SMTL ID : 7wrh.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

22 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: N.125, N.128, V.130, K.132, Y.160, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: T.111, T.112, N.236, T.238 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.282, E.283, N.284 Chain C: K.560 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.333, Q.582, L.584 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.711 Chain B: I.796, Y.798 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.719, L.924, Q.928, Q.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.803, S.805, Q.806 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.711 Chain C: I.796, Y.798 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.719, L.924, Q.928, Q.1073 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.924 NAG-NAG.12: 3 residues within 4Å: Chain B: N.803, S.805, Q.806 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: A.708, E.1074, N.1076 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.708 NAG-NAG.14: 4 residues within 4Å: Chain B: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.1136 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.282, E.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain A: I.796, Y.798 Chain C: N.711 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.719, L.924, Q.928, Q.1073 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.924 NAG-NAG.19: 3 residues within 4Å: Chain C: N.803, S.805, Q.806 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: S.706, A.708, E.1074, N.1076 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.708 NAG-NAG.21: 4 residues within 4Å: Chain C: N.1100, T.1102, H.1103, F.1105 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain C: N.1136 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain A: N.22, N.140 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.33, N.66 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: E.135, N.164, N.165 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: D.341, F.344, N.345, V.369, N.372 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: E.1074, N.1076 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.618, T.620 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.22, L.23, T.24, R.26, D.141 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.66 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.125, A.126, T.127 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Q.118, N.165 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: T.111, N.236 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.282, E.283, N.284 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.333, Q.582 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: F.340, D.341, F.344, N.345, N.372 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.618, Q.646 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.22 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.33, N.66 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: N.125, T.127, N.128, V.130 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain B: R.459, K.464, E.467 Chain C: N.236, T.238 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.333, Q.582 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: D.341, F.344, N.345 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.618 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.46: 3 residues within 4Å: Chain D: H.357, H.361, E.385 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.357, D:H.361, D:E.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s. Cell Discov (2022)

Release Date

2023-02-01

Peptides

Spike glycoprotein: ABC
Processed angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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