3FHB | pdb_00003fhb

Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor 3-aminobenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb3FHB/pdb
• Entry: 3FHB supersedes: 2PA9

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


• Deposited: 2008-12-09 Released: 2009-01-06 
• Deposition Author(s): Lehtio, L., Karlberg, T., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Johansson, I., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Schueler, H., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.

Lehtio, L., Jemth, A.S., Collins, R., Loseva, O., Johansson, A., Markova, N., Hammarstrom, M., Flores, A., Holmberg-Schiavone, L., Weigelt, J., Helleday, T., Schuler, H., Karlberg, T.

(2009) J Med Chem 52: 3108-3111

• PubMed: 19354255 
• DOI: https://doi.org/10.1021/jm900052j
• Primary Citation Related Structures: 
  3C49, 3C4H, 3CE0, 3FHB


• PubMed Abstract: 
  

  Poly(ADP-ribose) polymerases (PARPs) activate DNA repair mechanisms upon stress- and cytotoxin-induced DNA damage, and inhibition of PARP activity is a lead in cancer drug therapy. We present a structural and functional analysis of the PARP domain of human PARP-3 in complex with several inhibitors. Of these, KU0058948 is the strongest inhibitor of PARP-3 activity. The presented crystal structures highlight key features for potent inhibitor binding and suggest routes for creating isoenzyme-specific PARP inhibitors.

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Organizational Affiliation: 
• Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 39.89 kDa 
• Atom Count: 2,920 
• Modeled Residue Count: 357 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 3	A	357	Homo sapiens	Mutation(s): 0  Gene Names: PARP3, ADPRT3, ADPRTL3 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F1 (Homo sapiens) Explore Q9Y6F1  Go to UniProtKB:  Q9Y6F1
PHAROS:  Q9Y6F1 GTEx:  ENSG00000041880

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAB	B [auth A]	3-AMINOBENZOIC ACID C7 H7 N O2 XFDUHJPVQKIXHO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GAB	BindingDB:  3FHB	Kd: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.254 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.24	α = 90
b = 56.7	β = 112.86
c = 56.48	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Lehtio, L., Karlberg, T., Arrowsmith, C.H., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Johansson, I., Kotenyova, T., Moche, M., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Schueler, H., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)
• This entry supersedes: 2PA9

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations