1M3Y

The Structure of Major Capsid protein of a large, lipid containing, DNA virus

Structural Biology Knowledgebase: 1M3Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.352
  • R-Value Work: 0.342

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1M3Y

Classification: Viral protein

Total Structure Weight: 188706.13

Macromolecule Entities
Molecule Chains Length Organism Details
The Major capsid protein of PBCV-1, Vp54 A, B, C, D 413 Paramecium bursaria chlorella virus 1 Fragment: Residues 25-437
Gene Name(s): A430L
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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)
NDG
Query on NDG

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

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

A, B, C, D 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: 2.0 Å
  • R-Value Free: 0.352
  • R-Value Work: 0.342
  • Space Group: P 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 188.79 α = 90.00
b = 188.79 β = 90.00
c = 188.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-01
  • Released Date: 2002-12-04
  • 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: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4