3NW8

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

Structural Biology Knowledgebase: 3NW8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3NW8

Classification: VIRAL PROTEIN

Total Structure Weight: 319822.33

Macromolecule Entities
Molecule Chains Length Organism Details
Envelope glycoprotein B A, B, C, D 703 Human herpesvirus 1 Fragment: Ectodomain (UNP residues 30 to 730)
Mutation: P58A, Y179S, T313S, Q443L
Gene Name(s): gB UL27

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRY
Query on MRY

A, B, C, D MESO-ERYTHRITOL
C4 H10 O4
UNXHWFMMPAWVPI-ZXZARUISSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B, C, D SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.201
  • Space Group: P 3

Unit Cell:

Length (Å) Angle (°)
a = 117.99 α = 90.00
b = 117.99 β = 90.00
c = 321.54 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-07-09
  • Released Date: 2010-12-01
  • Deposition author(s): Stampfer, S.D., Lou, H., Cohen, G.H., Eisenberg, R.J., Heldwein, E.E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4