2Q7O

Structure of human purine nucleoside phosphorylase in complex with L-Immucillin-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

L-Enantiomers of transition state analogue inhibitors bound to human purine nucleoside phosphorylase.

Rinaldo-Matthis, A.Murkin, A.S.Ramagopal, U.A.Clinch, K.Mee, S.P.Evans, G.B.Tyler, P.C.Furneaux, R.H.Almo, S.C.Schramm, V.L.

(2008) J.Am.Chem.Soc. 130: 842-844

  • DOI: 10.1021/ja710733g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human purine nucleoside phosphorylase (PNP) was crystallized with transition-state analogue inhibitors Immucillin-H and DADMe-Immucillin-H synthesized with ribosyl mimics of l-stereochemistry. The inhibitors demonstrate that major driving forces for ...

    Human purine nucleoside phosphorylase (PNP) was crystallized with transition-state analogue inhibitors Immucillin-H and DADMe-Immucillin-H synthesized with ribosyl mimics of l-stereochemistry. The inhibitors demonstrate that major driving forces for tight binding of these analogues are the leaving group interaction and the cationic mimicry of the transition state, even though large geometric changes occur with d-Immucillins and l-Immucillins bound to human PNP.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
E
289Homo sapiensMutation(s): 0 
Gene 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
PO4
Query on PO4

Download SDF File 
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 143.457α = 90.00
b = 143.457β = 90.00
c = 166.248γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description