5FXZ | pdb_00005fxz

Crystal structure of JmjC domain of human histone demethylase UTY in complex with citrate

PDB DOI: https://doi.org/10.2210/pdb5FXZ/pdb

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

Deposited: 2016-03-03 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: 1.98 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (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 Citrate

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: 111.69 kDa
Atom Count: 7,914
Modelled Residue Count: 883
Deposited Residue Count: 956
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE DEMETHYLASE UTY	A, B	478	Homo sapiens	Mutation(s): 0 EC: 1.14.11.68
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14607
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain O [auth B]	D [auth A], O [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth B]	M [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.58	α = 90
b = 111.56	β = 90
c = 119.68	γ = 90

Software Package:

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

Structure Validation

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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