Structure Viewer: 6wps

>   Structure details

Structure of the Sars-Cov-2 Spike Glycoprotein in complex with the S309 Neutralizing antibody Fab Fragment

PDB6wps
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.1Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionFalse
AffinityNA
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>   Fv information

This PDB has 3 Fv(s).

>   F/G
Fv Details
Heavy chainF
Light chainG
Heavy subgroupIGHV1
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y P F T S Y G I S W V R Q A P G Q G L E W M G W I S T Y N G N T N Y A Q K F Q G R V T M T T D T S T T T G Y M E L R R L R S D D T A V Y Y C A R D Y T R G A W F G E S L I G G F D N W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 96 97 98 99 100 101 102 103 104 105 106 107
E I V L T Q S P G T L S L S P G E R A T L S C R A S Q T V S S T S L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q H D T S L T F G G G T K V E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namesars-cov-2 spike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GYPFTSY
CDRH2STYNGN
CDRH3DYTRGAWFGESLIGGFDN
CDRL1RASQTVSSTSLA
CDRL2GASSRAT
CDRL3QQHDTSLT

Orientation Angles (from ABangle)
HL-63.28°
HC170.7°
HC2118.38°
LC1123.54°
LC282.96°
dc16.14Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y P F T S Y G I S W V R Q A P G Q G L E W M G W I S T Y N G N T N Y A Q K F Q G R V T M T T D T S T T T G Y M E L R R L R S D D T A V Y Y C A R D Y T R G A W F G E S L I G G F D N W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 96 97 98 99 100 101 102 103 104 105 106 107
E I V L T Q S P G T L S L S P G E R A T L S C R A S Q T V S S T S L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q H D T S L T F G G G T K V E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namesars-cov-2 spike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GYPFTSY
CDRH2STYNGN
CDRH3DYTRGAWFGESLIGGFDN
CDRL1RASQTVSSTSLA
CDRL2GASSRAT
CDRL3QQHDTSLT

Orientation Angles (from ABangle)
HL-63.28°
HC170.7°
HC2118.38°
LC1123.54°
LC282.96°
dc16.14Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV1
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y P F T S Y G I S W V R Q A P G Q G L E W M G W I S T Y N G N T N Y A Q K F Q G R V T M T T D T S T T T G Y M E L R R L R S D D T A V Y Y C A R D Y T R G A W F G E S L I G G F D N W G Q G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 96 97 98 99 100 101 102 103 104 105 106 107
E I V L T Q S P G T L S L S P G E R A T L S C R A S Q T V S S T S L A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q H D T S L T F G G G T K V E I K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namesars-cov-2 spike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceMGILPSPGMPALLSLVSLLSVLLMGCVAETGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GYPFTSY
CDRH2STYNGN
CDRH3DYTRGAWFGESLIGGFDN
CDRL1RASQTVSSTSLA
CDRL2GASSRAT
CDRL3QQHDTSLT

Orientation Angles (from ABangle)
HL-63.28°
HC170.7°
HC2118.38°
LC1123.54°
LC282.96°
dc16.14Å
>   Occurences in auxilliary databases

Occurences of this structure in other OPIG databases.

>   CoVAbDab entry
Ab_or_Nb Ab
Binds_to SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV1
Does_not_bind_to None
Neutralising_vs SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV1
Not_Neutralising_vs None
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV1 Human Patient
VH_or_VHH QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVSS
VL EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIK
Heavy_V_Gene IGHV1-18 (Human)
Heavy_J_Gene IGHJ4 (Human)
Light_V_Gene IGKV3-20 (Human)
Light_J_Gene IGKJ4 (Human)
CDRH3 ARDYTRGAWFGESLIGGFDN
CDRL3 QQHDTSLT
Structures https://www.rcsb.org/structure/6WPS;
https://www.rcsb.org/structure/6WPT;
https://www.rcsb.org/structure/6WS6;
https://www.rcsb.org/structure/7JX3;
https://www.rcsb.org/structure/7L0N;
https://www.rcsb.org/structure/7BEP;
https://www.rcsb.org/structure/7R6W;
https://www.rcsb.org/structure/7R6X;
https://www.rcsb.org/structure/7SOB;
https://www.rcsb.org/structure/7TLY;
https://www.rcsb.org/structure/7TLZ;
https://www.rcsb.org/structure/7TM0;
https://www.rcsb.org/structure/7TN0
ABB_Homology_Model None
Sources Dora Pinto et al., 2020 (https://www.nature.com/articles/s41586-020-2349-y);
Luca Piccoli et al., 2020 (https://www.cell.com/cell/fulltext/S0092-8674(20);
Wanwisa Dejnirattisai et al., 2021 (https://www.cell.com/cell/fulltext/S0092-8674(21);
Tyler Starr et al., 2021 (https://www.nature.com/articles/s41586-021-03807-6);
Dhiraj Mannar et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473380v1);
Daniel Sheward et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473354v1);
Laura VanBlargan et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.15.472828v1);
Garrett Rappazzo et al., 2021 (https://www.science.org/doi/10.1126/science.abf4830);
Tongqing Zhou et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.27.474307v1);
Matthew McCallum et al., 2021 (https://dx.doi.org/10.1126/science.abn8652);
Bin Ju et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.19.476892v1);
Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1)
Date_Added May 4, 2020
Last_Updated Mar 4, 2022
Update_Description 28th May: Added sequence and crystal structure information. 15th June: Added 6ws6 structure. 16th October: Added more PDB structures. 28th Feb: Added 7L0N and new reference. 11th March: Added 7BEP. 24th July '21: Added new PDB structure and reference. 2nd Dec '21: Added new PDB structure. 28th Dec '21: Added Omicron-BA1 neturalisation data. 31st Jan '22: Added new neutralisation studies. 4th Mar '22: Added structures of S309 bound to Omicron-BA1 and Omicron-BA2 data.
Notes_Following_Up Extra variant binding data in Starr et al. Complete

TheraSAbDab link
>   Downloads

Additional links and files for download: see help for more details.

Chothia-numbered structure Download
IMGT-numbered structure Download
Non-annotated structure from the PDB Download
Summary file for this antibody Download

SAbDab papers

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

Dunbar, J., Krawczyk, K. et al. (2014) SAbDab: the Structural Antibody Database. Nucleic Acids Res. 42(D1):D1140-D1146 [link]

Thera-SAbDab paper

Raybould, M.I.J., Marks, C. et al (2020) Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48(D1):D383-D388. [link]

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