4LXL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.176

Literature

Macromolecules
Sequence Display for 4LXL

Classification: OXIDOREDUCTASE / PEPTIDE

Total Structure Weight: 43559.34

Macromolecule Entities
Molecule Chains Length Organism Details
Lysine-specific demethylase 4B A 368 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: Catalytic domain, UNP RESIDUES 1-348
Gene Name(s): KDM4B Gene View JHDM3B JMJD2B KIAA0876
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
H3 peptide D 8 Homo sapiens Gene Name(s): HIST1H3A Gene View H3FA HIST1H3B Gene View H3FL HIST1H3C Gene View H3FC HIST1H3D Gene View H3FB HIST1H3E Gene View H3FD HIST1H3F Gene View H3FI HIST1H3G Gene View H3FH HIST1H3H Gene View H3FK HIST1H3I Gene View H3FF HIST1H3J Gene View H3FJ
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PD2
Query on PD2

A PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NI
Query on NI

A NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
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
  • R-Value Work: 0.176
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 54.36 α = 90.00
b = 78.47 β = 90.00
c = 83.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

No revisions since initial release