SMTL ID : 8v5v.1

Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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.408, T.410, H.411, F.413 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.408, T.410, H.411, F.413 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.408, T.410, H.411, F.413 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.27, Q.236 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.19 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: K.105, D.106, N.111, S.113, Q.114 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: S.21, N.384 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.444 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain B: N.27, Q.236 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain B: N.19 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain B: K.105, D.106, N.111, S.113, Q.114 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: S.21, N.384 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain B: N.444 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: N.27, Q.236 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain C: N.19 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain C: K.105, D.106, N.111, S.113, Q.114 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: S.21, N.384 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain C: N.444 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olmedillas, E. et al., Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation. Cell Rep (2025)

Release Date

2024-12-18

Peptides

Spike protein S2,Fibritin: ABC
Variable domain of the light chain from the human antibody 6C10: DEH
Variable domain of the heavy chain from the human antibody 6C10: FGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
E

C
F

D
d

E
g

H
e

F
f

G
c

I
b

Spike protein S2,Fibritin

Variable domain of the light chain from the human antibody 6C10

Variable domain of the heavy chain from the human antibody 6C10