SMTL ID : 8dya.1

Structure of the SARS-CoV-2 spike glycoprotein S2 subunit

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: D.143, N.148, Q.151 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: I.479, N.481 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.445, F.450 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.56 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: A.53, E.419, N.421 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.64, F.65, Q.418 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain B: D.143, N.148, Q.151 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain B: I.479, N.481 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain B: N.445, F.450 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain B: N.56 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: A.53, E.419, N.421 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain B: N.64, F.65, Q.418 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: D.143, N.148, Q.151 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: I.479, N.481 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain C: N.445, F.450 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.56 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: A.53, E.419, N.421 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: N.64, F.65, Q.418 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bowen, J.E. et al., SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Sci Immunol (2022)

Release Date

2022-11-30

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein