SMTL ID : 7tn0.1 (1 other biounit)

SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

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

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: P.113, S.114, V.115, V.205, K.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.113, A:V.115 EDO.8: 4 residues within 4Å: Chain B: Q.3, L.4, W.117, Q.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.4, B:W.117, B:Q.119 EDO.19: 4 residues within 4Å: Chain D: T.5, S.7, T.22, R.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.7, D:T.22, D:T.22, D:R.24 EDO.20: 6 residues within 4Å: Chain D: Q.38, K.39, P.40, A.84, I.85, E.166 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.38, D:I.85

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

CL.2: 4 residues within 4Å: Chain A: V.115, F.116, I.117, K.207 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: Q.38, R.46 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.46, L.47 Chain B: D.115 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.98 Chain B: L.45, E.46, W.47 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: R.102 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: T.72, T.74 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: R.151, W.459, W.460, K.463, D.481 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: H.177, R.201 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: E.384, Y.497, R.500 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: P.328, E.357, E.384 Ligands: ZN.10 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain F: A.25, S.26 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain C: H.356, H.360, E.384 Ligands: CL.15 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.356, C:H.360, C:E.384, H2O.3

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

NAG.11: 4 residues within 4Å: Chain C: K.291, E.294, N.304 Chain E: R.86 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:R.86, C:K.291, C:N.304 NAG.14: 1 residues within 4Å: Chain C: N.414 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain C: K.8, N.72 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.8 NAG.17: 5 residues within 4Å: Chain C: N.35, T.37, E.39, N.40, Q.322 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.35, C:T.37, C:N.40 NAG.18: 4 residues within 4Å: Chain C: S.402, D.525, S.527, N.528 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.402, C:S.402, C:S.402, C:N.528 NAG.21: 6 residues within 4Å: Chain A: Y.50 Chain B: Y.100 Chain F: D.16, F.19, N.20, V.44 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:F.19, F:V.44 Hydrogen bonds: B:Y.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCallum, M. et al., Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science (2022)

Release Date

2022-02-02

Peptides

S309 light chain: A
S309 heavy chain: B
Angiotensin-converting enzyme 2: C
S304 Fab light chain: D
S304 Fab heavy chain: E
Spike protein S1: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
G

E
H

F
I

S309 light chain

S309 heavy chain

Angiotensin-converting enzyme 2

S304 Fab light chain

S304 Fab heavy chain

Spike protein S1

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