6G7X

Crystal structure of H. pylori purine nucleoside phosphorylase soaked in PO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.762 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Role of Phosphate Binding in Purine Nucleoside Phosphorylase of Helicobacter pylori

Bosnjakovic, M.Lescic Asler, I.Stefanic, Z.

(2018) Croatica Chemica Acta 91: --


Macromolecules

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
EC: 2.4.2.1
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56463
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B, C, D, E, F
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.762 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.320α = 90.00
b = 91.490β = 119.90
c = 93.410γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-06 
  • Released Date: 2018-08-08 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatia7423

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release