2AI2 | pdb_00002ai2

Purine nucleoside phosphorylase from calf spleen

• PDB DOI: https://doi.org/10.2210/pdb2AI2/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2005-07-28 Released: 2005-10-25 
• Deposition Author(s): Toms, A.V., Wang, W., Li, Y., Ganem, B., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Novel multisubstrate inhibitors of mammalian purine nucleoside phosphorylase.

Toms, A.V., Wang, W., Li, Y., Ganem, B., Ealick, S.E.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1449-1458

• PubMed: 16239721 
• DOI: https://doi.org/10.1107/S0907444905025503
• Primary Citation Related Structures: 
  2AI1, 2AI2, 2AI3


• PubMed Abstract: 
  

  In an effort to develop potent multisubstrate-analog inhibitors of purine nucleoside phosphorylase (PNP), three nucleoside phosphonates were designed utilizing structural information from the previously reported structures of complexes of bovine PNP with substrates and products. The nucleoside phosphonates contain an acetal linkage at the O2' and O3' positions and a two-C-atom spacer between the ribose and phosphate moieties. The linkage enables the compounds to simultaneously occupy the purine-, ribose- and phosphate-binding sites. The chemical syntheses, inhibition profiles and structural characterization of these novel multisubstrate analog inhibitors with bovine PNP are described.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.71 kDa 
• Atom Count: 2,409 
• Modeled Residue Count: 274 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	289	Bos taurus	Mutation(s): 0  EC: 2.4.2.1
UniProt
Find proteins for P55859 (Bos taurus) Explore P55859  Go to UniProtKB:  P55859

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P1D	E [auth A]	((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO L-2-YL)METHYLPHOSPHONIC ACID C13 H16 N3 O8 P ZOEDLCUBOBTIHG-USQSKNHBSA-N
144	D [auth A]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C4 H12 N O3 DRDCQJADRSJFFD-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.231 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.243	α = 90
b = 93.243	β = 90
c = 93.243	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-25 
Deposition Author(s): Toms, A.V., Wang, W., Li, Y., Ganem, B., Ealick, S.E.

Revision History  

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary