9I8O | pdb_00009i8o

Beta-Catenin R4 with Compound 1

PDB DOI: https://doi.org/10.2210/pdb9I8O/pdb

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

Deposited: 2025-02-05 Released: 2026-02-18
Deposition Author(s): Skowron, A.N., Klejnot, M., Pastok, M.W., Gorecka-Minakowska, K.M., Wisniewski, J., Walczak, M.J.
Funding Organization(s): National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.305 (Depositor), 0.297 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Beta-Catenin R4 with Compound 1

Skowron, A.N., Klejnot, M., Pastok, M.W., Gorecka-Minakowska, K.M., Wisniewski, J., Walczak, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 74.14 kDa
Atom Count: 5,008
Modeled Residue Count: 655
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catenin beta 1	A, B, C, D	169	Homo sapiens	Mutation(s): 0 Gene Names: CTNNB1
UniProt & NIH Common Fund Data Resources
Find proteins for A0A2R8Y815 (Homo sapiens) Explore A0A2R8Y815 Go to UniProtKB: A0A2R8Y815
GTEx: ENSG00000168036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2R8Y815
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I1A (Subject of Investigation/LOI) Query on A1I1A Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	(4~{a}~{R},10~{a}~{S})-1,1-dimethyl-5,6-bis(oxidanyl)-9-oxidanylidene-7-propan-2-yl-3,4,10,10~{a}-tetrahydro-2~{H}-phenanthrene-4~{a}-carboxylic acid C₂₀ H₂₆ O₅ GMLJOVLWUITZJA-VBKZILBWSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.305 (Depositor), 0.297 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.07	α = 90
b = 98.07	β = 90
c = 232.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Gorecka-Minakowska, K.M.

Funding Organization	Location	Grant Number
National Center for Research and Development (Poland)	Poland	POIR.01.02.00-00-0073/18

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release

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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.