4P1V

Structure of the P domain from a GI.7 Norovirus variant in complex with H-type 2 HBGA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5497 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.

Shanker, S.Czako, R.Sankaran, B.Atmar, R.L.Estes, M.K.Prasad, B.V.

(2014) J.Virol. 88: 6168-6180


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P domain of VPI
A, B, C, D
301Norovirus Hu/GI.7/TCH-060/USA/2003Mutation(s): 0 
Find proteins for G8FL04 (Norovirus Hu/GI.7/TCH-060/USA/2003)
Go to UniProtKB:  G8FL04
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

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

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

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5497 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.154 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 62.398α = 72.71
b = 63.150β = 82.24
c = 90.320γ = 60.75
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references
  • Version 2.0: 2017-11-01
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary