2XXZ

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8XQ	J [auth A], M [auth B]	8-hydroxyquinoline-5-carboxylic acid C10 H7 N O3 JGRPKOGHYBAVMW-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	C [auth A], E [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• 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

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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