3THT

Crystal structure and RNA binding properties of the RRM/AlkB domains in human ABH8, an enzyme catalyzing tRNA hypermodification, Northeast Structural Genomics Consortium Target HR5601B

Structural Biology Knowledgebase: 3THT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 3THT

Classification: OXIDOREDUCTASE

Total Structure Weight: 158505.95

Macromolecule Entities
Molecule Chains Length Organism Details
Alkylated DNA repair protein alkB homolog 8 A, B, C, D 345 Homo sapiens EC#: 1.14.11 IUBMB
Fragment: RRM and AlkB domains of ABH8
Gene Name(s): ALKBH8 Gene View ABH8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C, D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B, C, D MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.220
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 150.17 α = 90.00
b = 73.28 β = 112.73
c = 149.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-19
  • Released Date: 2011-11-02
  • Deposition author(s): Pastore, C., Topalidou, I., Forouhar, F., Yan, A.C., Levy, M., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History

  • 2012-10-10
    Type: Citation | Details: Citation update