2OX0

Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9

Structural Biology Knowledgebase: 2OX0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OX0

Classification: OXIDOREDUCTASE

Total Structure Weight: 90981.21

Macromolecule Entities
Molecule Chains Length Organism Details
JmjC domain-containing histone demethylation protein 3A A, B 381 Homo sapiens EC#: 1.14.11 IUBMB
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677
synthetic peptide C, 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

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

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

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-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)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OGA IC50: 250000 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MLY
Query on MLY
C, D L-PEPTIDE LINKING C8 H18 N2 O2 LYS
ALY
Query on ALY
C, D L-PEPTIDE LINKING C8 H16 N2 O3 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.169
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.21 α = 90.00
b = 150.00 β = 90.00
c = 57.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-02-19
  • Released Date: 2007-03-13
  • Deposition author(s): Pilka, E.S., Ng, S.S., Kavanagh, K.L., McDonough, M.A., Savitsky, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A., Sundstrom, M., Schofield, C.J., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4