SMTL ID : 7bem.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 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 Ligands: GOL.6 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Y.33, S.35, V.50, Y.52, D.98 Chain B: P.100 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:S.96, B:P.98 Hydrogen bonds: A:S.35, A:S.35, A:Y.52, A:D.98 GOL.6: 5 residues within 4Å: Chain C: N.20, S.50, F.51, W.113 Ligands: NAG-NAG-FUC.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.50, C:S.50

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

CL.3: 2 residues within 4Å: Chain A: G.65, F.67 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain C: F.54, K.55 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 7 residues within 4Å: Chain B: Q.40, K.48, P.62, R.64, F.65, E.84, D.85 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.40, B:R.64 Salt bridges: B:K.42, B:K.48 PO4.5: 6 residues within 4Å: Chain A: F.99, D.105 Chain B: Y.52, Q.58, S.59 Chain C: F.163 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.52, B:Q.58, B:Q.58, B:S.59, B:S.59

4 x PRO: PROLINE(Non-covalent)

PRO.7: 4 residues within 4Å: Chain C: T.53, G.81, R.85, Y.185 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:Y.185 Salt bridges: C:R.85 PRO.8: 3 residues within 4Å: Chain C: K.55, C.56, Y.57 1 PLIP interactions: 1 interactions with chain C, Hydrogen bonds: C:C.56 PRO.9: 2 residues within 4Å: Chain A: V.2 Chain C: F.163 5 PLIP interactions: 4 Ligand-Ligand interactions, 1 interactions with chain C Hydrogen bonds: P.9, P.9, P.9, P.9 Hydrophobic interactions: C:F.163 PRO.10: 4 residues within 4Å: Chain C: R.23, F.24, A.25, N.31 2 PLIP interactions: 2 interactions with chain C, Hydrophobic interactions: C:R.23 Hydrogen bonds: C:N.31

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-269 Vh domain: A
COVOX-269 Vl domain: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

COVOX-269 Vh domain

COVOX-269 Vl domain

Spike glycoprotein

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