2YBK

JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE

Structural Biology Knowledgebase: 2YBK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YBK

Classification: OXIDOREDUCTASE

Total Structure Weight: 89233.24

Macromolecule Entities
Molecule Chains Length Organism Details
LYSINE-SPECIFIC DEMETHYLASE 4A A, B 381 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 1-359
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677

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

A, B (2R)-2-hydroxypentanedioic acid
C5 H8 O5
HWXBTNAVRSUOJR-GSVOUGTGSA-N
Ligand Explorer
 
JSmol
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2HG IC50: 24000 nM (100) BindingDB

IC50: 24000 nM  BindingMOAD
IC50: 24000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.203
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.13 α = 90.00
b = 149.33 β = 90.00
c = 56.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-08
  • Released Date: 2011-04-06
  • Deposition author(s): Chowdhury, R., Mcdonough, M.A., Schofield, C.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4