1V45

Crystal Structure of human PNP complexed with 3-deoxyguanosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of human PNP complexed with ligands.

Canduri, F.Silva, R.G.dos Santos, D.M.Palma, M.S.Basso, L.A.Santos, D.S.de Azevedo Jr., W.F.

(2005) Acta Crystallogr.,Sect.D 61: 856-862

  • DOI: 10.1107/S0907444905005421
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration an ...

    Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration and exhibits a strong preference for purines containing a 6-keto group and ribosyl-containing nucleosides relative to the corresponding analogues. PNP was crystallized in complex with ligands and data collection was performed using synchrotron radiation. This work reports the structure of human PNP in complex with guanosine (at 2.80 A resolution), 3'-deoxyguanosine (at 2.86 A resolution) and 8-azaguanine (at 2.85 A resolution). These structures were compared with the PNP-guanine, PNP-inosine and PNP-immucillin-H complexes solved previously.


    Related Citations: 
    • Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir
      Dos Santos, D.M.,Canduri, F.,Pereira, J.H.,Dias, M.V.B.,Silva, R.G.,Mendes, M.A.,Palma, M.S.,Basso, L.A.,De Azevedo, W.F.,Santos, D.S.
      (2003) Biochem.Biophys.Res.Commun. 308: 553
    • Crystal Structure of Human Purine Nucleoside Phosphorylase at 2.3A Resolution
      De Azevedo Jr., W.F.,Canduri, F.,Dos Santos, D.M.,Silva, R.G.,De Oliveira, J.S.,De Carvalho, L.P.,Basso, L.A.,Mendes, M.A.,Palma, M.S.,Santos, D.S.
      (2003) Biochem.Biophys.Res.Commun. 308: 545


    Organizational Affiliation

    Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
E
288Homo sapiensGene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to Gene View: PNP
Go to UniProtKB:  P00491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3DG
Query on 3DG

Download SDF File 
Download CCD File 
E
9-(3-DEOXY-BETA-D-RIBOFURANOSYL)GUANINE
3-DEOXYGUANOSINE
C10 H13 N5 O4
OROIAVZITJBGSM-OBXARNEKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 141.320α = 90.00
b = 141.320β = 90.00
c = 162.620γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2014-04-16
    Type: Other, Refinement description