4D6Q

crystal structure of human JMJD2D in complex with 2,4-PDCA

• PDB DOI:  https://doi.org/10.2210/pdb4D6Q/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-14 Released: 2014-12-24 
• Deposition Author(s): Krojer, T., Vollmar, M., Bradley, A., Crawley, L., Szykowska, A., Burgess-Brown, N., Gileadi, C., Johansson, C., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.161 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 

Literature

Crystal Structure of Human Jmjd2D in Complex with 2,4-Pdca

Krojer, T., Vollmar, M., Bradley, A., Crawley, L., Szykowska, A., Burgess-Brown, N., Gileadi, C., Johansson, C., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 40.28 kDa 
• Atom Count: 3,300 
• Modelled Residue Count: 330 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4D	A	343	Homo sapiens	Mutation(s): 0  Gene Names: KDM4D, JHDM3D, JMJD2D EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for Q6B0I6 (Homo sapiens) Explore Q6B0I6  Go to UniProtKB:  Q6B0I6
PHAROS:  Q6B0I6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD2	D [auth A]	PYRIDINE-2,4-DICARBOXYLIC ACID C7 H5 N O4 MJIVRKPEXXHNJT-UHFFFAOYSA-N
SO4	J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PD2	BindingDB:  4D6Q	IC50: 2400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.161 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.91	α = 90
b = 71.91	β = 90
c = 151.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Krojer, T., Vollmar, M., Bradley, A., Crawley, L., Szykowska, A., Burgess-Brown, N., Gileadi, C., Johansson, C., Oppermann, U., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references