8Q06 | pdb_00008q06

EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A

PDB DOI: https://doi.org/10.2210/pdb8Q06/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-27 Released: 2025-02-12
Deposition Author(s): Armstrong, L.A., Kulathu, Y.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.247 (Depositor), 0.248 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

EF-hand of MINDY3 Deubiquitylase in Complex with UBL of RAD23A

Armstrong, L.A., Kulathu, Y.

To be published.

Macromolecule Content

Total Structure Weight: 37.59 kDa
Atom Count: 2,528
Modeled Residue Count: 296
Deposited Residue Count: 338
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase MINDY	A, B	80	Escherichia coli	Mutation(s): 0 Gene Names: MDA_GLEAN10008107 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48 Go to UniProtKB: P0CG48
PHAROS: P0CG48 GTEx: ENSG00000150991
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG48
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23 homolog A	C, D	89	Escherichia coli	Mutation(s): 0 Gene Names: RAD23A EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for P54725 (Homo sapiens) Explore P54725 Go to UniProtKB: P54725
PHAROS: P54725 GTEx: ENSG00000179262
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54725
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.247 (Depositor), 0.248 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.279	α = 90
b = 134.139	β = 114.67
c = 45.498	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-12

Deposition Author(s):

Armstrong, L.A.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2025-02-12
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.