5FBJ | pdb_00005fbj

Complex structure of JMJD5 and substrate

• PDB DOI: https://doi.org/10.2210/pdb5FBJ/pdb

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


• Deposited: 2015-12-14 Released: 2016-12-14 
• Deposition Author(s): Liu, H.L., Wang, Y., Wang, C., Zhang, G.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

to be published

Liu, H.L., Wang, Y., Wang, C., Dai, S.D., 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: 27.72 kDa 
• Atom Count: 2,041 
• Modeled 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
NMM	C [auth A]	(2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid C7 H16 N4 O2 NTNWOCRCBQPEKQ-YFKPBYRVSA-N
AKG	B [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.246 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.539	α = 90
b = 65.052	β = 90
c = 77.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Liu, H.L., Wang, Y., Wang, C., Zhang, G.Y.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description