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 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Jmjc Domain of Human Histone 3 Lysine-Specific Demethylase 3B (Kdm3B)

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.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 3BA349Homo sapiensMutation(s): 0 
Gene Names: KDM3BC5orf7JHDM2BJMJD1BKIAA1082
EC: 1.14.11 (PDB Primary Data), 1.14.11.65 (UniProt)
Find proteins for Q7LBC6 (Homo sapiens)
Explore Q7LBC6 
Go to UniProtKB:  Q7LBC6
NIH Common Fund Data Resources
PHAROS:  Q7LBC6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA

Download Ideal Coordinates CCD File 
C [auth A]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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E [auth A], F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.34α = 90
b = 85.61β = 90
c = 117.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Database references