SMTL ID : 3nwd.2 (3 other biounits)

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, low-pH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Q.113, N.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.114, A:N.114 NAG.2: 2 residues within 4Å: Chain A: A.399, N.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.403 NAG.3: 2 residues within 4Å: Chain A: N.647 Chain B: R.496 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.496, B:R.496 NAG.5: 2 residues within 4Å: Chain B: Q.113, N.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.114, B:N.114 NAG.6: 2 residues within 4Å: Chain B: A.399, N.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.403 NAG.7: 2 residues within 4Å: Chain B: N.647 Chain C: R.496 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.496, C:R.496 NAG.9: 2 residues within 4Å: Chain C: Q.113, N.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.114, C:N.114 NAG.10: 2 residues within 4Å: Chain C: A.399, N.403 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.403 NAG.11: 2 residues within 4Å: Chain A: R.496 Chain C: N.647 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.496, A:R.496

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.360, N.484 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: S.360, N.484 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: S.360, N.484 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stampfer, S.D. et al., Structural basis of local, pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1. J.Virol. (2010)

Release Date

2010-12-01

Peptides

Envelope glycoprotein B: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Envelope glycoprotein B

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