1V41

Crystal structure of human PNP complexed with 8-Azaguanine

• PDB DOI: https://doi.org/10.2210/pdb1V41/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-08 Released: 2004-12-14 
• Deposition Author(s): Dos Santos, D.M., Canduri, F., Silva, R.G., Mendes, M.A., Basso, L.A., Palma, M.S., De Azevedo Jr., W.F., Santos, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.263 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Structure of human PNP complexed with ligands.

Canduri, F., Silva, R.G., dos Santos, D.M., Palma, M.S., Basso, L.A., Santos, D.S., de Azevedo Jr., W.F.

(2005) Acta Crystallogr D Biol Crystallogr 61: 856-862

• PubMed: 15983407 
• DOI: https://doi.org/10.1107/S0907444905005421
• Primary Citation of Related Structures:  
  1RFG, 1V41, 1V45


• PubMed Abstract: 
  

  Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine-salvage pathway, which allows cells to utilize preformed bases and nucleosides in order to synthesize nucleotides. PNP is specific for purine nucleosides in the beta-configuration and exhibits a strong preference for purines containing a 6-keto group and ribosyl-containing nucleosides relative to the corresponding analogues. PNP was crystallized in complex with ligands and data collection was performed using synchrotron radiation. This work reports the structure of human PNP in complex with guanosine (at 2.80 A resolution), 3'-deoxyguanosine (at 2.86 A resolution) and 8-azaguanine (at 2.85 A resolution). These structures were compared with the PNP-guanine, PNP-inosine and PNP-immucillin-H complexes solved previously.

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Organizational Affiliation: 

Programa de Pós-Graduação em Biofísica Molecular, Departamento de Física, UNESP, São José do Rio Preto, SP 15054-000, Brazil.

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)

Macromolecule Content

• Total Structure Weight: 32.59 kDa 
• Atom Count: 2,301 
• Modelled Residue Count: 288 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A [auth E]	288	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZG	F [auth E]	5-AMINO-1H-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-7-OL C4 H4 N6 O LPXQRXLUHJKZIE-UHFFFAOYSA-N
SO4	B [auth E], C [auth E], D [auth E], E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
AZG	PDBBind:  1V41	Ki: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.263 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.28	α = 90
b = 139.28	β = 90
c = 161.42	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
X-PLOR	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Dos Santos, D.M., Canduri, F., Silva, R.G., Mendes, M.A., Basso, L.A., Palma, M.S., De Azevedo Jr., W.F., Santos, D.S.

Revision History  

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2014-04-16
  Changes: Other
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description