SMTL ID : 7neh.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 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, L.45 No protein-ligand interaction detected (PLIP)

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

EDO.2: 4 residues within 4Å: Chain A: N.30, R.71, N.73 Chain C: K.135 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: Y.33, Y.52, D.98, E.101, G.102 Chain C: K.94 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: S.35, W.47, V.50, D.98, G.102, F.104 Ligands: EDO.3, NO3.5 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: G.55, S.56, T.57, F.58 Chain C: T.92 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: A.24, S.25, G.26, N.76 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: S.124, V.125, F.126, V.211, K.213 Chain B: E.124 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: L.145, V.173, S.181, L.182, S.183 Chain B: T.179 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain B: P.120, Y.187, F.210, N.211, R.212, G.213, E.214, C.215 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: L.126, Y.187, E.188, R.212 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: R.143, A.145, E.162, L.176 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: Q.39, Y.94 Chain B: Q.38, K.39, P.40, G.41, K.42 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: Q.37, K.45, R.61, F.62, E.81, D.82 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: D.105, F.106, T.107, S.191, F.192, E.193 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: R.32, Y.73, F.141, S.191, E.193 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: G.81, D.82, R.85, V.180, Y.185 Ligands: NO3.22 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: F.19, N.20, F.51, W.113 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: N.92 Chain C: R.80, E.83, Q.86, K.94 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: W.30, R.32, R.143 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: S.52, T.53, F.54, K.55 Ligand excluded by PLIP

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

NO3.5: 4 residues within 4Å: Chain A: W.47, Y.52 Chain B: P.95 Ligands: EDO.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.52, B:P.95 NO3.12: 3 residues within 4Å: Chain B: S.157, G.158, S.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.158 Water bridges: B:N.159, B:S.160 NO3.22: 4 residues within 4Å: Chain C: S.52, T.53, Y.185 Ligands: EDO.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.53, C:T.53

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 4 residues within 4Å: Chain B: V.58, P.59, S.60, R.61 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.58, B:S.60, B:R.61, B:R.61

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.17: 1 residues within 4Å: Chain B: R.212 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.212

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

CL.26: 3 residues within 4Å: Chain A: R.31 Chain C: Y.150, Q.151 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Supasa, P. et al., Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell (2021)

Release Date

2021-03-03

Peptides

COVOX-269 Fab heavy chain: A
COVOX-269 fab light chain: B
Spike glycoprotein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
E

COVOX-269 Fab heavy chain

COVOX-269 fab light chain

Spike glycoprotein

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