SMTL ID : 7bel.2 (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: A.152, S.154, F.163, N.164 Chain C: N.48, R.65, Y.67, N.73, H.113, C.114, S.115 Chain D: N.44, D.107 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:N.44, A:S.154, A:S.154, A:N.164

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

ACT.2: 5 residues within 4Å: Chain A: P.103, D.104, P.140 Chain B: Y.53, Y.102 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.140 Hydrogen bonds: A:D.104, B:Y.53 Water bridges: B:Y.102 ACT.3: 2 residues within 4Å: Chain A: G.90, T.92 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.92 Hydrogen bonds: A:G.90 Salt bridges: A:K.101

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

NAG.4: 5 residues within 4Å: Chain A: F.15, G.16, N.20, V.44, L.45 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.15, A:L.45

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
X

B
C

C
E

D
F

E
D

Spike glycoprotein

COVOX-45 heavy chain

COVOX-88 heavy chain

COVOX-88 light chain

COVOX-45 light chain

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