9IFV | pdb_00009ifv

PARP15 catalytic domain mutant (R576E) in complex with 3-aminobenzamide

PDB DOI: https://doi.org/10.2210/pdb9IFV/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2025-02-18 Released: 2025-10-08
Deposition Author(s): Ebenwaldner, C., Logan, D.T., Schuler, H., Moche, M.
Funding Organization(s): Cancerfonden

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.225 (Depositor), 0.225 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

PARP15 catalytic domain mutant (R576E) in complex with 3-aminobenzamide

Ebenwaldner, C., Logan, D.T., Schuler, H., Moche, M.

To be published.

Macromolecule Content

Total Structure Weight: 51.1 kDa
Atom Count: 3,487
Modeled Residue Count: 396
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein mono-ADP-ribosyltransferase PARP15	A, B	221	Homo sapiens	Mutation(s): 1 Gene Names: PARP15, BAL3 EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens) Explore Q460N3 Go to UniProtKB: Q460N3
PHAROS: Q460N3 GTEx: ENSG00000173200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q460N3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3AB (Subject of Investigation/LOI) Query on 3AB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	3-aminobenzamide C₇ H₈ N₂ O GSCPDZHWVNUUFI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.225 (Depositor), 0.225 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.713	α = 90
b = 76.697	β = 90
c = 155.562	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Aimless	data scaling
autoPROC	data processing
autoPROC	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Ebenwaldner, C.

Funding Organization	Location	Grant Number
Cancerfonden	Sweden	23-3027Pj

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.