Structure Viewer: 7kmg

>   Structure details

Ly-Cov555 Neutralizing antibody against Sars-Cov-2

PDB7kmg
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.16Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
AffinityNA
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>   Fv information

This PDB has 2 Fv(s).

>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
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
Q V Q L V Q S G A E V K K P G S S V K V S C K A S G G T F S N Y A I S W V R Q A P G Q G L E W M G R I I P I L G I A N Y A Q K F Q G R V T I T A D K S T S T A Y M E L S S L R S E D T A V Y Y C A R G Y Y E A R H Y Y Y Y Y A M D V W G Q G T A 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 M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L S 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 T S L Q P E D F A T Y Y C Q Q S Y S T P R T F G Q G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPHHHHHH

CDR Sequences (chothia definition)
CDRH1GGTFSNY
CDRH2IPILGI
CDRH3GYYEARHYYYYYAMDV
CDRL1RASQSISSYLS
CDRL2AASSLQS
CDRL3QQSYSTPRT

Orientation Angles (from ABangle)
HL-61.72°
HC171.0°
HC2117.34°
LC1121.72°
LC283.32°
dc15.97Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV1
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
Q V Q L V Q S G A E V K K P G S S V K V S C K A S G G T F S N Y A I S W V R Q A P G Q G L E W M G R I I P I L G I A N Y A Q K F Q G R V T I T A D K S T S T A Y M E L S S L R S E D T A V Y Y C A R G Y Y E A R H Y Y Y Y Y A M D V W G Q G T A 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 M T Q S P S S L S A S V G D R V T I T C R A S Q S I S S Y L S 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 T S L Q P E D F A T Y Y C Q Q S Y S T P R T F G Q G T K V E I K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namespike protein s1
Antigen speciesSEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2
Antigen sequenceFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPHHHHHH

CDR Sequences (chothia definition)
CDRH1GGTFSNY
CDRH2IPILGI
CDRH3GYYEARHYYYYYAMDV
CDRL1RASQSISSYLS
CDRL2AASSLQS
CDRL3QQSYSTPRT

Orientation Angles (from ABangle)
HL-63.12°
HC170.69°
HC2116.88°
LC1121.23°
LC282.58°
dc15.97Å
>   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 (weak);SARS-CoV2_Gamma (weak);SARS-CoV2_Delta (weak)
Does_not_bind_to SARS-CoV2_Mu;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV2_Omicron-BA2.11;SARS-CoV2_Omicron-BA2.12.1;SARS-CoV2_Omicron-BA2.4;SARS-CoV2_Omicron-BA2.5
Neutralising_vs SARS-CoV2_WT;SARS-CoV2_Alpha;SARS-CoV2_Beta (weak);SARS-CoV2_Delta
Not_Neutralising_vs SARS-CoV2_Mu;SARS-CoV2_Omicron-BA1;SARS-CoV2_Omicron-BA2;SARS-CoV2_Omicron-BA2.11;SARS-CoV2_Omicron-BA2.12.1;SARS-CoV2_Omicron-BA2.4;SARS-CoV2_Omicron-BA2.5
Protein_and_Epitope S; RBD
Origin B-cells; SARS-CoV2_WT Human Patient
VH_or_VHH QVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYAISWVRQAPGQGLEWMGRIIPILGIANYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARGYYEARHYYYYYAMDVWGQGTAVTVSS
VL DIQMTQSPSSLSASVGDRVTITCRASQSISSYLSWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCQQSYSTPRTFGQGTKVEIK
Heavy_V_Gene IGHV1-69 (Human)
Heavy_J_Gene IGHJ6 (Human)
Light_V_Gene IGKV1-39 (Human)
Light_J_Gene IGKJ1 (Human)
CDRH3 ARGYYEARHYYYYYAMDV
CDRL3 QQSYSTPRT
Structures https://www.rcsb.org/structure/7KMG;
https://www.rcsb.org/structure/7L3N
ABB_Homology_Model None
Sources INN Proposed List P124 (https://www.who.int/medicines/publications/druginformation/innlists/PL124-COVID.pdf);
Bryan Jones et al., 2020 (https://www.biorxiv.org/content/10.1101/2020.09.30.318972v1);
Delphine Planas et al., 2021 (https://www.nature.com/articles/s41586-021-03777-9);
Daniel Sheward et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.19.473354v1);
Laura VanBlargan et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.15.472828v1);
Delphine Planas et al., 2021 (https://www.nature.com/articles/d41586-021-03827-2);
Lihong Liu et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.14.472719v3);
Xun Wang et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.24.474138v1);
Takuya Tada et al., 2021 (https://www.biorxiv.org/content/10.1101/2021.12.28.474369v1);
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);
Celine Boschi et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.01.03.474769v1);
Hang Ma et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.25.482049v1);
Hao Zhou et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.15.480166v2);
Sho Iketani et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.02.07.479306v1);
Prerna Arora et al., 2022 (https://www.sciencedirect.com/science/article/pii/S2211124722005186);
Daichi Yamasoba et al., 2022 (https://www.biorxiv.org/content/10.1101/2022.05.03.490409v1)
Date_Added Nov 11, 2020
Last_Updated Jun 14, 2022
Update_Description 14th Nov: Corrected CDRL3 sequence; 30th Jan: Added PDB structure and publication; 28th Dec '21: Added variant binding/neutralisation data; 31st Jan '22: Added new neutralisation study; 4th Mar '22: Added omicron BA2 data; 20th April '22: Added new reference and mu variant data; 14th Jun '22: Added new reference and omicron variant data.
Notes_Following_Up Therapeutic mAb. Also known as LY-CoV555. Debate as to whether completely loses neutralising ability versus Beta Gamma and Delta. 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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