SMTL ID : 7bej.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG-FUC.1: 5 residues within 4Å: Chain C: F.15, G.16, N.20, V.44, L.45 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: F.170, P.171, S.181, L.182, S.183 Chain B: Q.160, S.162, S.176, S.177, T.178 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.162, B:S.176, B:T.178, B:T.178, A:S.181, A:S.183 GOL.5: 4 residues within 4Å: Chain C: G.81, R.85, Y.185 Ligands: FMT.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.85

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain B: Q.37, Q.38, K.39, K.42, A.43, K.45 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.37, B:K.39 FMT.4: 2 residues within 4Å: Chain C: F.19, N.20 No protein-ligand interaction detected (PLIP) FMT.6: 7 residues within 4Å: Chain B: Y.32 Chain C: R.80, Y.172, G.173, F.174, N.178, Y.182 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.80, C:G.173, C:N.178 FMT.7: 1 residues within 4Å: Ligands: GOL.5 No protein-ligand interaction detected (PLIP) FMT.8: 1 residues within 4Å: Chain C: T.107 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.107 FMT.9: 4 residues within 4Å: Chain C: R.134, E.142, R.143, D.144 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.134, C:R.143 Water bridges: C:R.143, C:I.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., The antigenic anatomy of SARS-CoV-2 receptor binding domain. Cell (2021)

Release Date

2021-03-03

Peptides

COVOX-158 heavy chain: A
COVOX-158 light chain: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

COVOX-158 heavy chain

COVOX-158 light chain

Spike glycoprotein

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