SMTL ID : 7ya0.1

Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (S-6P-RRAR)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

15 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: 3 residues within 4Å: Chain A: N.315, I.316, Q.564 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.693 Chain B: Y.780 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.780 NAG-NAG.3: 3 residues within 4Å: Chain A: N.701, L.906, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.1082, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.315, Q.564, T.565 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.701, L.906, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.701, L.906, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: Y.15, N.48 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: E.265, N.266 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: D.323, F.326, N.327, V.351 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.587 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.600, T.602 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.1058 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: E.265, N.266 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: F.322, D.323, F.326, N.327 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.600, T.602 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.693 Chain C: Y.780 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: E.265, N.266 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.315, Q.564, T.565 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.600, T.602 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: Y.780 Chain C: N.693 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.1056, N.1058 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: N.35, T.37, E.39, Q.322 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain D: N.72 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.304 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain D: N.414 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain D: S.299, S.402, S.527, N.528 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain E: N.35, T.37, E.39, Q.322 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: K.8, Q.71, N.72 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.304, M.305 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain E: F.267, N.414, E.415, I.418, W.576 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain E: S.299, K.398, H.399, S.402, S.527, N.528 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain F: N.35, T.37, E.39, N.40, Q.322 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain F: E.4, K.8, N.72, V.75 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain F: N.304, M.305 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain F: N.414, W.576 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain F: S.402, D.525, S.527, N.528 Ligand excluded by PLIP

3 x ZN: ZINC ION(Non-covalent)

ZN.37: 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.43: 3 residues within 4Å: Chain E: H.356, H.360, E.384 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.356, E:H.360, E:E.384, E:E.384 ZN.49: 3 residues within 4Å: Chain F: H.356, H.360, E.384 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.356, F:H.360, F:E.384, F: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

2022-09-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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