2C36

Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 2C36

Classification: VIRAL PROTEIN

Total Structure Weight: 65157.13

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCOPROTEIN D HSV-1 A, B 285 Human alphaherpesvirus 1 Mutation: H307C
Details: N-ACETYL-GLUCOSAMINE LINKED TO ASN121 AND ASN94 IN BOTH SUBUNITS (CHAIN A, B)
Gene Name(s): gD US6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDG
Query on NDG

B 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 74.25 α = 90.00
b = 106.19 β = 90.00
c = 130.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-04
  • Released Date: 2005-11-23
  • Deposition author(s): Krummenacher, C., Supekar, V.M., Whitbeck, J.C., Lazear, E., Connolly, S.A., Eisenberg, R.J., Cohen, G.H., Wiley, D.C., Carfi, A.

Revision History

  • Version 1_0: 2005-11-23

    Type: Initial release

  • Version 1_1: 2011-05-07

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance