2XXZ

Crystal structure of the human JMJD3 jumonji domain

Structural Biology Knowledgebase: 2XXZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XXZ

Classification: OXIDOREDUCTASE

Total Structure Weight: 76262.39

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 6B A, B 332 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: JUMONJI DOMAIN, RESIDUES 1173-1502
Gene Name(s): KDM6B Gene View JMJD3 KIAA0346

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
8XQ
Query on 8XQ

A, B 8-hydroxyquinoline-5-carboxylic acid
C10 H7 N O3
JGRPKOGHYBAVMW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.183
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.76 α = 90.00
b = 71.43 β = 90.00
c = 159.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-12
  • Released Date: 2010-11-24
  • Deposition author(s): Che, K.H., Yue, W.W., Krojer, T., Muniz, J.R.C., Ng, S.S., Tumber, A., Daniel, M., Burgess-Brown, N., Savitsky, P., Ugochukwu, E., Filippakopoulos, P., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Revision History

  • 2015-01-14
    Type: Version format compliance | Details: REMARK 4
  • 2015-01-14
    Type: Non-polymer description | Details: FORMUL