6G7X

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 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) Croat Chem Acta 91


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase DeoD-type
A, B, C, D, E, F
A, B, C, D, E, F
233Helicobacter pylori 26695Mutation(s): 0 
Gene Names: deoDHP_1178
EC: 2.4.2.1
UniProt
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56463 
Go to UniProtKB:  P56463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56463
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth E],
IA [auth F],
J [auth A],
P [auth B],
U [auth C],
DA [auth E],
IA [auth F],
J [auth A],
P [auth B],
U [auth C],
Y [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
G [auth A],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
V [auth D],
W [auth D],
X [auth D],
Z [auth E]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.32α = 90
b = 91.49β = 119.9
c = 93.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Croatia7423

Revision History  (Full details and data files)

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