1JMA

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM

Structural Biology Knowledgebase: 1JMA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.236

Literature

Macromolecules
Sequence Display for 1JMA

Classification: Viral protein

Total Structure Weight: 50988.68

Macromolecule Entities
Molecule Chains Length Organism Details
HERPESVIRUS ENTRY MEDIATOR B 167 Human herpesvirus 1 Fragment: HVEA-162
Gene Name(s): TNFRSF14 Gene View HVEA HVEM UNQ329/PRO509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
GLYCOPROTEIN D A 290 Homo sapiens Fragment: GD-285
Gene Name(s): gD US6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259
  • R-Value Work: 0.236
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 129.15 α = 90.00
b = 129.15 β = 90.00
c = 80.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-07-17
  • Released Date: 2001-09-26
  • Deposition author(s): Carfi, A., Willis, S.H., Whitbeck, J.C., Krummenacker, C., Cohen, G.H., Eisenberg, R.J., Wiley, D.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update