2GP5

Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate

Structural Biology Knowledgebase: 2GP5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2GP5

Classification: Metal Binding Protein

Total Structure Weight: 81711.80

Macromolecule Entities
Molecule Chains Length Organism Details
Jumonji domain-containing protein 2A A, B 349 Homo sapiens EC#: 1.14.11 IUBMB
Gene Name(s): KDM4A Gene View JHDM3A JMJD2 JMJD2A KIAA0677

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

A, B 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-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)
FE2
Query on FE2

A, B FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.285
  • R-Value Work: 0.236
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.11 α = 90.00
b = 149.52 β = 90.00
c = 57.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-04-16
  • Released Date: 2006-05-23
  • Deposition author(s): Chen, Z., Zang, J., Whetstine, J., Hong, X., Davrazou, F., Kutateladze, T.G., Simpson, M., Dai, S., Hagman, J., Shi, Y., Zhang, G.

Revision History

  • 2013-11-27
    Type: Non-polymer description | Details: Change Fe+3 to Fe+2 based on citation
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update