1PAX

THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 3,4-DIHYDRO-5-METHYL-ISOQUINOLINONE

• PDB DOI: https://doi.org/10.2210/pdb1PAX/pdb

• Classification: TRANSFERASE
• Organism(s): Gallus gallus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1996-05-06 Released: 1997-05-15 
• Deposition Author(s): Ruf, A., Schulz, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 

Literature

Structure of the catalytic fragment of poly(ADP-ribose) polymerase from chicken.

Ruf, A., Mennissier de Murcia, J., de Murcia, G., Schulz, G.E.

(1996) Proc Natl Acad Sci U S A 93: 7481-7485

• PubMed: 8755499 
• DOI: https://doi.org/10.1073/pnas.93.15.7481
• Primary Citation of Related Structures:  
  1PAX


• PubMed Abstract: 
  

  The crystal structures of the catalytic fragment of chicken poly(ADP-ribose) polymerase [NAD+ ADP-ribosyltransferase; NAD+:poly(adenosine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyltransferase, EC 2.4.2.30] with and without a nicotinamide-analogue inhibitor have been elucidated. Because this enzyme is involved in the regulation of DNA repair, its inhibitors are of interest for cancer therapy. The inhibitor shows the nicotinamide site and also suggests the adenosine site. The enzyme is structurally related to bacterial ADP-ribosylating toxins but contains an additional alpha-helical domain that is suggested to relay the activation signal issued on binding to damaged DNA.

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Organizational Affiliation: 

Institut für Organische Chemie und Biochemie, Freiburg im Breisgau, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.58 kDa 
• Atom Count: 2,858 
• Modelled Residue Count: 350 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY(ADP-RIBOSE) POLYMERASE	A	361	Gallus gallus	Mutation(s): 0  EC: 2.4.2.30
UniProt
Find proteins for P26446 (Gallus gallus) Explore P26446  Go to UniProtKB:  P26446

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHQ	B [auth A]	3,4-DIHYDRO-5-METHYL-ISOQUINOLINONE C10 H11 N O RLLZPXDJYADIEU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DHQ	BindingDB:  1PAX	Ki: 70 (nM) from 1 assay(s)
		IC50: min: 160, max: 420 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.169 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.2	α = 90
b = 64.5	β = 90
c = 96.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-05-15 
Deposition Author(s): Ruf, A., Schulz, G.E.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-04
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other