7F41 | pdb_00007f41

PARP15 catalytic domain in complex with 3-AMINOBENZAMIDE

PDB DOI: https://doi.org/10.2210/pdb7F41/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2021-06-17 Released: 2022-06-22
Deposition Author(s): Zhou, X.L., Zhong, F.L., Li, J., Zhang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of the catalytic domain of human PARP15 in complex with small molecule inhibitors

Zhou, X., Yang, Y., Xu, Q., Zhou, H., Zhong, F., Deng, J., Zhang, J., Li, J.

(2022) Biochem Biophys Res Commun 622: 93-100

DOI: https://doi.org/10.1016/j.bbrc.2022.06.070

Macromolecule Content

Total Structure Weight: 45.64 kDa
Atom Count: 3,359
Modeled Residue Count: 387
Deposited Residue Count: 396
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	198	Homo sapiens	Mutation(s): 0 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 B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	3-aminobenzamide C₇ H₈ N₂ O GSCPDZHWVNUUFI-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.313	α = 90
b = 68.498	β = 90
c = 158.404	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2022-06-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2025-03-26
Changes: Database references, Structure summary

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.