SMTL ID : 7lm9.1

Crystal structure of SARS-CoV spike protein receptor-binding domain in complex with a cross-neutralizing antibody CV38-142 Fab isolated from COVID-19 patient

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 13 residues within 4Å: Chain A: F.20, G.21, F.24, N.25, V.49, L.50 Chain B: R.100, Y.103 Chain C: S.31, Y.49, S.53 Ligands: EDO.3, EDO.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:R.100, C:S.31 Hydrogen bonds: C:S.53, C:S.53 Hydrophobic interactions: B:Y.103

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: K.28, F.29, P.30, S.31, N.132, Y.133 6 PLIP interactions: 6 interactions with chain A Water bridges: A:S.31, A:S.31, A:S.31, A:N.130, A:N.132, A:Y.133 EDO.3: 7 residues within 4Å: Chain A: F.24, N.25, F.55, W.118 Chain B: S.104 Ligands: NAG-NAG-BMA-FUC.1, EDO.4 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.104, A:N.25, A:W.118 EDO.4: 5 residues within 4Å: Chain A: S.53, F.55 Ligands: NAG-NAG-BMA-FUC.1, NAG-NAG-BMA-FUC.1, EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.53 EDO.5: 5 residues within 4Å: Chain A: R.37, Y.78, F.146, S.195, E.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:E.197, A:E.197 EDO.6: 6 residues within 4Å: Chain B: L.151, V.179, S.187, L.188, S.189 Chain C: T.180 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.189 Water bridges: B:S.189, B:S.189, B:S.189, C:T.180, C:T.180 EDO.7: 5 residues within 4Å: Chain B: S.7, K.19, I.20, S.21, Y.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.21, B:S.21 EDO.8: 6 residues within 4Å: Chain C: Q.37, K.45, R.61, F.62, E.81, D.82 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.37, C:K.45, C:K.45, C:D.82, C:D.82 Water bridges: C:K.39 EDO.9: 3 residues within 4Å: Chain C: S.65, G.66, S.67 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.66, C:S.67 Water bridges: C:G.64, C:S.67 EDO.10: 9 residues within 4Å: Chain C: P.121, L.127, Y.188, F.211, N.212, R.213, G.214, E.215, C.216 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.214, C:E.215 EDO.11: 4 residues within 4Å: Chain C: L.156, Q.157, S.158, N.160 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.158, C:S.158, C:N.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection. Cell Host Microbe (2021)

Release Date

2021-03-31

Peptides

Spike glycoprotein: A
CV38-142 Fab heavy chain: B
CV38-142 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

CV38-142 Fab heavy chain

CV38-142 Fab light chain

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