7Y1P | pdb_00007y1p

CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na

PDB DOI: https://doi.org/10.2210/pdb7Y1P/pdb

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

Deposited: 2022-06-08 Released: 2023-12-13
Deposition Author(s): He, Z., Yuchi, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.208 (Depositor), 0.209 (DCC)
R-Value Observed:
0.209 (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 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF THE RGS-HOMOLOGOUS DOMAIN OF AXIN IN COMPLEX WITH LZ-22Na

He, Z., Yuchi, Z.

To be published.

Macromolecule Content

Total Structure Weight: 67.45 kDa
Atom Count: 4,383
Modeled Residue Count: 556
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin-1	A, B, C, D	147	Homo sapiens	Mutation(s): 0 Gene Names: AXIN1, AXIN
UniProt & NIH Common Fund Data Resources
Find proteins for O15169 (Homo sapiens) Explore O15169 Go to UniProtKB: O15169
PHAROS: O15169 GTEx: ENSG00000103126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I5L (Subject of Investigation/LOI) Query on I5L Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	(2~{Z},4~{Z})-2-methyl-5-(8-oxidanyldibenzofuran-4-yl)penta-2,4-dienal C₁₈ H₁₄ O₃ FWMQKXGLKVAFDC-FYOBGJLRSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.208 (Depositor), 0.209 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.343	α = 90
b = 155.343	β = 90
c = 107.061	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32022073
National Natural Science Foundation of China (NSFC)	China	31972287

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.