SMTL ID : 7or9.1

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-1-1-1-1-1-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 A: N.20, A.21, L.118, R.186 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: G.81, D.82, R.85, V.180, Y.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.82, A:R.85, A:Y.185 GOL.6: 4 residues within 4Å: Chain C: G.9, Y.88, G.100, G.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.88, C:Y.88, C:G.101

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

CL.3: 2 residues within 4Å: Chain A: F.106, T.107 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Q.86, K.94 Chain B: Y.52 Chain C: Y.92 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: Y.151, E.154, P.155, V.156, A.174 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain C: P.60, R.62 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 7 residues within 4Å: Chain C: Y.50, T.54 Chain D: S.52, N.54, N.55, Y.57, Y.106 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.50, D:N.54, D:N.54, D:N.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell (2021)

Release Date

2021-07-07

Peptides

Spike protein S1: A
COVOX-222 Fab heavy chain: B
COVOX-222 Fab light chain: C
COVOX-278 Fab heavy chain: D
COVOX-278 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
B

D
H

E
L

Spike protein S1

COVOX-222 Fab heavy chain

COVOX-222 Fab light chain

COVOX-278 Fab heavy chain

COVOX-278 Fab light chain

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