SMTL ID : 7wpa.1

SARS-CoV-2 Omicron Variant SPIKE trimer complexed with ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-mer

Ligands

12 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.328, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: N.328, P.576, Q.577, T.578, L.579 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.579 Hydrogen bonds: B:T.578 NAG-NAG.6: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.328, Q.577, T.578, L.579 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.579 NAG-NAG.10: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.613, T.615 Chain C: I.831, Q.833 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: S.705, N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.703, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: I.831 Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: Y.793 Chain B: S.705, N.706 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: I.831, K.832 Chain C: N.613, T.615 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: I.791, Y.793 Chain C: S.705, N.706 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: Q.892 Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.90, T.92 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: N.322, M.323, T.324, Q.325 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.546, T.548 Ligand excluded by PLIP

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

CL.31: 3 residues within 4Å: Chain D: M.455, W.477, M.480 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.32: 3 residues within 4Å: Chain D: H.374, E.375, H.378 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Spike glycoprotein

Angiotensin-converting enzyme 2

Related Entries With Identical Sequence