8HKO

Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib

• PDB DOI: https://doi.org/10.2210/pdb8HKO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-11-27 Released: 2024-05-01 
• Deposition Author(s): Wang, X.Y., Zhou, J., Xu, B.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Starting Model: in silico

Literature

Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib

Wang, X.Y., Zhou, J., Xu, B.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 81.13 kDa 
• Atom Count: 6,309 
• Modelled Residue Count: 706 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 2	A, B	353	Homo sapiens	Mutation(s): 4  Gene Names: PARP2, ADPRT2, ADPRTL2 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGN5 (Homo sapiens) Explore Q9UGN5  Go to UniProtKB:  Q9UGN5
PHAROS:  Q9UGN5 GTEx:  ENSG00000129484

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RPB (Subject of Investigation/LOI)	H [auth A], J [auth B]	Rucaparib C19 H18 F N3 O HMABYWSNWIZPAG-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RPB	BindingDB:  8HKO	Ki: 0.7 (nM) from 1 assay(s)
		Kd: 26 (nM) from 1 assay(s)
		IC50: min: 0.4, max: 172 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.761	α = 90
b = 86.286	β = 90.39
c = 96.047	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Wang, X.Y., Zhou, J., Xu, B.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82003657
National Natural Science Foundation of China (NSFC)	China	81673300
National Natural Science Foundation of China (NSFC)	China	82173693

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release