5FYM | pdb_00005fym

Crystal structure of JmjC domain of human histone demethylase UTY in complex with D-2-hydroxyglutarate

PDB DOI: https://doi.org/10.2210/pdb5FYM/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-03-08 Released: 2016-03-16
Deposition Author(s): Nowak, R., Krojer, T., Johansson, C., Gileadi, C., Kupinska, K., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.245 (Depositor), 0.246 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2- Hydroxyglutarate

Nowak, R., Krojer, T., Johansson, C., Gileadi, C., Kupinska, K., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 112.29 kDa
Atom Count: 7,949
Modeled Residue Count: 890
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE DEMETHYLASE UTY	A, B	478	Homo sapiens	Mutation(s): 0 EC: 1.14.11 (PDB Primary Data), 1.14.11.68 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14607 (Homo sapiens) Explore O14607 Go to UniProtKB: O14607
PHAROS: O14607 GTEx: ENSG00000183878
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14607
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2HG Query on 2HG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain D [auth A]	D [auth A], U [auth B]	(2R)-2-hydroxypentanedioic acid C₅ H₈ O₅ HWXBTNAVRSUOJR-GSVOUGTGSA-N		Interactions Focus chain D [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain U [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain JA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain JA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain JA [auth B]	JA [auth B], S [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain S [auth A] Interactions & Density Focus chain JA [auth B] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain C [auth A]	C [auth A], T [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.245 (Depositor), 0.246 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.48	α = 90
b = 109.34	β = 90
c = 117.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
DIMPLE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description