Crystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin A

Experimental Data Snapshot

  • Resolution: 2.293 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history


Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.

Narczyk, M.Bertosa, B.Papa, L.Vukovic, V.Lescic Asler, I.Wielgus-Kutrowska, B.Bzowska, A.Luic, M.Stefanic, Z.

(2018) FEBS J. 285: 1305-1325


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-type
A, B, C, D, E, F
233Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: deoD
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56463
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on FMC

Download SDF File 
Download CCD File 
A, B, C, D, E, F
C10 H13 N5 O4
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 2.293 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.051α = 90.00
b = 84.801β = 90.00
c = 274.462γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-30 
  • Released Date: 2018-02-14 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatian Science FounataionCroatia7423
National Science Center of PolandPoland2015/18/M/NZ1/00776
Polish Ministry for Science and Higher EducationPolandBST-173300/BF

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references