1IYW Ligase date Sep 10, 2002
title Preliminary Structure Of Thermus Thermophilus Ligand-Free Va Synthetase
authors S.Fukai, O.Nureki, S.Sekine, A.Shimada, D.G.Vassylyev, S.Yokoyama Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Valyl-Trna Synthetase
Chain: A, B
Ec: 6.1.1.9
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.316 R_Free 0.383
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.562 207.328 59.235 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.00 Å
ligand
enzyme Ligase E.C.6.1.1.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • aminoacyl-tRNA editing activ...


    • Primary referenceMechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S, RNA 2003 Jan;9(1):100-11. PMID:12554880
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (1iyw.pdb1.gz) 20 Kb
  • Biological Unit Coordinates (1iyw.pdb2.gz) 20 Kb
  • CSU: Contacts of Structural Units for 1IYW
  • Likely Quarternary Molecular Structure file(s) for 1IYW
  • Retrieve 1IYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IYW from S2C, [Save to disk]
    • View 1IYW 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 1IYW
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1IYW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1iywa4, region A:1-189,A:343-578 [Jmol] [rasmolscript] [script source]
        - Domain d1iywa3, region A:190-342 [Jmol] [rasmolscript] [script source]
        - Domain d1iywa2, region A:579-796 [Jmol] [rasmolscript] [script source]
        - Domain d1iywa1, region A:797-862 [Jmol] [rasmolscript] [script source]
        - Domain d1iywb4, region B:1-189,B:343-578 [Jmol] [rasmolscript] [script source]
        - Domain d1iywb3, region B:190-342 [Jmol] [rasmolscript] [script source]
        - Domain d1iywb2, region B:579-796 [Jmol] [rasmolscript] [script source]
        - Domain d1iywb1, region B:797-862 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1iyw_A] [1iyw] [1iyw_B]
  • SWISS-PROT database: [P96142]
  • Domain organization of [SYV_THETH] by SWISSPFAM
    • Other resources with information on 1IYW
  • Community annotation for 1IYW 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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