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

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

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

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 13 residues within 4Å: Chain A: K.135, A.152, G.153, S.154, N.164 Chain C: N.48, R.65, Y.67, N.73, H.113, C.114, S.115, Y.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.154, A:S.154, A:N.164

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

ACT.2: 4 residues within 4Å: Chain A: P.103, D.104, P.140 Chain B: Y.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.104

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.16, E.17, N.20, A.21, T.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.22, A:T.22

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

NAG.4: 4 residues within 4Å: Chain A: F.15, G.16, N.20, V.44 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.15

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-45 heavy chain: B
COVOX-88 heavy chain: C
COVOX-88 light chain: D
COVOX-45 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
A

C
H

D
L

E
B

Spike glycoprotein

COVOX-45 heavy chain

COVOX-88 heavy chain

COVOX-88 light chain

COVOX-45 light chain

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