2YU1 | pdb_00002yu1

Crystal structure of hJHDM1A complexed with a-ketoglutarate

• PDB DOI: https://doi.org/10.2210/pdb2YU1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-04-05 Released: 2007-04-24 
• Deposition Author(s): Han, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.238 (Depositor) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Structural basis for histone demethylation by JHDM1

Han, Z., Liu, P., Gu, L., Zhang, Y., Li, H., Chen, S., Chai, 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)

Macromolecule Content 

• Total Structure Weight: 53.12 kDa 
• Atom Count: 3,255 
• Modeled Residue Count: 386 
• Deposited Residue Count: 451 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JmjC domain-containing histone demethylation protein 1A	A	451	Homo sapiens	Mutation(s): 1  Gene Names: hJHDM1A 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
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.238 (Depositor) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.255	α = 90
b = 81.255	β = 90
c = 124.01	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Han, Z.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2024-05-29
  Changes: Data collection