SMTL ID : 7beh.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 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: 3 residues within 4Å: Chain A: F.15, G.16, N.20 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.2: 10 residues within 4Å: Chain A: T.155, P.156, C.157, N.158, V.160 Chain B: T.71, N.72 Chain C: Y.106, S.109, N.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.156, A:N.158

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.19, N.20, S.50, F.51, W.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 GOL.4: 4 residues within 4Å: Chain B: Q.56, D.102, L.192 Chain C: E.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.56, B:L.192

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 8 residues within 4Å: Chain B: Y.167, E.170, P.171, V.172, F.188, P.189, A.190, L.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.167, B:E.170, B:V.172, B:V.172, B:F.188, B:A.190 TRS.6: 6 residues within 4Å: Chain B: G.55 Chain C: P.21, D.100, Y.102, G.116, G.117 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.21, C:D.100, C:G.117, C:V.161

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

Spike glycoprotein: A
COVOX-316 heavy chain: B
COVOX-316 light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

Spike glycoprotein

COVOX-316 heavy chain

COVOX-316 light chain

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