1V3Q

Structure of human PNP complexed with DDI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of human purine nucleoside phosphorylase complexed with inosine and ddI

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

(2004) Biochem Biophys Res Commun 313: 907-914

  • DOI: 10.1016/j.bbrc.2003.11.179
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human purine nucleoside phosphorylase (PNP) is a ubiquitous enzyme which plays a key role in the purine salvage pathway, and PNP deficiency in humans leads to an impairment of T-cell function, usually with no apparent effect on B-cell function. PNP i ...

    Human purine nucleoside phosphorylase (PNP) is a ubiquitous enzyme which plays a key role in the purine salvage pathway, and PNP deficiency in humans leads to an impairment of T-cell function, usually with no apparent effect on B-cell function. PNP is highly specific for 6-oxopurine nucleosides and exhibits negligible activity for 6-aminopurine nucleosides. The catalytic efficiency for inosine is 350,000-fold greater than for adenosine. Adenine nucleosides and nucleotides are deaminated by adenosine deaminase and AMP deaminase to their corresponding inosine derivatives which, in turn, may be further degraded. Here we report the crystal structures of human PNP in complex with inosine and 2('),3(')-dideoxyinosine, refined to 2.8A resolution using synchrotron radiation. The present structures provide explanation for ligand binding, refine the purine-binding site, and can be used for future inhibitor design.


    Related Citations: 
    • 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

    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 sapiensMutation(s): 0 
Gene Names: PNPNP
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS  P00491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2DI
Query on 2DI

Download CCD File 
E
9-[(2R,5R)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-2-YL]-1,9-DIHYDRO-6H-PURIN-6-ONE
C10 H12 N4 O3
BXZVVICBKDXVGW-NKWVEPMBSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.33α = 90
b = 141.33β = 90
c = 161.45γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-07-18
    Changes: Non-polymer description