2XXZ | pdb_00002xxz

Crystal structure of the human JMJD3 jumonji domain

PDB DOI: https://doi.org/10.2210/pdb2XXZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-12 Released: 2010-11-24
Deposition Author(s): Che, K.H., Yue, W.W., Krojer, T., Muniz, J.R.C., Ng, S.S., Tumber, A., Daniel, M., Burgess-Brown, N., Savitsky, P., Ugochukwu, E., Filippakopoulos, P., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor), 0.245 (DCC)
R-Value Work:
0.183 (Depositor), 0.213 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Human Jmjd3 Jumonji Domain

Che, K.H., Yue, W.W., Krojer, T., Muniz, J.R.C., Ng, S.S., Tumber, A., Daniel, M., Burgess-Brown, N., Savitsky, P., von Delft, F., Ugochukwu, E., Filippakopoulos, P., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 76.26 kDa
Atom Count: 5,082
Modeled Residue Count: 578
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 6B	A, B	332	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 O15054 (Homo sapiens) Explore O15054 Go to UniProtKB: O15054
PHAROS: O15054 GTEx: ENSG00000132510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15054
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8XQ Query on 8XQ Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B]	8-hydroxyquinoline-5-carboxylic acid C₁₀ H₇ N O₃ JGRPKOGHYBAVMW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	C [auth A], E [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8XQ	BindingDB: 2XXZ	IC50: min: 100, max: 200 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216 (Depositor), 0.245 (DCC)
R-Value Work: 0.183 (Depositor), 0.213 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.757	α = 90
b = 71.431	β = 90
c = 159.698	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-11-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-24
Type: Initial release
Version 1.1: 2015-01-14
Changes: Non-polymer description, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other