1H3F Ligase date Aug 28, 2002
title Tyrosyl-Trna Synthetase From Thermus Thermophilus Complexed Tyrosinol
authors S.Cusack, A.Yaremchuk, I.Kriklivyi, M.Tukalo
compound source
Molecule: Tyrosyl-Trna Synthetase
Chain: A, B
Synonym: Tyrosine--Trna Ligase
Ec: 6.1.1.1
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet29b
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.794 111.050 141.226 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand SO4, TYE enzyme Ligase E.C.6.1.1.1 BRENDA
related structures by homologous chain: 1H3E
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceClass I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition., Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S, EMBO J 2002 Jul 15;21(14):3829-40. PMID:12110594
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (1h3f.pdb1.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 1H3F
  • CSU: Contacts of Structural Units for 1H3F
  • Likely Quarternary Molecular Structure file(s) for 1H3F
  • Structure Factors (531 Kb)
  • Retrieve 1H3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1H3F from S2C, [Save to disk]
  • Re-refined 1h3f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1H3F 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 1H3F
  • 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 1H3F, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h3fa2, region A:352-432 [Jmol] [rasmolscript] [script source]
        - Domain d1h3fa1, region A:5-347 [Jmol] [rasmolscript] [script source]
        - Domain d1h3fb2, region B:353-432 [Jmol] [rasmolscript] [script source]
        - Domain d1h3fb1, region B:5-343 [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: [1h3f] [1h3f_B] [1h3f_A]
  • SWISS-PROT database: [P83453]
  • Domain organization of [SYY_THET2] by SWISSPFAM
  • Domain found in 1H3F: [S4 ] by SMART
  • Other resources with information on 1H3F
  • Community annotation for 1H3F 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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