4O61

Structure of human ALKBH5 crystallized in the presence of citrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.174

Literature

Macromolecules
Sequence Display for 4O61

Classification: OXIDOREDUCTASE

Total Structure Weight: 51246.46

Macromolecule Entities
Molecule Chains Length Organism Details
RNA demethylase ALKBH5 A, B 222 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: UNP residues 74-294
Gene Name(s): ALKBH5 Gene View ABH5 OFOXD1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNL
Query on UNL

Unknown ligand
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

UNKNOWN ATOM OR ION
X
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CIT N/A in BindingDB
IC50: 488000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230
  • R-Value Work: 0.174
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 50.47 α = 90.00
b = 57.17 β = 102.23
c = 78.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-12-20
  • Released Date: 2014-02-26
  • Deposition author(s): Tempel, W., Chao, X., Liu, K., Dong, A., Cerovina, T., He, H., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History

  • 2014-05-07
    Type: Database references
  • 2014-06-04
    Type: Database references
  • 2015-07-01
    Type: Database references