4BBQ

Crystal structure of the CXXC and PHD domain of Human Lysine-specific Demethylase 2A (KDM2A)(FBXL11)

• PDB DOI: https://doi.org/10.2210/pdb4BBQ/pdb

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


• Deposited: 2012-09-27 Released: 2012-10-10 
• Deposition Author(s): Allerston, C.K., Watson, A.A., Edlich, C., Li, B., Chen, Y., Ball, L., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Laue, E.D., Gileadi, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Crystal Structure of the Cxxc and Phd Domain of Human Lysine-Specific Demethylase 2A (Kdm2A)(Fbxl11)

Allerston, C.K., Watson, A.A., Edlich, C., Li, B., Chen, Y., Ball, L., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Laue, E.D., Gileadi, O.

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: 27.22 kDa 
• Atom Count: 1,682 
• Modelled Residue Count: 217 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 2A	A, B	117	Homo sapiens	Mutation(s): 0  EC: 1.14.11.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2K7 (Homo sapiens) Explore Q9Y2K7  Go to UniProtKB:  Q9Y2K7
PHAROS:  Q9Y2K7 GTEx:  ENSG00000173120

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.024	α = 90
b = 30.053	β = 91.66
c = 90.824	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
AP_SCALE	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Allerston, C.K., Watson, A.A., Edlich, C., Li, B., Chen, Y., Ball, L., Krojer, T., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Laue, E.D., Gileadi, O.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description