SMTL ID : 7xch.1

Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human ACE2 ectodomain (two-RBD-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: N.107, N.110, V.112, F.139, Y.142 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.142 Hydrogen bonds: A:Y.142, A:Y.142, A:Y.142 NAG-NAG.2: 5 residues within 4Å: Chain A: T.93, T.94, N.218, T.220, R.221 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.264, E.265, N.266 Chain C: K.542 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.315, Q.564 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.693 Chain B: Y.780 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.701, L.906, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.693 Chain C: I.778, Y.780 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.701, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: K.542 Chain C: N.264, E.265, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain A: Y.780 Chain C: N.693 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.701, L.906, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: A.690, E.1056, N.1058 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.690 NAG-NAG.20: 4 residues within 4Å: Chain C: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain D: K.398, S.402, D.525, S.527, N.528 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: S.402, D.525, S.527, N.528 No protein-ligand interaction detected (PLIP)

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

NAG.24: 2 residues within 4Å: Chain A: N.4, N.122 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: A.690, E.1056, K.1057, N.1058 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.600, T.602 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.107, A.108, T.109, S.137 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.147 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: T.93, N.218 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: K.542 Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.315, Q.564 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.600, T.602, Q.628, R.630 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.146, N.147 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.218 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain D: K.8, N.72, V.75 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.304 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain D: Q.63, Q.83, N.85, V.89 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.414, E.415, W.576 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain E: N.35, T.37, E.39, Q.322 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.72 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: E.294, N.304 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: Q.63, Q.83, N.85, V.89 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.40: 3 residues within 4Å: Chain D: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.356, D:H.360, D:E.384 ZN.44: 3 residues within 4Å: Chain E: H.356, H.360, E.384 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.356, E:H.360, E:E.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Z. et al., Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun (2022)

Release Date

2022-08-31

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Processed angiotensin-converting enzyme 2

Related Entries With Identical Sequence