1PF7

CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

Starting Model: experimental
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This is version 2.1 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

  • DOI: https://doi.org/10.1016/j.bbrc.2003.08.094
  • Primary Citation of Related Structures:  
    1PF7

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PURINE NUCLEOSIDE PHOSPHORYLASEA [auth E]289Homo sapiensMutation(s): 0 
EC: 2.4.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
PHAROS:  P00491
GTEx:  ENSG00000198805 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00491
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
IMH BindingDB:  1PF7 Ki: min: 0.06, max: 72 (nM) from 6 assay(s)
Kd: min: 0.02, max: 0.06 (nM) from 3 assay(s)
IC50: min: 0.06, max: 100 (nM) from 3 assay(s)
ΔH: -3.50e+1 (kJ/mol) from 1 assay(s)
ΔG: -4.56e+1 (kJ/mol) from 1 assay(s)
PDBBind:  1PF7 Ki: 0.07 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.39α = 90
b = 139.39β = 90
c = 161.31γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2022-10-05
    Changes: Atomic model, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description