1PF7

CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for inhibition of human PNP by immucillin-H

De Azevedo Jr., W.F.Canduri, F.Dos Santos, D.M.Pereira, J.H.Dias, M.V.B.Silva, R.G.Mendes, M.A.Palma, M.S.Basso, L.A.Santos, D.S.

(2003) Biochem.Biophys.Res.Commun. 309: 917-922


  • PubMed Abstract: 
  • Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. PNP is a target for inhibitor development aiming at T-cell immune response modulation. This work reports on the cr ...

    Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. PNP is a target for inhibitor development aiming at T-cell immune response modulation. This work reports on the crystallographic study of the complex of human PNP-immucillin-H (HsPNP-ImmH) solved at 2.6A resolution using synchrotron radiation. Immucillin-H (ImmH) inhibits the growth of malignant T-cell lines in the presence of deoxyguanosine without affecting non-T-cell tumor lines. ImmH inhibits activated normal human T cells after antigenic stimulation in vitro. These biological effects of ImmH suggest that this agent may have utility in the treatment of certain human diseases characterized by abnormal T-cell growth or activation. This is the first structural report of human PNP complexed with immucillin-H. The comparison of the complex HsPNP-ImmH with recent crystallographic structures of human PNP explains the high specificity of immucillin-H for human PNP.


    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.S.,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. walterfa@df.ibilce.unesp.br




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PURINE NUCLEOSIDE PHOSPHORYLASE
E
289Homo 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
IMH
Query on IMH

Download SDF File 
Download CCD File 
E
1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
C11 H14 N4 O4
IWKXDMQDITUYRK-KUBHLMPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMHKi: 0.072 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 139.390α = 90.00
b = 139.390β = 90.00
c = 161.310γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance