3BGS

Structure of human purine nucleoside phosphorylase with L-DADMe-ImmH and phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 

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
A
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 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DIH
Query on DIH

Download SDF File 
Download CCD File 
A
3-HYDROXY-4-HYDROXYMETHYL-1-(4-OXO-4,4A,5,7A-TETRAHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YLMETHYL)-PYRROLIDINIUM
4'-DEAZA-1'-AZA-2'-DEOXY-1'-(9-METHYLENE)-IMMUCILLIN-H, (3R,4R)-N-[9-DEAZAHYPOXANTHIN-9-YL)METHYL]-4-HYDROXYMETHYL-PYRROLIDIN-3-OL
C12 H19 N4 O3
WFVGWLHAOKEIOJ-MFQSTILNSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DIHKi: 0.38 nM BINDINGMOAD
DIHKi: 0.38 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 142.801α = 90.00
b = 142.801β = 90.00
c = 167.348γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description