Structure Viewer: 7e8m

>   Structure details

Crystal Structure of Sars-Cov-2 antibody P2C-1F11 with Mutated Rbd

PDB7e8m
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.09Å
Number of Fvs1
In complexTrue
Light chain typeKappa
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 subgroupIGHV3
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 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 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 I T V S S N Y M N W V R Q A P G K G L E W V S L I Y S G G S T Y Y A D S V K G R F T I S R D N S K N T L Y L Q M N S L R A E D T A V Y H C A R D L V V 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 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 I 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 G S S P T F G Q G T K L E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGP

CDR Sequences (chothia definition)
CDRH1GITVSSN
CDRH2YSGGS
CDRH3DLVVYGMDV
CDRL1RASQSVSSSYLA
CDRL2GASSRAT
CDRL3QQYGSSPT

Orientation Angles (from ABangle)
HL-57.94°
HC171.16°
HC2118.81°
LC1122.06°
LC283.93°
dc16.3Å
>   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 (weak);SARS-CoV2_Omicron-BA2 (weak)
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 (weak);SARS-CoV2_Omicron-BA2 (weak)
Not_Neutralising_vs None
Protein_and_Epitope S; RBD
Origin ND
VH_or_VHH EVQLVESGGGLVQPGGSLRLSCAASGITVSSNYMNWVRQAPGKGLEWVSLIYSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYHCARDLVVYGMDVWGQGTTVTVSS
VL EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPTFGQGTKLEIK
Heavy_V_Gene IGHV3-11 (Human)
Heavy_J_Gene IGHJ5 (Human)
Light_V_Gene IGKV1-9 (Human)
Light_J_Gene IGKJ4 (Human)
CDRH3 ARDLVVYGMDV
CDRL3 QQYGSSPT
Structures http://www.rcsb.org/structure/7CDI;
https://www.rcsb.org/structure/7E8M
ABB_Homology_Model None
Sources PDB (http://www.rcsb.org/structure/7CDI);
Lihong Liu et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.14.472719v3);
Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1)
Date_Added Nov 22, 2020
Last_Updated Mar 4, 2022
Update_Description 27th May '21: Added extra structure (7e8m). 28th Dec '21: Added variant neutralisation data. 4th Mar '22: Added Omicron-BA2 data
Notes_Following_Up Awaiting publication for full reference and neutralisation data (X. Wang et al.). Therapeutic antibody Amubarvimab. Also known as Brii-196.

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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