3JZT

Structure of a cubic crystal form of X (ADRP) domain from FCoV with ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the X (ADRP) domain of nsp3 from feline coronavirus

Wojdyla, J.A.Manolaridis, I.Snijder, E.J.Gorbalenya, A.E.Coutard, B.Piotrowski, Y.Hilgenfeld, R.Tucker, P.A.

(2009) Acta Crystallogr.,Sect.D 65: 1292-1300

  • DOI: 10.1107/S0907444909040074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2 A resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was ...

    The structure of the X (or ADRP) domain of a pathogenic variant of feline coronavirus (FCoV) has been determined in tetragonal and cubic crystal forms to 3.1 and 2.2 A resolution, respectively. In the tetragonal crystal form, glycerol-3-phosphate was observed in the ADP-ribose-binding site. Both crystal forms contained large solvent channels and had a solvent content of higher than 70%. Only very weak binding of this domain to ADP-ribose was detected in vitro. However, the structure with ADP-ribose bound was determined in the cubic crystal form at 3.9 A resolution. The structure of the FCoV X domain had the expected macro-domain fold and is the first structure of this domain from a coronavirus belonging to subgroup 1a.


    Organizational Affiliation

    EMBL Hamburg Outstation, c/o DESY, D-22603 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
macro domain of Non-structural protein 3
A, B, C, D, E, F, G, H
168Feline coronavirus (strain FIPV WSU-79/1146)Mutation(s): 0 
Gene Names: rep
Find proteins for Q98VG9 (Feline coronavirus (strain FIPV WSU-79/1146))
Go to UniProtKB:  Q98VG9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download SDF File 
Download CCD File 
B, C, D
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 220.236α = 90.00
b = 220.236β = 90.00
c = 220.236γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction
COMBATdata reduction
Auto-Rickshawphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance