1YFT Ligase date Jan 03, 2005
title The Crystal Structure Of The Catalytic Fragment Of Alanyl-Tr Synthetase In Complex Wtih Glycine
authors M.A.Swairjo, P.R.Schimmel
compound source
Molecule: Alanyl-Trna Synthetase
Chain: A
Synonym: Alanine-Trna Ligase, Alars
Ec: 6.1.1.7
Engineered: Yes
 Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363
Gene: Alas
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet20b+
symmetry Space Group: P 41 21 2
R_factor 0.207 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.912 73.912 172.905 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.23 Å
ligand GLY enzyme Ligase E.C.6.1.1.7 BRENDA
related structures by homologous chain: 1YFR, 1YGB
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBreaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase., Swairjo MA, Schimmel PR, Proc Natl Acad Sci U S A 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:15657145
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (1yft.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1yft.pdb2.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 1YFT
  • CSU: Contacts of Structural Units for 1YFT
  • Likely Quarternary Molecular Structure file(s) for 1YFT
  • Structure Factors (231 Kb)
  • Retrieve 1YFT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YFT from S2C, [Save to disk]
  • Re-refined 1yft structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YFT 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 1YFT
  • 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 1YFT, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yft] [1yft_A]
  • SWISS-PROT database: [O67323]
  • Domain organization of [SYA_AQUAE] by SWISSPFAM
    • Other resources with information on 1YFT
  • Community annotation for 1YFT 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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