211 Conformation | ||||||
| Method | Electron microscopy | Resolution | 2.90 Å | Mutation | Yes | [7] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPCD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 EVPVAIHADQ 628 LTPTWRVYST638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ 690 SIIAYTMSLG700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM 740 YICGDSTECS750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK 790 TPPIKDFGGF800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLAD830 AGFIKQYGDC 840 LGDIAARDLI850 CAQKFNGLTV860 LPPLLTDEMI870 AQYTSALLAG880 TITSGWTFGA 890 GAALQIPFAM900 QMAYRFNGIG910 VTQNVLYENQ920 KLIANQFNSA930 IGKIQDSLSS 940 TASALGKLQD950 VVNQNAQALN960 TLVKQLSSNF970 GAISSVLNDI980 LSRLDKCEAE 990 VQIDRLITGR1000 LQSLQTYVTQ1010 QLIRAAEIRA1020 SANLAATKMS1030 ECVLGQSKRV 1040 DFCGKGYHLM1050 SFPQSAPHGV1060 VFLHVTYVPA1070 QEKNFTTAPA1080 ICHDGKAHFP 1090 REGVFVSNGT1100 HWFVTQRNFY1110 EPQIITTDNT1120 FVSGNCDVVI1130 GIVNNTVYDP 1140
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:336 or .A:337 or .A:338 or .A:341 or .A:342 or .A:356 or .A:358 or .A:361 or .A:363 or .A:365 or .A:368 or .A:369 or .A:372 or .A:373 or .A:374 or .A:377 or .A:379 or .A:387 or .A:392 or .A:395 or .A:397 or .A:408 or .A:409 or .A:415 or .A:416 or .A:417 or .A:432 or .A:434 or .A:513 or .A:515 or .A:524; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
CYS336
2.842
PRO337
2.805
PHE338
2.758
VAL341
2.270
PHE342
2.801
LYS356
4.660
ILE358
2.326
CYS361
4.327
ALA363
2.386
TYR365
2.572
LEU368
2.331
TYR369
2.765
ALA372
4.319
SER373
4.086
PHE374
2.150
PHE377
2.524
|
|||||
| PDB ID: 7XU2 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [7] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPCD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQDVNCT618 EVPVAIHADQ 628 LTPTWRVYST638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ 690 SIIAYTMSLG700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM 740 YICGDSTECS750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK 790 TPPIKDFGGF800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLAD830 IKQYGDCLGD 843 IAARDLICAQ853 KFNGLTVLPP863 LLTDEMIAQY873 TSALLAGTIT883 SGWTFGAGAA 893 LQIPFAMQMA903 YRFNGIGVTQ913 NVLYENQKLI923 ANQFNSAIGK933 IQDSLSSTAS 943 ALGKLQDVVN953 QNAQALNTLV963 KQLSSNFGAI973 SSVLNDILSR983 LDKCEAEVQI 993 DRLITGRLQS1003 LQTYVTQQLI1013 RAAEIRASAN1023 LAATKMSECV1033 LGQSKRVDFC 1043 GKGYHLMSFP1053 QSAPHGVVFL1063 HVTYVPAQEK1073 NFTTAPAICH1083 DGKAHFPREG 1093 VFVSNGTHWF1103 VTQRNFYEPQ1113 IITTDNTFVS1123 GNCDVVIGIV1133 NNTVYDP |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EIC or .EIC2 or .EIC3 or :3EIC;style chemicals stick;color identity;select .A:408 or .A:409 or .A:415 or .A:416 or .A:417; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7XU4 Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [7] |
| PDB Sequence |
QCVNLTTRTQ
23 LPPAYTNSFT33 RGVYYPDKVF43 RSSVLHSTQD53 LFLPFFSNVT63 WFHAIHVTKR 78 FDNPVLPFND88 GVYFASTEKS98 NIIRGWIFGT108 TLDSKTQSLL118 IVNNATNVVI 128 KVCEFQFCND138 PFLGVYYHKN148 NKSWMESEFR158 VYSSANNCTF168 EYVSQPFLMD 178 LEGKQGNFKN188 LREFVFKNID198 GYFKIYSKHT208 PINLVRDLPQ218 GFSALEPLVD 228 LPIGINITRF238 QTLLALHRSY248 LTPGDSSSGW258 TAGAAAYYVG268 YLQPRTFLLK 278 YNENGTITDA288 VDCALDPLSE298 TKCTLKSFTV308 EKGIYQTSNF318 RVQPTESIVR 328 FPNITNLCPF338 GEVFNATRFA348 SVYAWNRKRI358 SNCVADYSVL368 YNSASFSTFK 378 CYGVSPTKLN388 DLCFTNVYAD398 SFVIRGDEVR408 QIAPGQTGKI418 ADYNYKLPCD 428 FTGCVIAWNS438 NNLDSKVGGN448 YNYLYRLFRK458 SNLKPFERDI468 STEIYQAGST 478 PCNGVEGFNC488 YFPLQSYGFQ498 PTNGVGYQPY508 RVVVLSFELL518 HAPATVCGPK 528 KSTNLVKNKC538 VNFNFNGLTG548 TGVLTESNKK558 FLPFQQFGRD568 IADTTDAVRD 578 PQTLEILDIT588 PCSFGGVSVI598 TPGTNTSNQV608 AVLYQGVNCT618 EVPVAIHADQ 628 LTPTWRVYST638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ 690 SIIAYTMSLG700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM 740 YICGDSTECS750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK 790 TPPIKDFGGF800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLAD830 AGFIKQYGDC 840 LGDIAARDLI850 CAQKFNGLTV860 LPPLLTDEMI870 AQYTSALLAG880 TITSGWTFGA 890 GAALQIPFAM900 QMAYRFNGIG910 VTQNVLYENQ920 KLIANQFNSA930 IGKIQDSLSS 940 TASALGKLQD950 VVNQNAQALN960 TLVKQLSSNF970 GAISSVLNDI980 LSRLDKCEAE 990 VQIDRLITGR1000 LQSLQTYVTQ1010 QLIRAAEIRA1020 SANLAATKMS1030 ECVLGQSKRV 1040 DFCGKGYHLM1050 SFPQSAPHGV1060 VFLHVTYVPA1070 QEKNFTTAPA1080 ICHDGKAHFP 1090 REGVFVSNGT1100 HWFVTQRNFY1110 EPQIITTDNT1120 FVSGNCDVVI1130 GIVNNTVYDP 1140
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Click to Show 3D Structure of This Binding Site
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Science. 2020 Nov 27;370(6520):1089-1094. | ||||
| REF 2 | Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2. Nat Commun. 2022 Jan 11;13(1):222. | ||||
| REF 3 | Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2. Cell Res. 2021 Jun;31(6):717-719. | ||||
| REF 4 | Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD. Cell Discov. 2022 Feb 15;8(1):16. | ||||
| REF 5 | Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science. 2022 Jul 22;377(6604):eabm3125. | ||||
| REF 6 | Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein. Science. 2020 Nov 6;370(6517):725-730. | ||||
| REF 7 | Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike. PLoS Pathog. 2022 Jul 29;18(7):e1010583. | ||||
| REF 8 | A thermostable, closed SARS-CoV-2 spike protein trimer. Nat Struct Mol Biol. 2020 Oct;27(10):934-941. | ||||
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