4GAZ | pdb_00004gaz

Crystal Structure of a Jumonji Domain-containing Protein JMJD5

• PDB DOI: https://doi.org/10.2210/pdb4GAZ/pdb

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


• Deposited: 2012-07-26 Released: 2013-08-14 
• Deposition Author(s): Wang, H., Zhou, X., Zhang, X., Tao, Y., Chen, N., Zang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal Structure of a Jumonji Domain-containing Protein JMJD5

Wang, H., Zhou, X., Zhang, X., Tao, Y., Chen, N., Zang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59.08 kDa 
• Atom Count: 3,893 
• Modeled Residue Count: 470 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 8	A, B	252	Homo sapiens	Mutation(s): 0  Gene Names: JMJD5, KDM8 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OGA	D [auth A], F [auth B]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.431	α = 90
b = 69.431	β = 90
c = 270.052	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Wang, H., Zhou, X., Zhang, X., Tao, Y., Chen, N., Zang, J.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary