3BGS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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): 1 
Gene Names: NPPNP
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS  P00491
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DIH
Query on DIH

Download CCD File 
A
7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one
C12 H17 N4 O3
AFNHHLILYQEHKK-BDAKNGLRSA-O
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DIHKi:  0.3800000250339508   nM  Binding MOAD
DIHKi:  0.3800000250339508   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.801α = 90
b = 142.801β = 90
c = 167.348γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 2.0: 2018-12-12
    Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary