1J5Q

The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.

Structural Biology Knowledgebase: 1J5Q SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.269

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1J5Q

Classification: Viral protein

Total Structure Weight: 103738.58

Macromolecule Entities
Molecule Chains Length Organism Details
Major capsid protein A, B 437 Paramecium bursaria chlorella virus 1 Gene Name(s): A430L

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

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

A, B MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.309
  • R-Value Work: 0.269
  • Space Group: P 41 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 188.76 α = 90.00
b = 188.76 β = 90.00
c = 188.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-06-27
  • Released Date: 2002-11-20
  • Deposition author(s): Nandhagopal, N., Simpson, A.A., Gurnon, J.R., Yan, X., Baker, T.S., Graves, M.V., Van Etten, J.L., Rossmann, M.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values