9I8W | pdb_00009i8w

Beta-catenin armadillo with cyclic peptide and Compound 3

PDB DOI: https://doi.org/10.2210/pdb9I8W/pdb

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

Deposited: 2025-02-06 Released: 2026-02-18
Deposition Author(s): Klejnot, M., Skowron, A.N., 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: 2.20 Å
R-Value Free:
0.244 (Depositor), 0.199 (DCC)
R-Value Work:
0.183 (Depositor), 0.198 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Beta-catenin armadillo with cyclic peptide and Compound 3

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

To be published.

Macromolecule Content

Total Structure Weight: 61.09 kDa
Atom Count: 4,105
Modeled Residue Count: 527
Deposited Residue Count: 554
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catenin beta-1	A	538	Homo sapiens	Mutation(s): 0 Gene Names: CTNNB1, CTNNB, OK/SW-cl.35, PRO2286
UniProt & NIH Common Fund Data Resources
Find proteins for P35222 (Homo sapiens) Explore P35222 Go to UniProtKB: P35222
PHAROS: P35222 GTEx: ENSG00000168036
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35222
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic peptide	B	16	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HHT (Subject of Investigation/LOI) Query on HHT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-(4-bromanyl-2-methoxy-phenyl)ethanoic acid C₉ H₉ Br O₃ RNRCAQYXOAHKGD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.244 (Depositor), 0.199 (DCC)
R-Value Work: 0.183 (Depositor), 0.198 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 90.47	β = 90
c = 120.79	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

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Klejnot, M.

Skowron, A.N.

Pastok, M.W.

Gorecka-Minakowska, K.M.

Wisniewski, J.

Walczak, M.J.

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
Version 2.0: 2026-04-22
Type: Coordinate replacement
Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Refinement description, Structure summary
Version 2.1: 2026-05-06
Changes: Database references, Structure summary