SMTL ID : 7beo.1 (1 other biounit)

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 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: 5 residues within 4Å: Chain B: H.100, N.102, T.104, S.105, Y.107 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.107 Hydrogen bonds: B:S.105

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

NAG.2: 4 residues within 4Å: Chain A: F.15, G.16, F.19, N.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.19 Hydrogen bonds: A:N.20

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain B: N.57, T.58 Chain D: A.119, N.121, Y.123 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.57, B:T.58, B:T.58

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: V.160 Chain C: Y.33, G.93 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.33 ACT.5: 4 residues within 4Å: Chain D: T.192, F.193, P.194, L.205 No protein-ligand interaction detected (PLIP) ACT.6: 6 residues within 4Å: Chain A: Q.175 Chain D: S.65, Q.66, N.70, Y.123, Y.124 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.175, D:Q.66 ACT.7: 4 residues within 4Å: Chain D: H.191 Chain E: T.177, E.178, D.180 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:T.177 Hydrogen bonds: E:E.178 Salt bridges: D:H.191

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

Spike glycoprotein: A
COVOX-253H55L heavy chain: B
COVOX-253H55L light chain: C
COVOX-75 heavy chain: D
COVOX-75 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
H

C
L

D
A

E
B

Spike glycoprotein

COVOX-253H55L heavy chain

COVOX-253H55L light chain

COVOX-75 heavy chain

COVOX-75 light chain

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