Structure Viewer: 7cm4

>   Structure details

Crystal Structure of Covid-19 Virus Spike Receptor-Binding Domain complexed with a Neutralizing antibody Ct-P59

PDB7cm4
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.71Å
Number of Fvs1
In complexTrue
Light chain typeLambda
Has constant regionTrue
AffinityNA
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>   Fv information

This PDB has 1 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV2
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 31A 31B 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 100E 100F 100G 100H 100I 100J 101 102 103 104 105 106 107 108 109 110 111 112 113
Q I T L K E S G P T L V K P T Q T L T L T C S F S G F S L S T S G V G V G W I R Q P P G K A L E W L A L I D W D D N K Y H T T S L K T R L T I S K D T S K N Q V V L T M T N M D P V D T A T Y Y C A R I P G F L R Y R N R Y Y Y Y G M D V W G Q G T T V T 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 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 96 97 98 99 100 101 102 103 104 105 106 107
E L V L T Q P P S V S A A P G Q K V T I S C S G S S S N I G N N Y V S W Y Q Q L P G T A P K L L I Y D N N K R P S G I P D R F S G S K S G T S A T L G I T G L Q T G D E A D Y Y C G T W D S S L S A G V F G G G T E L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namespike glycoprotein
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNHHHHHHHH

CDR Sequences (chothia definition)
CDRH1GFSLSTSGV
CDRH2DWDDN
CDRH3IPGFLRYRNRYYYYGMDV
CDRL1SGSSSNIGNNYVS
CDRL2DNNKRPS
CDRL3GTWDSSLSAGV

Orientation Angles (from ABangle)
HL-53.77°
HC169.81°
HC2120.06°
LC1119.92°
LC283.51°
dc15.87Å
>   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
Does_not_bind_to SARS-CoV2_Omicron-BA1
Neutralising_vs SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta;SARS-CoV2_Gamma;SARS-CoV2_Delta
Not_Neutralising_vs SARS-CoV2_Omicron-BA1
Protein_and_Epitope S; RBD
Origin Phage Display (Ab, human, immune - SARS-CoV2)
VH_or_VHH QITLKESGPTLVKPTQTLTLTCSFSGFSLSTSGVGVGWIRQPPGKALEWLALIDWDDNKYHTTSLKTRLTISKDTSKNQVVLTMTNMDPVDTATYYCARIPGFLRYRNRYYYYGMDVWGQGTTVTVSS
VL ELVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAGVFGGGTELTVL
Heavy_V_Gene IGHV2-70 (Human)
Heavy_J_Gene IGHJ6 (Human)
Light_V_Gene IGLV1-51 (Human)
Light_J_Gene IGLJ3 (Human)
CDRH3 ARIPGFLRYRNRYYYYGMDV
CDRL3 GTWDSSLSAGV
Structures https://www.rcsb.org/structure/7CM4
ABB_Homology_Model None
Sources INN Proposed List P124 (https://www.who.int/medicines/publications/druginformation/innlists/PL124-COVID.pdf);
Dong Kyun-Ryu et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.07.08.451696v1);
Laura VanBlargan et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.15.472828v1);
Xun Wang et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.24.474138v1);
Tongqing Zhou et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.27.474307v1);
Cheolmin Kim et al., 2021 (https://www.nature.com/articles/s41467-020-20602-5);
Matthew McCallum et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.28.474380v1);
Franck Touret et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.01.474639v1)
Date_Added Nov 11, 2020
Last_Updated Jan 31, 2022
Update_Description 30th Jan: Added PDB structure; 24th July '21: Added new publication with variant binding data; 28th Dec '21: Added Omicron-BA1 neutralisation data; 31st Jan '22: Added new neutralisation study and origin
Notes_Following_Up Therapeutic mAb. Also known as CT-P59. Variant binding data in Ryu 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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