3R6K

Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)

Structural Biology Knowledgebase: 3R6K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3R6K

Classification: VIRAL PROTEIN

Total Structure Weight: 34027.38

Macromolecule Entities
Molecule Chains Length Organism Details
VP1 protein A 305 Norwalk virus Fragment: unp residues 225-525
Gene Name(s):

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

A ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.237
  • R-Value Work: 0.219
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 73.39 α = 90.00
b = 100.28 β = 90.00
c = 82.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-21
  • Released Date: 2011-05-11
  • Deposition author(s): Hansman, G.S., Biertumpfel, C., McLellan, J.S., Georgiev, I., Chen, L., Zhou, T., Katayama, K., Kwong, P.D.

Revision History

  • 2011-11-02
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4