9SA1 | pdb_00009sa1

The RING domain of IDOL

PDB DOI: https://doi.org/10.2210/pdb9SA1/pdb

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

Deposited: 2025-08-07 Released: 2025-09-10
Deposition Author(s): Bradshaw, W.J., He, L., Guenther, F., Murphy, E.J.
Funding Organization(s): Alzheimers Research UK (ARUK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free:
0.177 (Depositor), 0.177 (DCC)
R-Value Work:
0.130 (Depositor), 0.130 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9SA1

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

Literature

The RING domain of IDOL

Bradshaw, W.J., He, L., Guenther, F., Murphy, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 17.9 kDa
Atom Count: 1,526
Modeled Residue Count: 156
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase MYLIP	A, B	78	Homo sapiens	Mutation(s): 0 Gene Names: MYLIP, BZF1, IDOL, BM-023, PP5242 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WY64 (Homo sapiens) Explore Q8WY64 Go to UniProtKB: Q8WY64
PHAROS: Q8WY64 GTEx: ENSG00000007944
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WY64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free: 0.177 (Depositor), 0.177 (DCC)
R-Value Work: 0.130 (Depositor), 0.130 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.534	α = 90
b = 51.958	β = 90
c = 55.328	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Alzheimers Research UK (ARUK)	United Kingdom	ARUK2020DDI-OX
Alzheimers Research UK (ARUK)	United Kingdom	520909

Revision History (Full details and data files)

Version 1.0: 2025-09-10
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.