SMTL ID : 7thk.1

Cryo-EM structure of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.277, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.11: 7 residues within 4Å: Chain A: T.106, N.231, T.233 Chain B: R.454, S.456, N.457, K.459 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain A: E.130, N.159, N.160 Chain B: Y.348, I.465, T.467 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: Q.892 Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.277, N.279 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain B: T.106, N.231, T.233 Chain C: S.456, K.459, E.462 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: I.791, Y.793 Chain B: S.705, N.706 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain B: D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.798, Q.801 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: F.339, N.340, V.364, L.368 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.120, T.122, N.123, V.125 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: T.106, N.231, T.233 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Cryo-EM structure of the SARS-CoV-2 Omicron spike. Cell Rep (2022)

Release Date

2022-03-02

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein