8WD3 | pdb_00008wd3

The Crystal Structure of JMJD2A(M1-L359) from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8WD3/pdb

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


• Deposited: 2023-09-14 Released: 2023-11-22 
• Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Bao, C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.250 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of JMJD2A(M1-L359) from Biortus.

Wang, F., Cheng, W., Yuan, Z., Shang, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.9 kDa 
• Atom Count: 5,512 
• Modeled Residue Count: 683 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A EC: 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
PHAROS:  O75164 GTEx:  ENSG00000066135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.250 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.641	α = 90
b = 97.111	β = 90
c = 141.083	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Ju, C., Bao, C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release