4C8D

Crystal structure of JmjC domain of human histone 3 Lysine-specific demethylase 3B (KDM3B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 4C8D

Classification: OXIDOREDUCTASE

Total Structure Weight: 40726.20

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 3B A 349 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JMJC DOMAIN, RESIDUES 1380-1720
Gene Name(s): KDM3B Gene View C5orf7 JHDM2B JMJD1B KIAA1082
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OGA
Query on OGA

A N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.194
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 83.34 α = 90.00
b = 85.61 β = 90.00
c = 117.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-30
  • Released Date: 2013-10-16
  • Deposition author(s): Vollmar, M., Johansson, C., Gileadi, C., Goubin, S., Szykowska, A., Krojer, T., Crawley, L., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History

  • Version 1_0: 2013-10-16

    Type: Initial release

  • Version 1_1: 2013-12-11

    Type: Database references