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

Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

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

Ligands

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

NAG-NAG-BMA-MAN-MAN-FUC.1: 15 residues within 4Å: Chain A: F.15, G.16, F.19, N.20, V.44 Chain D: Q.1, Y.32, R.98, Y.100, G.112, G.113, D.115 Chain E: Y.50, R.55, T.57 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.100, E:Y.50 Hydrogen bonds: D:Y.32, D:Y.32, D:D.115

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: F.19, N.20, S.50, F.51, W.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:S.50 pi-Stacking: A:W.113 IMD.11: 7 residues within 4Å: Chain D: W.47, W.50, N.59, T.101, R.102 Chain E: S.95, L.96 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.59, D:T.101, D:T.101 pi-Cation interactions: D:R.102 IMD.13: 5 residues within 4Å: Chain D: T.53, Y.54, N.55, T.72, T.74 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.72

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain B: E.59, W.60 Chain C: T.110, F.111 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain B: R.65, S.67, G.68, H.69 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: I.15, K.103, N.106 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: Q.16, T.110 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: H.178 Chain E: D.167 Ligand excluded by PLIP

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 6 residues within 4Å: Chain B: I.71, Y.72, Y.73, K.78 Chain C: L.2, F.3 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:Y.72, C:F.3 Hydrogen bonds: B:I.71, B:Y.73, C:L.2 Salt bridges: B:K.78

3 x GLY: GLYCINE(Non-covalent)

GLY.6: 3 residues within 4Å: Chain B: S.67, R.85, N.87 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.85, B:N.87 GLY.12: 1 residues within 4Å: Chain D: R.85 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.85 GLY.16: 5 residues within 4Å: Chain D: L.45, E.46, W.47 Chain E: T.97, F.98 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:F.98, D:L.45, D:W.47

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 6 residues within 4Å: Chain C: S.22, T.98, Y.100, Q.113, G.114, K.116 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: R.23, A.25 Chain D: E.108 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.108

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.15: 6 residues within 4Å: Chain D: Q.43 Chain E: G.9, T.10, Y.88, G.100, G.101 No protein-ligand interaction detected (PLIP)

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-384 heavy chain: B
COVOX-384 light chain: C
S309 heavy chain: D
S309 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
A

C
B

D
H

E
L

Spike glycoprotein

COVOX-384 heavy chain

COVOX-384 light chain

S309 heavy chain

S309 light chain

Related Entries With Identical Sequence