Structure Viewer: 7r6w

>   Structure details

Sars-Cov-2 Spike Receptor-Binding Domain (Rbd) in complex with S2X35 Fab and S309 Fab

PDB7r6w
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution1.83Å
Number of Fvs2
In complexTrue
Light chain typeKappa,Lambda
Has constant regionTrue
AffinityNA
>   Structure visualisation
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>   Fv information

This PDB has 2 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-61.58°
HC169.77°
HC2117.06°
LC1122.92°
LC284.85°
dc16.09Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGLV1
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 100K 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 T F T N Y G I S W V R Q A P G Q G L E W M G W I S A Y K G N T N Y A Q K L Q G R V T M T T D T S T S T A Y M E L R S L R S D D T A V Y Y C A R P D Y Q V L G Y D F W I G Y Y G M D V W G Q G T T V I V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 30A 30B 30C 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 95B 95C 95D 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q P P S V S G A P G Q R V T I S C T G S S S N I G A G Y D V H W Y Q Q L P G T A P K L L I Y G N T N R P S G V P D R F S G S K S G T S A S L A I T G L Q A E D E A D Y Y C Q S Y D S S L S G S E V V F G G G T K L T V L

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

CDR Sequences (chothia definition)
CDRH1GYTFTNY
CDRH2SAYKGN
CDRH3PDYQVLGYDFWIGYYGMDV
CDRL1TGSSSNIGAGYDVH
CDRL2GNTNRPS
CDRL3QSYDSSLSGSEVV

Orientation Angles (from ABangle)
HL-59.4°
HC172.71°
HC2118.38°
LC1117.87°
LC281.18°
dc15.67Å
>   Occurences in auxilliary databases

Occurences of this structure in other OPIG databases.

>   CoVAbDab entry
Ab_or_Nb Ab
Binds_to SARS-CoV2_WT
Does_not_bind_to SARS-CoV2_Omicron-BA1
Neutralising_vs SARS-CoV2_WT
Not_Neutralising_vs SARS-CoV2_Omicron-BA1
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV2_WT Human Patient
VH_or_VHH QVQLVQSGAEVKKPGASVKVSCKASGYTFTNYGISWVRQAPGQGLEWMGWISAYKGNTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARPDYQVLGYDFWIGYYGMDVWGQGTTVIVSS
VL QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNTNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSEVVFGGGTKLTVL
Heavy_V_Gene IGHV1-18 (Human)
Heavy_J_Gene IGHJ6 (Human)
Light_V_Gene IGLV1-40 (Human)
Light_J_Gene IGLJ3 (Human)
CDRH3 ARPDYQVLGYDFWIGYYGMDV
CDRL3 QSYDSSLSGSEVV
Structures https://www.rcsb.org/structure/7JXE;
https://www.rcsb.org/structure/7R6W
ABB_Homology_Model None
Sources Luca Piccoli et al., 2020 (https://www.cell.com/cell/fulltext/S0092-8674(20);
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)
Date_Added Oct 16, 2020
Last_Updated Dec 28, 2021
Update_Description 24th July '21: Added new PDB structure and reference. 28th Dec '21: Added Omicron-BA1 binding data
Notes_Following_Up 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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