1QF6 Ligase Rna date Apr 06, 1999
title Structure Of E. Coli Threonyl-Trna Synthetase Complexed With Cognate Trna
authors R.Sankaranarayanan, A.C.Dock-Bregeon, B.Rees, D.Moras
compound source
Molecule: Threonine Trna
Chain: B
Synonym: Trna (Thr)
Other_details: Complexed With Adenosine Monophosphate
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Threonyl-Trna Synthetase
Chain: A
Synonym: Thrrs
Ec: 6.1.1.3
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.195 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
162.670 162.670 128.570 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand 5MU, AET, AMP, G7M, H2U, PSU, ZN enzyme Ligase E.C.6.1.1.3 BRENDA
note 1QF6 (Molecule of the Month:pdb16)
related structures by homologous chain: 1EVK
Gene
Ontology
ChainFunctionProcessComponent
A
  • aminoacyl-tRNA editing activ...


    • Primary referenceThe structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site., Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D, Cell 1999 Apr 30;97(3):371-81. PMID:10319817
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (1qf6.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 1QF6
  • CSU: Contacts of Structural Units for 1QF6
  • Likely Quarternary Molecular Structure file(s) for 1QF6
  • Structure Factors (395 Kb)
  • Retrieve 1QF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QF6 from S2C, [Save to disk]
  • Re-refined 1qf6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1QF6 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 1QF6
  • 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 1QF6, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qf6a2, region A:2-62 [Jmol] [rasmolscript] [script source]
        - Domain d1qf6a4, region A:242-532 [Jmol] [rasmolscript] [script source]
        - Domain d1qf6a1, region A:533-642 [Jmol] [rasmolscript] [script source]
        - Domain d1qf6a3, region A:63-241 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1qf6_B] [1qf6_A] [1qf6]
  • SWISS-PROT database: [P0A8M3]
  • Domain organization of [SYT_ECOLI] by SWISSPFAM
  • Domain found in 1QF6: [tRNA_SAD ] by SMART
    • Other resources with information on 1QF6
  • Community annotation for 1QF6 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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