4WZE

Crystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Ley (tetraglycan)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human noroviruses' fondness for histo-blood group antigens.

Singh, B.K.Leuthold, M.M.Hansman, G.S.

(2015) J.Virol. 89: 2024-2040


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A, B
308Norovirus Hu/GII-4/Saga4/2006/JPMutation(s): 0 
Find proteins for B5BTR7 (Norovirus Hu/GII-4/Saga4/2006/JP)
Go to UniProtKB:  B5BTR7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A, B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.020α = 90.00
b = 58.500β = 108.10
c = 113.860γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Database references
  • Version 1.2: 2015-03-04
    Type: Derived calculations