3RY8

Structural basis for norovirus inhibition and fucose mimicry by citrate

Structural Biology Knowledgebase: 3RY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.151
  • R-Value Work: 0.139

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RY8

Classification: VIRAL PROTEIN

Total Structure Weight: 70482.45

Macromolecule Entities
Molecule Chains Length Organism Details
Capsid protein A, B 319 Norwalk virus Fragment: P domain (UNP residues 225-538)
Gene Name(s):

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

A CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FLC N/A in BindingDB
Kd: 460000 nM  BindingMOAD
Kd: 460000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.151
  • R-Value Work: 0.139
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 63.76 α = 90.00
b = 79.81 β = 96.84
c = 69.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-11
  • Released Date: 2011-11-09
  • Deposition author(s): Hansman, G.S., McLellan, J.S., Kwong, P.D

Revision History

  • 2012-07-25
    Type: Citation | Details: Citation update