SMTL ID : 7tgw.1

Omicron spike at 3.0 A (open form)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: 4 residues within 4Å: Chain A: N.107, T.109, N.110, V.112 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.701, L.906 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.906 NAG-NAG.3: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.701, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.1082, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.146, N.147 Ligand excluded by PLIP NAG.14: 7 residues within 4Å: Chain A: T.93, N.218 Chain C: R.441, S.443, N.444, K.446, E.449 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.600, E.603, Q.628 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: E.265, N.266 Chain C: K.542 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.693 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: E.1056, N.1058 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.48, P.615 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.15, N.48 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.600, Q.628 Chain C: Q.820 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.315 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.641 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.693 Chain C: I.778 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1058 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: Q.820 Chain C: N.600, Q.628 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: N.701, L.906, Q.910, Q.1055 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: L.906 Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: E.265, N.266 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.693 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.1056, N.1058 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain. Nat Commun (2022)

Release Date

2022-03-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein