3THT Oxidoreductase date Aug 19, 2011
title Crystal Structure And Rna Binding Properties Of The Rrmalkb In Human Abh8, An Enzyme Catalyzing Trna Hypermodification, Structural Genomics Consortium Target Hr5601b
authors C.Pastore, I.Topalidou, F.Forouhar, A.C.Yan, M.Levy, J.F.Hunt, Nor Structural Genomics Consortium (Nesg)
compound source
Molecule: Alkylated Dna Repair Protein Alkb Homolog 8
Chain: A, B, C, D
Fragment: Rrm And Alkb Domains Of Abh8
Synonym: Probable Alpha-Ketoglutarate-Dependent Dioxygenase
Ec: 1.14.11.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Abh8, Alkbh8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26
symmetry Space Group: C 1 2 1
R_factor 0.220 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
150.166 73.279 149.814 90.00 112.73 90.00
method X-Ray Diffractionresolution 3.01 Å
ligand AKG, MN, ZN enzyme Oxidoreductase E.C.1.14.11 BRENDA
A, D, C, B

Primary referenceCrystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification., Pastore C, Topalidou I, Forouhar F, Yan AC, Levy M, Hunt JF, J Biol Chem. 2012 Jan 13;287(3):2130-43. Epub 2011 Nov 7. PMID:22065580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (205 Kb) [Save to disk]
  • Biological Unit Coordinates (3tht.pdb1.gz) 52 Kb
  • Biological Unit Coordinates (3tht.pdb2.gz) 54 Kb
  • Biological Unit Coordinates (3tht.pdb3.gz) 51 Kb
  • Biological Unit Coordinates (3tht.pdb4.gz) 53 Kb
  • Biological Unit Coordinates (3tht.pdb5.gz) 201 Kb
  • Biological Unit Coordinates (3tht.pdb6.gz) 102 Kb
  • Biological Unit Coordinates (3tht.pdb7.gz) 195 Kb
  • Biological Unit Coordinates (3tht.pdb8.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 3THT
  • CSU: Contacts of Structural Units for 3THT
  • Structure Factors (423 Kb)
  • Retrieve 3THT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3THT from S2C, [Save to disk]
  • Re-refined 3tht structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3THT in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3THT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3THT, from MSDmotif at EBI
  • Fold representative 3tht from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tht_B] [3tht_D] [3tht_C] [3tht_A] [3tht]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3THT
  • Community annotation for 3THT at PDBWiki (http://pdbwiki.org)
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