5FZO

Crystal structure of the catalytic domain of human JmjD1C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 5FZO

Classification: OXIDOREDUCTASE

Total Structure Weight: 81141.34

Macromolecule Entities
Molecule Chains Length Organism Details
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C A 352 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500
Gene Name(s): JMJD1C Gene View JHDM2C KIAA1380 TRIP8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROBABLE JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROT EIN 2C B 352 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JUMONJI DOMAIN, UNP RESIDUES 2157-2500
Mutation: S2340D
Gene Name(s): JMJD1C Gene View JHDM2C KIAA1380 TRIP8

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

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

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

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSD
Query on CSD
A, B L-PEPTIDE LINKING C3 H7 N O4 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.192
  • Space Group: P 2 21 21

Unit Cell:

Length (Å) Angle (°)
a = 45.32 α = 90.00
b = 110.92 β = 90.00
c = 165.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-03-15
  • Released Date: 2016-03-30
  • Deposition author(s): Nowak, R., Talon, R., Krojer, T., Goubin, S., McDonough, M., Fairhead, M., Oppermann, U., Johansson, C.

Revision History

  • Version 1_0: 2016-03-30

    Type: Initial release

  • Version 1_1: 2016-04-06

    Type: Structure summary