SMTL ID : 7bei.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 4 residues within 4Å: Chain C: F.15, G.16, N.20, V.44 No protein-ligand interaction detected (PLIP)

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 3 residues within 4Å: Chain A: S.43, R.84, S.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.43, A:R.84 Water bridges: A:R.84 NO3.3: 4 residues within 4Å: Chain A: P.136, S.137, V.138 Chain B: E.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.138, A:V.138 NO3.7: 5 residues within 4Å: Chain B: S.44, Y.45 Chain C: Y.126, S.171, Y.172 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.126, B:S.44

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: T.70 Chain C: T.92 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: I.25, S.30 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: G.179, V.180 Chain B: D.182 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: Q.50, Q.51, K.52, K.55, A.56 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: P.109, G.110 Ligand excluded by PLIP

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-150 heavy chain: A
COVOX-150 light chain: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

COVOX-150 heavy chain

COVOX-150 light chain

Spike glycoprotein

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