SMTL ID : 9q9n.1

HSV-1 prefusion glycoprotein B bound by Nb1_gbHSV

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

12 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.398, L.443, N.445 Chain B: D.103, E.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.103 NAG-NAG.2: 4 residues within 4Å: Chain A: D.103, I.104 Chain C: N.398, L.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.103 NAG-NAG.3: 5 residues within 4Å: Chain A: Q.140, N.141, E.379, F.508, T.509 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.509 NAG-NAG.4: 5 residues within 4Å: Chain B: Q.140, N.141, E.379, F.508, T.509 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.509 NAG-NAG.5: 5 residues within 4Å: Chain C: Q.140, N.141, E.379, F.508, T.509 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.509 NAG-NAG.6: 1 residues within 4Å: Chain C: N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.430 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain B: N.398, L.443, N.445 Chain C: D.103, I.104, E.107 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.103 NAG-NAG.10: 3 residues within 4Å: Chain A: L.673, N.674 Chain B: R.136 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.136 NAG-NAG.11: 3 residues within 4Å: Chain B: L.673, N.674 Chain C: R.136 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.136 NAG-NAG.12: 1 residues within 4Å: Chain C: N.674 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vollmer, B. et al., A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2. Nature (2025)

Release Date

2025-09-03

Peptides

Glycoprotein B: ABC
Nb1_gbHSV: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
d

E
e

F
f

Membrane

We predict this structure to be a membrane protein.
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Glycoprotein B

Nb1_gbHSV

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