8Y0P | pdb_00008y0p

Beta-Catenin in complex with peptide 301

PDB DOI: https://doi.org/10.2210/pdb8Y0P/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-01-22 Released: 2024-04-17
Deposition Author(s): Tim, F.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.279 (Depositor), 0.277 (DCC)
R-Value Work:
0.239 (Depositor), 0.236 (DCC)
R-Value Observed:
0.241 (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 1.0 of the entry. See complete history.

Literature

Beta-Catenin in complex with peptide 301

Tim, F.

To be published.

Macromolecule Content

Total Structure Weight: 123.92 kDa
Atom Count: 7,755
Modeled Residue Count: 1,034
Deposited Residue Count: 1,122
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catenin beta-1	A, B	549	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
B-cell CLL/lymphoma 9 protein	C [auth L]	24	Homo sapiens	Mutation(s): 1 Gene Names: BCL9
UniProt & NIH Common Fund Data Resources
Find proteins for O00512 (Homo sapiens) Explore O00512 Go to UniProtKB: O00512
PHAROS: O00512 GTEx: ENSG00000116128
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00512
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRO (Subject of Investigation/LOI) Query on PRO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	D [auth A], E [auth A], F [auth A], G [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NAL Query on NAL	C [auth L]	L-PEPTIDE LINKING	C₁₃ H₁₃ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.279 (Depositor), 0.277 (DCC)
R-Value Work: 0.239 (Depositor), 0.236 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.921	α = 90
b = 100.758	β = 90
c = 187.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-04-17
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.