4QU1

Crystal structure of human JMJD5 jmj-c domain

• PDB DOI: https://doi.org/10.2210/pdb4QU1/pdb

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


• Deposited: 2014-07-10 Released: 2015-07-15 
• Deposition Author(s): Liu, H.L., Wang, C., Zhang, G.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.174 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 

Literature

The Histone Arginine Demethylase JMJD5

Liu, H.L., Wang, C., Dege, C., Ning, F.K., Weisz, J., Hansen, K., Zang, J.Y., Pan, C.H., Marrack, P., Kappler, J., Hagmen, J., Zhang, G.Y.

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: 27.62 kDa 
• Atom Count: 2,240 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 8	A	236	Homo sapiens	Mutation(s): 0  Gene Names: KDM8, JMJD5 EC: 1.14.11.27 (PDB Primary Data), 3.4 (UniProt), 1.14.11.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N371 (Homo sapiens) Explore Q8N371  Go to UniProtKB:  Q8N371
PHAROS:  Q8N371 GTEx:  ENSG00000155666

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.174 
• R-Value Work: 0.149 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.627	α = 90
b = 65.03	β = 90
c = 77.782	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Liu, H.L., Wang, C., Zhang, G.Y.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations