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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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 B: H.100, N.102, S.105, Y.107 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.107 Hydrogen bonds: B:S.105

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 2 residues within 4Å: Chain A: R.32, R.34 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.32 IMD.11: 3 residues within 4Å: Chain D: V.101 Chain E: Y.49, Q.55 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.55

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: W.30, N.31, R.32, R.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.32, A:R.32 GOL.4: 8 residues within 4Å: Chain A: C.157, V.160, E.161, G.162, F.163, C.165 Chain C: Y.33, G.93 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.158, A:F.163, C:G.93 GOL.10: 5 residues within 4Å: Chain A: Y.126, N.127 Chain D: V.104 Chain E: A.50, S.53 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.53, E:S.53, A:N.127 GOL.12: 12 residues within 4Å: Chain D: F.180, P.181, V.183, S.191, L.192, S.193 Chain E: Q.160, E.161, S.162, S.176, S.177, T.178 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:S.191, D:S.193, E:S.162, E:S.176, E:T.178

6 x BR: BROMIDE ION(Non-covalent)

BR.5: 2 residues within 4Å: Chain B: G.56, T.58 Ligand excluded by PLIP BR.6: 6 residues within 4Å: Chain B: R.44, L.45, E.46, W.47 Chain C: T.98, F.99 Ligand excluded by PLIP BR.8: 2 residues within 4Å: Chain D: Q.53, Y.111 Ligand excluded by PLIP BR.9: 4 residues within 4Å: Chain D: I.51, K.58, S.71, R.72 Ligand excluded by PLIP BR.13: 2 residues within 4Å: Chain E: H.189, R.211 Ligand excluded by PLIP BR.14: 2 residues within 4Å: Chain E: G.28, S.30 Ligand excluded by PLIP

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.7: 11 residues within 4Å: Chain B: G.42, Q.43 Chain C: T.10, Q.39, P.41, G.42, V.86, Y.88, Q.101, G.102, K.104 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.42, C:Y.88

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-253 heavy chain: B
COVOX-253 light chain: C
COVOX-75 heavy chain: D
COVOX-75 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
H

C
L

D
A

E
B

Spike glycoprotein

COVOX-253 heavy chain

COVOX-253 light chain

COVOX-75 heavy chain

COVOX-75 light chain

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