Structure Viewer: 7r6x

>   Structure details

Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) in complex with S2E12 Fab, S309 Fab, and S304 Fab

PDB7r6x
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.95Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
AffinityNA
>   Structure visualisation
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>   Fv information

This PDB has 3 Fv(s).

>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 chainsR
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGTRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHH

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

Orientation Angles (from ABangle)
HL-61.31°
HC169.62°
HC2118.55°
LC1122.36°
LC282.88°
dc15.97Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V Q P G G S L R L S C A A S G F T F S S Y D M H W V R Q T T G K G L E W V S T I G T A G D T Y Y P D S V K G R F T I S R E D A K N S L Y L Q M N S L R A G D T A V Y Y C A R G D S S G Y Y Y Y F D Y W G Q G T L L 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 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 95 95A 96 97 98 99 100 101 102 103 104 105 106 107
D I Q M T Q S P S S L S A A V G D R V T I T C R A S Q S I G S Y L N W Y Q Q K P G K A P K L L I Y A A S S L Q S G V P S R F S G S G S G T D F T L T I S S L Q P E D F A I Y Y C Q Q S Y V S P T Y T F G P G T K V D I K

Antigen Details
Antigen chainsR
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGTRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTFSSY
CDRH2GTAGD
CDRH3GDSSGYYYYFDY
CDRL1RASQSIGSYLN
CDRL2AASSLQS
CDRL3QQSYVSPTYT

Orientation Angles (from ABangle)
HL-66.36°
HC172.41°
HC2116.41°
LC1119.63°
LC283.28°
dc16.21Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV1
Light subgroupIGKV3
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G P E V K K P G T S V R V S C K A S G F T F T S S A V Q W V R Q A R G Q R L E W V G W I V V G S G N T N Y A Q K F H E R V T I T R D M S T S T A Y M E L S S L R S E D T A V Y Y C A S P Y C S G G S C S D G F D I W G Q G T M 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 95 95A 96 97 98 99 100 101 102 103 104 105 106 107
D I V L T Q T P G T L S L S P G E R A T L S C R A S Q S V S S S Y 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 Y V G L T G W T F G Q G T K V E I K

Antigen Details
Antigen chainsR
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGTRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GFTFTSS
CDRH2VVGSGN
CDRH3PYCSGGSCSDGFDI
CDRL1RASQSVSSSYLA
CDRL2GASSRAT
CDRL3QQYVGLTGWT

Orientation Angles (from ABangle)
HL-58.82°
HC168.59°
HC2117.09°
LC1120.61°
LC281.54°
dc15.93Å
>   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
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
Not_Neutralising_vs None
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV2_WT Human Patient
VH_or_VHH QVQLVQSGPEVKKPGTSVRVSCKASGFTFTSSAVQWVRQARGQRLEWVGWIVVGSGNTNYAQKFHERVTITRDMSTSTAYMELSSLRSEDTAVYYCASPYCSGGSCSDGFDIWGQGTMVTVSS
VL DIVLTQTPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYVGLTGWTFGQGTKVEIK
Heavy_V_Gene IGHV1-58 (Human)
Heavy_J_Gene IGHJ3 (Human)
Light_V_Gene IGKV3-20 (Human)
Light_J_Gene IGKJ1 (Human)
CDRH3 ASPYCSGGSCSDGFDI
CDRL3 QQYVGLTGWT
Structures https://www.rcsb.org/structure/7K4N;
https://www.rcsb.org/structure/7K45;
https://www.rcsb.org/structure/7K3Q;
https://www.rcsb.org/structure/7R6X
ABB_Homology_Model None
Sources M. Alejandra Tortorici et al., 2020 (https://science.sciencemag.org/content/early/2020/09/23/science.abe3354);
Tyler Starr et al., 2021 (https://www.nature.com/articles/s41586-021-03807-6);
Elisabetta Cameroni et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.12.472269v1);
Tongqing Zhou et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.27.474307v1)
Date_Added Nov 11, 2020
Last_Updated Jan 31, 2022
Update_Description 26th Nov: Added PDB structure and sequence information; 24th July '21: Added new PDB structure and reference with variant binding data. 28th Dec '21: Added Omicron-BA1 binding data. 31st Jan '22: Added more variant neutralisation data
Notes_Following_Up Variant binding data in Starr et al. Debate as to strength of Omicron-BA1 neutralisation. 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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