SMTL ID : 7qny.1

The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with COVOX-58 and COVOX-158 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain B: A.79, G.80, S.170, N.171, N.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.170 GOL.4: 3 residues within 4Å: Chain E: T.206, K.207, S.208 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.207, E:S.208, E:S.208

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain C: G.13, F.16, N.17, L.42 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.16, C:L.42 Hydrogen bonds: C:N.17

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain D: L.99, S.101, D.103 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.101, D:D.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dejnirattisai, W. et al., SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell (2022)

Release Date

2022-01-19

Peptides

COVOX-58 heavy chain: A
COVOX-58 light chain: B
Surface glycoprotein: C
COVOX-158 heavy chain: D
COVOX-158 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
H

E
L

COVOX-58 heavy chain

COVOX-58 light chain

Surface glycoprotein

COVOX-158 heavy chain

COVOX-158 light chain

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