SMTL ID : 9ddc.1

Cryo-EM structure of gB-Ecto.516P, an HSV-1 glycoprotein B extracellular domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

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: 3 residues within 4Å: Chain A: N.398, L.443, N.445 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.398, L.443, N.445 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.398, L.443, N.445 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: E.138, N.141 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.430 NAG.6: 2 residues within 4Å: Chain A: D.672, N.674 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: E.138, N.141 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain B: N.430 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.430 NAG.9: 2 residues within 4Å: Chain B: D.672, N.674 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain C: E.138, N.141 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain C: N.430 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.430 NAG.12: 2 residues within 4Å: Chain C: D.672, N.674 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roark, R.S. et al., Prefusion structure, evasion and neutralization of HSV-1 glycoprotein B. Nat Microbiol (2025)

Release Date

2025-09-10

Peptides

Glycoprotein B: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Glycoprotein B

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