3RVH | pdb_00003rvh

Crystal Structure of JMJD2A Complexed with Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3RVH/pdb

• Classification: Oxidoreductase/Oxidoreductase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-06 Released: 2012-05-09 
• Deposition Author(s): King, O.N.F., Maloney, D.J., Tumber, A., Rai, G., Jadhav, A., Clifton, I.J., Heightman, T.D., Simeonov, A., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.224 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of JMJD2A Complexed with Inhibitor

King, O.N.F., Maloney, D.J., Tumber, A., Rai, G., Jadhav, A., Clifton, I.J., Heightman, T.D., Simeonov, A., McDonough, M.A., Schofield, C.J.

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: 89.63 kDa 
• Atom Count: 6,123 
• Modeled Residue Count: 701 
• 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: JHDM3A, JMJD2, JMJD2A, KDM4A, 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
HQ2	E [auth A], I [auth B]	8-hydroxy-3-(piperazin-1-yl)quinoline-5-carboxylic acid C14 H15 N3 O3 TUTIPJBLHAOGRW-UHFFFAOYSA-N
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.224 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.82	α = 90
b = 149.34	β = 90
c = 57.154	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): King, O.N.F., Maloney, D.J., Tumber, A., Rai, G., Jadhav, A., Clifton, I.J., Heightman, T.D., Simeonov, A., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description