6HXR | pdb_00006hxr

Human PARP16 (ARTD15) IN COMPLEX WITH EB-47

PDB DOI: https://doi.org/10.2210/pdb6HXR/pdb

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

Deposited: 2018-10-18 Released: 2019-10-30
Deposition Author(s): Karlberg, T., Pinto, A.F., Thorsell, A.G., Schuler, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.230 (Depositor), 0.216 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Human PARP16 (ARTD15) IN COMPLEX WITH EB-47

Karlberg, T., Pinto, A.F., Thorsell, A.G., Schuler, H.

To be published.

Macromolecule Content

Total Structure Weight: 101.82 kDa
Atom Count: 5,634
Modeled Residue Count: 706
Deposited Residue Count: 894
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mono [ADP-ribose] polymerase PARP16	A, B, C	298	Homo sapiens	Mutation(s): 0 Gene Names: PARP16, ARTD15, C15orf30 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Y8 (Homo sapiens) Explore Q8N5Y8 Go to UniProtKB: Q8N5Y8
PHAROS: Q8N5Y8 GTEx: ENSG00000138617
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N5Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UHB Query on UHB Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide C₂₄ H₂₇ N₉ O₆ QEUOCRGVJJDDTK-VBFAUCSFSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.230 (Depositor), 0.216 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.064	α = 90
b = 148.064	β = 90
c = 99.73	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-10-30
Type: Initial release
Version 1.1: 2022-12-07
Changes: Database references, Derived calculations
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.