3PAX | pdb_00003pax

THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH 3-METHOXYBENZAMIDE

• PDB DOI: https://doi.org/10.2210/pdb3PAX/pdb

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


• Deposited: 1997-11-25 Released: 1998-05-27 
• 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 Work: 
  0.171 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Inhibitor and NAD+ binding to poly(ADP-ribose) polymerase as derived from crystal structures and homology modeling.

Ruf, A., de Murcia, G., Schulz, G.E.

(1998) Biochemistry 37: 3893-3900

• PubMed: 9521710 
• DOI: https://doi.org/10.1021/bi972383s
• Primary Citation Related Structures: 
  2PAW, 2PAX, 3PAX, 4PAX


• PubMed Abstract: 
  

  Inhibitors of poly(ADP-ribose) polymerase (PARP, EC 2.4.2.30) are of clinical interest because they have potential for improving radiation therapy and chemotherapy of cancer. The refined binding structures of four such inhibitors are reported together with the refined structure of the unligated catalytic fragment of the enzyme. Following their design, all inhibitors bind at the position of the nicotinamide moiety of the substrate NAD+. The observed binding mode suggests inhibitor improvements that avoid other NAD(+)-binding enzymes. Because the binding pocket of NAD+ has been strongly conserved during evolution, the homology with ADP-ribosylating bacterial toxins could be used to extend the bound nicotinamide, which is marked by the inhibitors, to the full NAD+ molecule.

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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: 40.57 kDa 
• Atom Count: 2,850 
• Modeled 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 (PDB Primary Data), 2.4.2 (UniProt)
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
3MB	B [auth A]	3-METHOXYBENZAMIDE C8 H9 N O2 VKPLPDIMEREJJF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3MB	BindingDB:  3PAX	IC50: min: 1.70e+4, max: 3.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.171 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.93	α = 90
b = 64.31	β = 90
c = 96.03	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Ruf, A., Schulz, G.E.

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection