SMTL ID : 3nw8.3 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

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.371, L.416, N.418 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.371, L.416, N.418 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.371, L.416, N.418 No protein-ligand interaction detected (PLIP)

9 x MRY: MESO-ERYTHRITOL(Non-covalent)

MRY.2: 6 residues within 4Å: Chain A: N.126, A.128, Y.257, S.335, V.336, C.337 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.126, A:A.128, A:Y.257, A:S.335, A:C.337 Water bridges: A:S.335 MRY.3: 2 residues within 4Å: Chain A: R.218, E.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.248 Water bridges: A:R.218 MRY.6: 4 residues within 4Å: Chain A: F.196, D.199, D.200, H.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.199, A:D.199, A:D.200, A:H.201 MRY.10: 6 residues within 4Å: Chain B: N.126, A.128, Y.257, S.335, V.336, C.337 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.126, B:A.128, B:Y.257, B:S.335, B:C.337 Water bridges: B:S.335 MRY.11: 2 residues within 4Å: Chain B: R.218, E.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.248 Water bridges: B:R.218 MRY.14: 4 residues within 4Å: Chain B: F.196, D.199, D.200, H.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.199, B:D.199, B:D.200, B:H.201 MRY.18: 6 residues within 4Å: Chain C: N.126, A.128, Y.257, S.335, V.336, C.337 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.126, C:A.128, C:Y.257, C:S.335, C:C.337 Water bridges: C:S.335 MRY.19: 2 residues within 4Å: Chain C: R.218, E.248 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.248 Water bridges: C:R.218 MRY.22: 4 residues within 4Å: Chain C: F.196, D.199, D.200, H.201 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.199, C:D.199, C:D.200, C:H.201

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

NAG.4: 2 residues within 4Å: Chain A: A.399, N.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.403 NAG.5: 3 residues within 4Å: Chain A: N.647, T.649 Chain B: R.496 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain B: A.399, N.403 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.403 NAG.13: 3 residues within 4Å: Chain B: N.647, T.649 Chain C: R.496 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain C: A.399, N.403 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.403 NAG.21: 3 residues within 4Å: Chain A: R.496 Chain C: N.647, T.649 No protein-ligand interaction detected (PLIP)

6 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Chain A: R.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.277 NA.8: 5 residues within 4Å: Chain A: K.131, F.132, K.133, D.250, A.251 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.251, A:A.251 NA.15: 1 residues within 4Å: Chain B: R.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.277 NA.16: 5 residues within 4Å: Chain B: K.131, F.132, K.133, D.250, A.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.250, B:A.251 NA.23: 1 residues within 4Å: Chain C: R.277 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.277 NA.24: 5 residues within 4Å: Chain C: K.131, F.132, K.133, D.250, A.251 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.250, C:A.251

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
C

B
C

C
C

Envelope glycoprotein B

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