SMTL ID : 8dm1.1

Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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: 5 residues within 4Å: Chain A: N.119, T.121, N.122, V.124, E.151 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain B: N.119, T.121, N.122, V.124, E.151 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain C: N.119, T.121, N.122, V.124, E.151 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.122 NAG-NAG.14: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain A: Q.892 Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.25, N.58 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: T.105, N.231, T.233 Chain C: K.459, E.462 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.162 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: T.105, N.231, T.233 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.162 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.340 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.706, G.1128 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural analysis of receptor engagement and antigenic drift within the BA.2 spike protein. Cell Rep (2023)

Release Date

2023-01-25

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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