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 | Biliverdine Ix Alpha | Ligand Info | |||
| Canonical SMILES | CC1=C(C(=CC2=C(C(=C(N2)C=C3C(=C(C(=O)N3)C)C=C)C)CCC(=O)O)NC1=CC4=NC(=O)C(=C4C)C=C)CCC(=O)O | ||||
| InChI | 1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,34-35H,1-2,9-12H2,3-6H3,(H,37,42)(H,38,39)(H,40,41)/b24-13-,27-14-,28-15- | ||||
| InChIKey | RCNSAJSGRJSBKK-NSQVQWHSSA-N | ||||
| PubChem Compound ID | 5280353 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7NT9 Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation) | ||||||
| Method | Electron microscopy | Resolution | 3.36 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 DVNCWRVYST 638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ690 SIIAYTMSLG 700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM740 YICGDSTECS 750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK790 TPPIKDFGGF 800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLDL849 ICAQKFNGLT859 VLPPLLTDEM 869 IAQYTSALLA879 GTITSGWTFG889 AGAALQIPFA899 MQMAYRFNGI909 GVTQNVLYEN 919 QKLIANQFNS929 AIGKIQDSLS939 STASALGKLQ949 DVVNQNAQAL959 NTLVKQLSSN 969 FGAISSVLND979 ILSRLDPPEA989 EVQIDRLITG999 RLQSLQTYVT1009 QQLIRAAEIR 1019 ASANLAATKM1029 SECVLGQSKR1039 VDFCGKGYHL1049 MSFPQSAPHG1059 VVFLHVTYVP 1069 AQEKNFTTAP1079 AICHDGKAHF1089 PREGVFVSNG1099 THWFVTQRNF1109 YEPQIITTDN 1119 TFVSGNCDVV1129 IGIVNNTVYD1139 PLQPELD
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| PDB ID: 7NTA Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect) | ||||||
| Method | Electron microscopy | Resolution | 3.50 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 DVNCWRVYST 638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ690 SIIAYTMSLG 700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM740 YICGDSTECS 750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK790 TPPIKDFGGF 800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLDL849 ICAQKFNGLT859 VLPPLLTDEM 869 IAQYTSALLA879 GTITSGWTFG889 AGAALQIPFA899 MQMAYRFNGI909 GVTQNVLYEN 919 QKLIANQFNS929 AIGKIQDSLS939 STASALGKLQ949 DVVNQNAQAL959 NTLVKQLSSN 969 FGAISSVLND979 ILSRLDPPEA989 EVQIDRLITG999 RLQSLQTYVT1009 QQLIRAAEIR 1019 ASANLAATKM1029 SECVLGQSKR1039 VDFCGKGYHL1049 MSFPQSAPHG1059 VVFLHVTYVP 1069 AQEKNFTTAP1079 AICHDGKAHF1089 PREGVFVSNG1099 THWFVTQRNF1109 YEPQIITTDN 1119 TFVSGNCDVV1129 IGIVNNTVYD1139 PLQPELD
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| PDB ID: 7NTC Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab | ||||||
| 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 DVNCWRVYST 638 GSNVFQTRAG648 CLIGAEHVNN658 SYECDIPIGA668 GICASYQTSQ690 SIIAYTMSLG 700 AENSVAYSNN710 SIAIPTNFTI720 SVTTEILPVS730 MTKTSVDCTM740 YICGDSTECS 750 NLLLQYGSFC760 TQLNRALTGI770 AVEQDKNTQE780 VFAQVKQIYK790 TPPIKDFGGF 800 NFSQILPDPS810 KPSKRSFIED820 LLFNKVTLDL849 ICAQKFNGLT859 VLPPLLTDEM 869 IAQYTSALLA879 GTITSGWTFG889 AGAALQIPFA899 MQMAYRFNGI909 GVTQNVLYEN 919 QKLIANQFNS929 AIGKIQDSLS939 STASALGKLQ949 DVVNQNAQAL959 NTLVKQLSSN 969 FGAISSVLND979 ILSRLDPPEA989 EVQIDRLITG999 RLQSLQTYVT1009 QQLIRAAEIR 1019 ASANLAATKM1029 SECVLGQSKR1039 VDFCGKGYHL1049 MSFPQSAPHG1059 VVFLHVTYVP 1069 AQEKNFTTAP1079 AICHDGKAHF1089 PREGVFVSNG1099 THWFVTQRNF1109 YEPQIITTDN 1119 TFVSGNCDVV1129 IGIVNNTVYD1139 PLQPELD
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| 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 | [2] |
| 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
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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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .C:94 or .C:96 or .C:99 or .C:100 or .C:101 or .C:102 or .C:103 or .C:104 or .C:119 or .C:120 or .C:121 or .C:126 or .C:128 or .C:175 or .C:177 or .C:188 or .C:190 or .C:192 or .C:194 or .C:203 or .C:205 or .C:207 or .C:226 or .C:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER94
4.746
GLU96
3.325
ASN99
2.474
ILE100
4.843
ILE101
2.587
ARG102
2.423
GLY103
2.608
TRP104
2.454
ILE119
2.458
VAL120
4.641
ASN121
1.767
VAL126
2.791
|
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| PDB ID: 6ZOZ Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Locked State | ||||||
| Method | Electron microscopy | Resolution | 3.50 Å | Mutation | Yes | [3] |
| PDB Sequence |
CVNLTTRTQL
24 PPAYTNSFTR34 GVYYPDKVFR44 SSVLHSTQDL54 FLPFFSNVTW64 FHAIHDNPVL 84 PFNDGVYFAS94 TEKSNIIRGW104 IFGTTLDSKT114 QSLLIVNNAT124 NVVIKVCEFQ 134 FCNDPFLGME154 SEFRVYSSAN164 NCTFEYVSQP174 FLNFKNLREF192 VFKNIDGYFK 202 IYSKHTPINL212 VRDLPQGFSA222 LEPLVDLPIG232 INITRFQTLL242 ALAAAYYVGY 269 LQPRTFLLKY279 NENGTITDAV289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR 319 VQPTESIVRF329 PNITNLCPFG339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY 369 NSASFSTFKC379 YGVCPTKLND389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA 419 DYNYKLPDDF429 TGCVIAWNSN439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS 469 TEIYQAGSTP479 CNGVEGFNCY489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH 519 APATVCGPKK529 STNLVKNKCV539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI 569 ADTTDAVRDP579 QTLEILDITP589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTE 619 VPVAIHADQL629 TPTWRVYSTG639 SNVFQTRAGC649 LIGAEHVNNS659 YECDIPIGAG 669 ICASYQTSQS687 IIAYTMSLGA697 ENSVAYSNNS707 IAIPTNFTIS717 VTTEILPVSM 727 TKTSVDCTMY737 ICGDSTECSN747 LLLQYGSFCT757 QLNRALTGIA767 VEQDKNTQEV 777 FAQVKQIYKT787 PPIKDFGGFN797 FSQILPDPSK807 PSKRSFIEDL817 LFNKVTLADA 827 GFIKQYGDCL837 GDIAARDLIC847 AQKFNGLTVL857 PPLLTDEMIA867 QYTSALLAGT 877 ITSGWTFGAG887 AALQIPFAMQ897 MAYRFNGIGV907 TQNVLYENQK917 LIANQFNSAI 927 GKIQDSLSST937 ASALGKLQDV947 VNQNAQALNT957 LVKQLSSNFG967 AISSVLNDIL 977 SRLCPPEAEV987 QIDRLITGRL997 QSLQTYVTQQ1007 LIRAAEIRAS1017 ANLAATKMSE 1027 CVLGQSKRVD1037 FCGKGYHLMS1047 FPQSAPHGVV1057 FLHVTYVPAQ1067 EKNFTTAPAI 1077 CHDGKAHFPR1087 EGVFVSNGTH1097 WFVTQRNFYE1107 PQIITTDNTF1117 VSGNCDVVIG 1127 IVNNTVYDP
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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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:99 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:190 or .A:192 or .A:207 or .A:226; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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||||||
| 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 | [3] |
| 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
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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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:177 or .A:190 or .A:192 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| 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 | [2] |
| 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
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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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:94 or .A:96 or .A:99 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:128 or .A:173 or .A:175 or .A:177 or .A:178 or .A:190 or .A:192 or .A:203 or .A:205 or .A:207 or .A:226 or .A:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER94
4.852
GLU96
2.949
ASN99
2.512
ILE100
4.440
ILE101
2.621
ARG102
2.370
GLY103
2.573
TRP104
2.903
ILE119
2.381
VAL120
3.824
ASN121
2.050
VAL126
2.642
|
|||||
| 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 | [2] |
| 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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:92 or .A:94 or .A:96 or .A:99 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:173 or .A:175 or .A:177 or .A:178 or .A:188 or .A:190 or .A:192 or .A:194 or .A:203 or .A:205 or .A:207 or .A:226 or .A:227; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
PHE92
4.958
SER94
4.775
GLU96
3.210
ASN99
2.592
ILE100
4.779
ILE101
2.428
ARG102
2.251
GLY103
2.636
TRP104
2.920
ILE119
2.427
VAL120
3.900
ASN121
1.652
VAL126
2.557
|
|||||
| PDB ID: 7XU6 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 Conformation | ||||||
| Method | Electron microscopy | Resolution | 2.90 Å | Mutation | Yes | [2] |
| PDB Sequence |
NLTTRTQLPP
26 AYTNSFTRGV36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 AIHVTKRFDN 81 PVLPFNDGVY91 FASTEKSNII101 RGWIFGTTLD111 SKTQSLLIVN121 NATNVVIKVC 131 EFQFCNDPFL141 GVYYHKNNKS151 WMESEFRVYS161 SANNCTFEYV171 SQPFLMDLEG 181 KQGNFKNLRE191 FVFKNIDGYF201 KIYSKHTPIN211 LVRDLPQGFS221 ALEPLVDLPI 231 GINITRFQTL241 LALHRSSGWT259 AGAAAYYVGY269 LQPRTFLLKY279 NENGTITDAV 289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF329 PNITNLCPFG 339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC379 YGVSPTKLND 389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPCDF429 TGCVIAWNSN 439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP479 CNGVEGFNCY 489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK529 STNLVKNKCV 539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP579 QTLEILDITP 589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTE619 VPVAIHADQL629 TPTWRVYSTG 639 SNVFQTRAGC649 LIGAEHVNNS659 YECDIPIGAG669 ICASYQTSQS691 IIAYTMSLGA 701 ENSVAYSNNS711 IAIPTNFTIS721 VTTEILPVSM731 TKTSVDCTMY741 ICGDSTECSN 751 LLLQYGSFCT761 QLNRALTGIA771 VEQDKNTQEV781 FAQVKQIYKT791 PPIKDFGGFN 801 FSQILPDPSK811 PSKRSFIEDL821 LFNKVTLIKQ836 YGDCLGDLIC851 AQKFNGLTVL 861 PPLLTDEMIA871 QYTSALLAGT881 ITSGWTFGAG891 AALQIPFAMQ901 MAYRFNGIGV 911 TQNVLYENQK921 LIANQFNSAI931 GKIQDSLSST941 ASALGKLQDV951 VNQNAQALNT 961 LVKQLSSNFG971 AISSVLNDIL981 SRLDKCEAEV991 QIDRLITGRL1001 QSLQTYVTQQ 1011 LIRAAEIRAS1021 ANLAATKMSE1031 CVLGQSKRVD1041 FCGKGYHLMS1051 FPQSAPHGVV 1061 FLHVTYVPAQ1071 EKNFTTAPAI1081 CHDGKAHFPR1091 EGVFVSNGTH1101 WFVTQRNFYE 1111 PQIITTDNTF1121 VSGNCDVVIG1131 IVNNTVYDP
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:96 or .A:99 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:128 or .A:173 or .A:175 or .A:177 or .A:190 or .A:192 or .A:203 or .A:205 or .A:207 or .A:226 or .A:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLU96
4.693
ASN99
2.350
ILE100
4.197
ILE101
2.639
ARG102
2.413
GLY103
3.207
TRP104
3.109
ILE119
2.441
VAL120
3.548
ASN121
2.363
VAL126
2.388
|
|||||
| PDB ID: 7XU3 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation | ||||||
| Method | Electron microscopy | Resolution | 3.00 Å | Mutation | Yes | [2] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 AIHDNPVLPF86 NDGVYFASTE 96 KSNIIRGWIF106 GTTLSLLIVN121 NATNVVIKVC131 EFQFCNDPFL141 GVMESEFRVY 160 SSANNCTFEY170 VSQPFLFKNL189 REFVFKNIDG199 YFKIYSKHTP209 ILPQGFSALE 224 PLVDLPIGIN234 ITRFQTLLAL244 HGAAAYYVGY269 LQPRTFLLKY279 NENGTITDAV 289 DCALDPLSET299 KCTLKSFTVE309 KGIYQTSNFR319 VQPTESIVRF329 PNITNLCPFG 339 EVFNATRFAS349 VYAWNRKRIS359 NCVADYSVLY369 NSASFSTFKC379 YGVSPTKLND 389 LCFTNVYADS399 FVIRGDEVRQ409 IAPGQTGKIA419 DYNYKLPCDF429 TGCVIAWNSN 439 NLDSKVGGNY449 NYLYRLFRKS459 NLKPFERDIS469 TEIYQAGSTP479 CNGVEGFNCY 489 FPLQSYGFQP499 TNGVGYQPYR509 VVVLSFELLH519 APATVCGPKK529 STNLVKNKCV 539 NFNFNGLTGT549 GVLTESNKKF559 LPFQQFGRDI569 ADTTDAVRDP579 QTLEILDITP 589 CSFGGVSVIT599 PGTNTSNQVA609 VLYQDVNCTE619 VNVFQTRAGC649 LIGAEHVNNS 659 YECDIPIGAG669 ICASYQTSQS691 IIAYTMSLGA701 ENSVAYSNNS711 IAIPTNFTIS 721 VTTEILPVSM731 TKTSVDCTMY741 ICGDSTECSN751 LLLQYGSFCT761 QLNRALTGIA 771 VEQDKNTQEV781 FAQVKQIYKT791 PPIKDFGGFN801 FSQILPDPSK811 PSKRSFIEDL 821 LFNKVTFNGL858 TVLPPLLTDE868 MIAQYTSALL878 AGTITSGWTF888 GAGAALQIPF 898 AMQMAYRFNG908 IGVTQNVLYE918 NQKLIANQFN928 SAIGKIQDSL938 SSTASALGKL 948 QDVVNQNAQA958 LNTLVKQLSS968 NFGAISSVLN978 DILSRLDKCE988 AEVQIDRLIT 998 GRLQSLQTYV1008 TQQLIRAAEI1018 RASANLAATK1028 MSECVLGQSK1038 RVDFCGKGYH 1048 LMSFPQSAPH1058 GVVFLHVTYV1068 PAQEKNFTTA1078 PAICHDGKAH1088 FPREGVFVSN 1098 GTHWFVTQRN1108 FYEPQIITTD1118 NTFVSGNCDV1128 VIGIVNNTVY1138 DP |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .B:94 or .B:96 or .B:98 or .B:99 or .B:102 or .B:104 or .B:121 or .B:123 or .B:126 or .B:173 or .B:175 or .B:176 or .B:190 or .B:192 or .B:194 or .B:203 or .B:205 or .B:207 or .B:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 7XU5 Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | Yes | [2] |
| PDB Sequence |
AYTNSFTRGV
36 YYPDKVFRSS46 VLHSTQDLFL56 PFFSNVTWFH66 AINPVLPFND88 GVYFASTEKS 98 NIIRGWIFGS116 LLIVNNATNV126 VIKVCEFQSE156 FRVYSFEYVS172 QPKNLREFVF 194 KNIDGYFKIY204 SKHTPILPQG219 FSALEPLVDL229 PIITRFQTLL242 ALAAYYVGYL 270 QPRTFLLKYN280 ENGTITDAVD290 CALDPLSETK300 CTLKSFTVEK310 GIYQTSNFRV 320 QPTESIVRFP330 NITNLCPFGE340 VFNATRFASV350 YAWNRKRISN360 CVADYSVLYN 370 SASFSTFKCY380 GVSPTKLNDL390 CFTNVYADSF400 VIRGDEVRQI410 APGQTGKIAD 420 YNYKLPCDFT430 GCVIAWNSNN440 LNYNYLYRLF456 RKSNLKPFER466 DPLQSYGFQP 499 GYQPYRVVVL513 SFELLHAPAT523 VCGPKKSTNL533 VKNKCVNFNF543 NGLTGTGVLT 553 ESNKKFLPFQ563 QFGRDIADTT573 DAVRDPQTLE583 ILDITPCSFG593 GVSVITPGTN 603 TSNQVAVLYQ613 GVNCTEVNVF643 QTRAGCLIGA653 EHVNNSYECD663 IPIGAGICAS 673 YQTSQSIIAY695 TMSLGAENSV705 AYSNNSIAIP715 TNFTISVTTE725 ILPVSMTKTS 735 VDCTMYICGD745 STECSNLLLQ755 YGSFCTQLNR765 ALTGIAVEQD775 KNTQEVFAQV 785 KQIYKTPPIK795 DFGGFNFSQI805 LPDPSKPSKR815 SFIEDLLFNK825 VTFNGLTVLP 862 PLLTDEMIAQ872 YTSALLAGTI882 TSGWTFGAGA892 ALQIPFAMQM902 AYRFNGIGVT 912 QNVLYENQKL922 IANQFNSAIG932 KIQDSLSSTA942 SALGKLQDVV952 NQNAQALNTL 962 VKQLSSNFGA972 ISSVLNDILS982 RLDKCEAEVQ992 IDRLITGRLQ1002 SLQTYVTQQL 1012 IRAAEIRASA1022 NLAATKMSEC1032 VLGQSKRVDF1042 CGKGYHLMSF1052 PQSAPHGVVF 1062 LHVTYVPAQE1072 KNFTTAPAIC1082 HDGKAHFPRE1092 GVFVSNGTHW1102 FVTQRNFYEP 1112 QIITTDNTFV1122 SGNCDVVIGI1132 VNNTVYDP
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .B:96 or .B:97 or .B:98 or .B:99 or .B:102 or .B:104 or .B:121 or .B:122 or .B:123 or .B:124 or .B:126 or .B:188 or .B:190 or .B:192 or .B:203 or .B:205 or .B:207 or .B:224 or .B:226 or .B:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| 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 | [2] |
| 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 .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:94 or .A:96 or .A:99 or .A:100 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:128 or .A:175 or .A:177 or .A:178 or .A:188 or .A:190 or .A:192 or .A:203 or .A:205 or .A:207 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
SER94
4.413
GLU96
3.397
ASN99
2.432
ILE100
4.214
ILE101
2.686
ARG102
2.683
GLY103
3.038
TRP104
2.674
ILE119
2.478
VAL120
3.998
ASN121
1.971
VAL126
2.674
|
|||||
| 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 | [2] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:128 or .A:175 or .A:177 or .A:178 or .A:188 or .A:190 or .A:192 or .A:194 or .A:203 or .A:205 or .A:207 or .A:226 or .A:227; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ASN99
2.423
ILE101
2.429
ARG102
2.263
GLY103
2.892
TRP104
2.645
ILE119
2.365
VAL120
3.830
ASN121
2.154
VAL126
2.836
ILE128
4.720
PHE175
4.800
|
|||||
| PDB ID: 7B62 Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin | ||||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [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 KSFTVEKGSS313 GLEVLF |
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BLA or .BLA2 or .BLA3 or :3BLA;style chemicals stick;color identity;select .A:99 or .A:101 or .A:102 or .A:103 or .A:104 or .A:119 or .A:120 or .A:121 or .A:126 or .A:177 or .A:188 or .A:190 or .A:192 or .A:203 or .A:207 or .A:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity. Sci Adv. 2021 May 28;7(22):eabg7607. | ||||
| REF 2 | Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike. PLoS Pathog. 2022 Jul 29;18(7):e1010583. | ||||
| REF 3 | A thermostable, closed SARS-CoV-2 spike protein trimer. Nat Struct Mol Biol. 2020 Oct;27(10):934-941. | ||||
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