4AAP | pdb_00004aap

Crystal structure of JMJD5 domain of human Lysine-specific demethylase 8 (KDM8) in complex with N-oxalylglycine (NOG)

• PDB DOI: https://doi.org/10.2210/pdb4AAP/pdb

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


• Deposited: 2011-12-05 Released: 2012-02-29 
• Deposition Author(s): Vollmar, M., Johansson, C., Krojer, T., Canning, P., Allerston, C., Gadhave, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal Structure of Jmjd5 Domain of Human Lysine- Specific Demethylase 8 (Kdm8) in Complex with N- Oxalylglycine (Nog)

Vollmar, M., Johansson, C., Krojer, T., Canning, P., Allerston, C., Gadhave, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.08 kDa 
• Atom Count: 3,725 
• Modeled Residue Count: 468 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 8	A, B	239	Homo sapiens	Mutation(s): 0  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], G [auth B]	N-OXALYLGLYCINE C4 H5 N O5 BIMZLRFONYSTPT-UHFFFAOYSA-N
ZN	C [auth A], E [auth A], F [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.575	α = 90
b = 68.575	β = 90
c = 269.003	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Vollmar, M., Johansson, C., Krojer, T., Canning, P., Allerston, C., Gadhave, A., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other