2AI3

Purine nucleoside phosphorylase from calf spleen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase.

Toms, A.V.Wang, W.Li, Y.Ganem, B.Ealick, S.E.

(2005) Acta Crystallogr.,Sect.D 61: 1449-1458

  • DOI: 10.1107/S0907444905025503
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In an effort to develop potent multisubstrate-analog inhibitors of purine nucleoside phosphorylase (PNP), three nucleoside phosphonates were designed utilizing structural information from the previously reported structures of complexes of bovine PNP ...

    In an effort to develop potent multisubstrate-analog inhibitors of purine nucleoside phosphorylase (PNP), three nucleoside phosphonates were designed utilizing structural information from the previously reported structures of complexes of bovine PNP with substrates and products. The nucleoside phosphonates contain an acetal linkage at the O2' and O3' positions and a two-C-atom spacer between the ribose and phosphate moieties. The linkage enables the compounds to simultaneously occupy the purine-, ribose- and phosphate-binding sites. The chemical syntheses, inhibition profiles and structural characterization of these novel multisubstrate analog inhibitors with bovine PNP are described.


    Related Citations: 
    • Calf Spleen Purine Nucleoside Phosphorylase Complexed with Substrates and Substrate Analogs.
      Mao, C.,Cook, W.J.,Zhou, M.,Fedorov, A.A.,Almo, S.C.,Ealick, S.E.
      (1998) Biochemistry 37: 7135


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A
289Bos taurusMutation(s): 0 
Gene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P55859 (Bos taurus)
Go to Gene View: PNP
Go to UniProtKB:  P55859
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
144
Query on 144

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Download CCD File 
A
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
P2G
Query on P2G

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Download CCD File 
A
(2S,4R,6R,6AS)-4-(2-AMINO-6-OXO-1,6-DIHYDROPURIN-9-YL)-6-(HYDROXYMETHYL)-TETRAHYDROFURO[3,4-D][1,3]DIOXOL-2-YLPHOSPHONIC ACID
GUANOSINE-2',3'-O-METHYLIDENEPHOSPHONATE
C11 H14 N5 O8 P
GKAPYWCOOQBBHV-KXSYMAMXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P2GIC50: 5000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 93.992α = 90.00
b = 93.992β = 90.00
c = 93.992γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance