9QZL | pdb_00009qzl

Structure of NONO bound to (R)-SKBG-1 in P43212

PDB DOI: https://doi.org/10.2210/pdb9QZL/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-23 Released: 2025-12-17
Deposition Author(s): Fribourg, S.
Funding Organization(s): Institut National de la Sante et de la Recherche Medicale (INSERM)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9QZL

Ligand Structure Quality Assessment

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

Literature

Structure of NONO bound to (R)-SKBG-1

Fribourg, S.

To be published.

Macromolecule Content

Total Structure Weight: 61.29 kDa
Atom Count: 3,995
Modeled Residue Count: 483
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-POU domain-containing octamer-binding protein	A, B	260	Homo sapiens	Mutation(s): 0 Gene Names: NONO, NRB54
UniProt & NIH Common Fund Data Resources
Find proteins for Q15233 (Homo sapiens) Explore Q15233 Go to UniProtKB: Q15233
PHAROS: Q15233 GTEx: ENSG00000147140
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15233
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JB9 (Subject of Investigation/LOI) Query on A1JB9 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	4-(2-chloranylethanoyl)-~{N}-[(4-methoxyphenyl)methyl]-1-(4-methoxyphenyl)sulfonyl-piperazine-2-carboxamide C₂₂ H₂₆ Cl N₃ O₆ S SXQZEMXQTRNLRZ-HXUWFJFHSA-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: 2.90 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.069	α = 90
b = 87.069	β = 90
c = 138.587	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Institut National de la Sante et de la Recherche Medicale (INSERM)	France	--

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.