SMTL ID : 7xo8.1

SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three human ACE2 Bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.1069, N.1071 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.1095, G.1096, H.1098, F.1100 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.706, G.1128 Chain C: Y.793 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: E.651, Y.652, N.654 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: E.306, N.600 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: E.1069, N.1071 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.1095, G.1096, H.1098, F.1100 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: E.306, N.600 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: Y.25, N.27, N.58 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: N.119, A.120, T.121, N.122 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: I.791, Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.1095, G.1096, H.1098, F.1100 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.798, S.800 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: Y.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.118, N.119, N.122 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: S.420, D.543, S.545, N.546 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain D: E.22, K.26, Q.89, N.90 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: S.420, S.545, N.546 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain E: E.22, K.26, Q.89, N.90 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain F: S.420, D.543, S.545, N.546 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain F: E.22, K.26, Q.89, N.90 Ligand excluded by PLIP

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

CL.34: 4 residues within 4Å: Chain D: R.169, W.477, K.481, D.499 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain E: R.169, W.477, K.481, D.499 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain F: R.169, W.477, K.481, D.499 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.35: 3 residues within 4Å: Chain D: H.374, H.378, E.402 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.374, D:E.402 ZN.39: 3 residues within 4Å: Chain E: H.374, H.378, E.402 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.374, E:E.402 ZN.43: 3 residues within 4Å: Chain F: H.374, H.378, E.402 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.374, F:E.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins. Cell Res. (2022)

Release Date

2022-06-15

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
E

Spike glycoprotein

Angiotensin-converting enzyme 2

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