4GD4 | pdb_00004gd4

Crystal Structure of JMJD2A Complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GD4/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-31 Released: 2012-08-15 
• Deposition Author(s): King, O.N.F., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., McDonough, M.A., Schofield, C.J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.218 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal Structure of JMJD2A Complexed with Inhibitor

King, O.N.F., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., McDonough, M.A., Schofield, C.J., Structural Genomics Consortium (SGC)

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: 89.42 kDa 
• Atom Count: 5,994 
• Modeled Residue Count: 697 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
PHAROS:  O75164 GTEx:  ENSG00000066135

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0WS	F [auth A], L [auth B]	2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid C9 H7 N3 O2 NTNYOLXCVCDWFY-UHFFFAOYSA-N
ZN	D [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A], G [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.218 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.75	α = 90
b = 150.03	β = 90
c = 57.49	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): King, O.N.F., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., McDonough, M.A., Schofield, C.J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Other
• Version 1.2: 2014-10-08
  Changes: Database references
• Version 1.3: 2014-12-03
  Changes: Structure summary
• Version 1.4: 2018-01-24
  Changes: Database references
• Version 1.5: 2018-01-31
  Changes: Database references
• Version 1.6: 2024-02-28
  Changes: Data collection, Database references, Derived calculations