RCSB PDB - 1PF7: CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH IMMUCILLIN H

 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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Ligand Structure Quality Assessment 

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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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IMHClick on this verticalbar to view details

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