2CYA Ligase date Jul 06, 2005
title Crystal Structure Of Tyrosyl-Trna Synthetase From Aeropyrum
authors M.Kuratani, H.Sakai, M.Takahashi, T.Yanagisawa, T.Kobayashi, K.Mu L.Chen, Z.J.Liu, B.C.Wang, C.Kuroishi, S.Kuramitsu, T.Terada, Y.B M.Shirouzu, S.I.Sekine, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Tyrosyl-Trna Synthetase
Chain: A
Ec: 6.1.1.1
Engineered: Yes
Organism_scientific: Aeropyrum Pernix
Organism_taxid: 56636
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 43 21 2
R_factor 0.211 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.912 65.912 196.168 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand SO4 enzyme Ligase E.C.6.1.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structures of Tyrosyl-tRNA Synthetases from Archaea., Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S, J Mol Biol 2006 Jan 20;355(3):395-408. Epub 2005 Nov 14. PMID:16325203
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2cya.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 2CYA
  • CSU: Contacts of Structural Units for 2CYA
  • Likely Quarternary Molecular Structure file(s) for 2CYA
  • Structure Factors (324 Kb)
  • Retrieve 2CYA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2CYA from S2C, [Save to disk]
  • Re-refined 2cya structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2CYA 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 2CYA
  • 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 2CYA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2cya] [2cya_A]
  • SWISS-PROT database: [Q9YA64]
  • Domain organization of [SYY_AERPE] by SWISSPFAM
  • Other resources with information on 2CYA
  • Community annotation for 2CYA 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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