5AIL | pdb_00005ail

Human PARP9 2nd macrodomain

PDB DOI: https://doi.org/10.2210/pdb5AIL/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-15 Released: 2015-02-25
Deposition Author(s): Sieg, C., Shrestha, L., Talon, R., Sorrell, F., Williams, E., von Delft, F., Bountra, C., Arrowsmith, C., Edwards, A.M., Knapp, S., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.215 (Depositor), 0.221 (DCC)
R-Value Work:
0.169 (Depositor), 0.183 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Parp9 2Nd Macrodomain

Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 47.49 kDa
Atom Count: 3,403
Modeled Residue Count: 362
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLY [ADP-RIBOSE] POLYMERASE 9	A, B	186	Homo sapiens	Mutation(s): 0 EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXQ6 (Homo sapiens) Explore Q8IXQ6 Go to UniProtKB: Q8IXQ6
PHAROS: Q8IXQ6 GTEx: ENSG00000138496
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IXQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], L [auth B]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] H [auth B] I [auth B] J [auth B] C [auth A], D [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.215 (Depositor), 0.221 (DCC)
R-Value Work: 0.169 (Depositor), 0.183 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.489	α = 90
b = 74.01	β = 90
c = 94.369	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-02-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-25
Type: Initial release
Version 1.1: 2017-09-13
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description