4LXL | pdb_00004lxl

Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3

• PDB DOI: https://doi.org/10.2210/pdb4LXL/pdb

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


• Deposited: 2013-07-30 Released: 2014-07-30 
• Deposition Author(s): Wang, W.-C., Chu, C.-H., Chen, C.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3

Wang, W.-C., Chu, C.-H., Chen, C.-C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.56 kDa 
• Atom Count: 3,025 
• Modeled Residue Count: 337 
• Deposited Residue Count: 376 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4B	A	368	Homo sapiens	Mutation(s): 0  Gene Names: KDM4B EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O94953 (Homo sapiens) Explore O94953  Go to UniProtKB:  O94953
PHAROS:  O94953 GTEx:  ENSG00000127663

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 peptide	B [auth D]	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD2	C [auth A]	PYRIDINE-2,4-DICARBOXYLIC ACID C7 H5 N O4 MJIVRKPEXXHNJT-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B [auth D]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.364	α = 90
b = 78.475	β = 90
c = 83.893	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Wang, W.-C., Chu, C.-H., Chen, C.-C.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description