Structure Viewer: 7bep

>   Structure details

Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in a Ternary complex with Covox-384 and S309 Fabs

PDB7bep
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.61Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
AffinityNA
>   Structure visualisation
Please note the WebGL plugin needs to be enabled to use PV Viewer.

Display options:














>   Fv information

This PDB has 4 Fv(s).

>   D/F
Fv Details
Heavy chainD
Light chainF
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 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 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 K P G E S L R L S C A A S G F T F S D Y Y M T W I R Q A P G K G L E W V S Y I R S S G H T I Y Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R V E D T A V Y Y C A R G G V L R F L E W P L N A 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 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q L T Q S P S S L S A S V G D R V T I T C R A S Q G I S N Y L A W Y Q Q K P G K V P K L L I Y A A S T 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 V A T Y Y C Q K Y N N A L G T F G Q G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2RSSGHT
CDRH3GGVLRFLEWPLNAFDI
CDRL1RASQGISNYLA
CDRL2AASTLQS
CDRL3QKYNNALGT

Orientation Angles (from ABangle)
HL-47.26°
HC172.02°
HC2117.6°
LC1118.66°
LC286.18°
dc16.12Å
>   A/B
Fv Details
Heavy chainA
Light chainB
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 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 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 K P G E S L R L S C A A S G F T F S D Y Y M T W I R Q A P G K G L E W V S Y I R S S G H T I Y Y A D S V K G R F T I S R D N A K N S L Y L Q M N S L R V E D T A V Y Y C A R G G V L R F L E W P L N A 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 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q L T Q S P S S L S A S V G D R V T I T C R A S Q G I S N Y L A W Y Q Q K P G K V P K L L I Y A A S T 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 V A T Y Y C Q K Y N N A L G T F G Q G T K V E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

CDR Sequences (chothia definition)
CDRH1GFTFSDY
CDRH2RSSGHT
CDRH3GGVLRFLEWPLNAFDI
CDRL1RASQGISNYLA
CDRL2AASTLQS
CDRL3QKYNNALGT

Orientation Angles (from ABangle)
HL-49.63°
HC171.04°
HC2117.39°
LC1119.52°
LC285.22°
dc16.13Å
>   H/L
Fv Details
Heavy chainH
Light chainL
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 chainsE
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

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

Orientation Angles (from ABangle)
HL-60.7°
HC169.81°
HC2118.41°
LC1122.26°
LC284.31°
dc16.15Å
>   G/I
Fv Details
Heavy chainG
Light chainI
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 chainsC
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK

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

Orientation Angles (from ABangle)
HL-61.5°
HC169.76°
HC2117.68°
LC1122.44°
LC283.93°
dc16.06Å
>   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_Delta
Does_not_bind_to None
Neutralising_vs SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Delta
Not_Neutralising_vs SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA1.1;SARS-CoV2_Omicron-BA2;SARS-CoV2_Beta;SARS-CoV2_Gamma
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV2_WT Human Patient
VH_or_VHH EVQLVESGGGLVKPGESLRLSCAASGFTFSDYYMTWIRQAPGKGLEWVSYIRSSGHTIYYADSVKGRFTISRDNAKNSLYLQMNSLRVEDTAVYYCARGGVLRFLEWPLNAFDIWGQGTMVTVSS
VL DIQLTQSPSSLSASVGDRVTITCRASQGISNYLAWYQQKPGKVPKLLIYAASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQKYNNALGTFGQGTKVEIK
Heavy_V_Gene IGHV3-11 (Human)
Heavy_J_Gene IGHJ3 (Human)
Light_V_Gene IGKV1-27 (Human)
Light_J_Gene IGKJ1 (Human)
CDRH3 ARGGVLRFLEWPLNAFDI
CDRL3 QKYNNALGT
Structures https://www.rcsb.org/structure/7BEP;
https://www.rcsb.org/structure/7ND8
ABB_Homology_Model None
Sources Wanwisa Dejnirattisai et al., 2021 (https://www.sciencedirect.com/science/article/pii/S009286742100221X);
Wanwisa Dejnirattisai et al., 2022 (https://www.sciencedirect.com/science/article/pii/S0092867421015786);
Rungtiwa Nutalai et al., 2022 (https)
Date_Added Mar 11, 2021
Last_Updated Jun 14, 2022
Update_Description 31st Jan '22: Added variant data. 14th Jun '22: Added new omicron data.
Notes_Following_Up 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]

Our privacy policy