2E1B Ligase, Hydrolase date Oct 20, 2006
title Crystal Structure Of The Alax-M Trans-Editing Enzyme From Py Horikoshii
authors R.Fukunaga, S.Yokoyama, Riken Structural Genomicsproteomics I (Rsgi)
compound source
Molecule: 216aa Long Hypothetical Alanyl-Trna Synthetase
Chain: A
Synonym: Ph0108
Ec: 6.1.1.7, 3.1.1.29
Engineered: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 62
R_factor 0.227 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.223 80.223 72.269 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand ZN enzyme Ligase E.C.6.1.1.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • aminoacyl-tRNA editing activ...


  • Primary referenceStructure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii., Fukunaga R, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):390-400. Epub 2007, Feb 21. PMID:17327676
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (2e1b.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 2E1B
  • CSU: Contacts of Structural Units for 2E1B
  • Likely Quarternary Molecular Structure file(s) for 2E1B
  • Structure Factors (56 Kb)
  • Retrieve 2E1B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E1B from S2C, [Save to disk]
  • Re-refined 2e1b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E1B 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 2E1B
  • 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
  • 3D motif for 2E1B, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e1b_A] [2e1b]
  • SWISS-PROT database: [O57848]
  • Domain organization of [ALAXM_PYRHO] by SWISSPFAM
  • Domain found in 2E1B: [tRNA_SAD ] by SMART
  • Other resources with information on 2E1B
  • Community annotation for 2E1B at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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