Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2325 
• Modelled Residue Count: 288 
• Deposited Residue Count: 288 
• Unique protein chains: 1

1PWY

CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH ACYCLOVIR

• PDB DOI: 10.2210/pdb1PWY/pdb

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


• Deposited: 2003-07-02 Released: 2004-03-23 
• Deposition Author(s): Dos Santos, D.M., Canduri, F., Pereira, J.H., Vinicius Bertacine Dias, M., Silva, R.G., Mendes, M.A., Palma, M.S., Basso, L.A., De Azevedo, W.F., Santos, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.301 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 

Literature

Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir.

dos Santos, D.M., Canduri, F., Pereira, J.H., Vinicius Bertacine Dias, M., Silva, R.G., Mendes, M.A., Palma, M.S., Basso, L.A., de Azevedo, W.F., Santos, D.S.

(2003) Biochem Biophys Res Commun 308: 553-559

• PubMed: 12914786 
• DOI: 10.1016/s0006-291x(03)01433-5
• Primary Citation of Related Structures:  
  1PWY


• PubMed Abstract: 
  

In human, purine nucleoside phosphorylase (HsPNP) is responsible for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. This work reports the first crystallographic study of human PNP complexed with acyclovir (HsPNP:Acy). Acyclovir is a potent clinically useful inhibitor of replicant herpes simplex virus that also inhibits human PNP but with a relatively lower inhibitory activity (K(i)=90 microM). Analysis of the structural differences among the HsPNP:Acy complex, PNP apoenzyme, and HsPNP:Immucillin-H provides explanation for inhibitor binding, refines the purine-binding site, and can be used for future inhibitor design.

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Related Citations: 

• Application of Crystallographic and Modeling Methods in the Design of Purine Nucleoside Phosphorylase Inhibitors
  Ealick, S.E., Babu, Y.S., Bugg, C.E., Erion, M.D., Guida, W.C., Montgomery, J.A., Secrist III, J.A.
  (1991) Proc Natl Acad Sci U S A 88: 11540

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Organizational Affiliation: 

Departamento de Física, UNESP, São José do Rio Preto, SP, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A [auth E]	288	Homo sapiens	Mutation(s): 0  Gene Names: PNP, NP 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
AC2	E	9-HYROXYETHOXYMETHYLGUANINE C8 H11 N5 O3 MKUXAQIIEYXACX-UHFFFAOYSA-N
SO4	B [auth E], C [auth E], D [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
AC2	PDBBind:  1PWY	Ki: 9.00e+4 (nM) from 1 assay(s)
	BindingDB:  1PWY	Ki: 1.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.301 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.06	α = 90
b = 139.06	β = 90
c = 160.57	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

• Deposited Date: 2003-07-02 
• Released Date: 2004-03-23 
Deposition Author(s): Dos Santos, D.M., Canduri, F., Pereira, J.H., Vinicius Bertacine Dias, M., Silva, R.G., Mendes, M.A., Palma, M.S., Basso, L.A., De Azevedo, W.F., Santos, D.S.

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references