2IY5 Ligase date Jul 12, 2006
title Phenylalanyl-Trna Synthetase From Thermus Thermophilus Compl Trna And A Phenylalanyl-Adenylate Analog
authors N.Moor, O.Kotik-Kogan, D.Tworowski, M.Sukhanova, M.Safro
compound source
Molecule: Phenylalanyl-Trna Synthetase Alpha Chain
Chain: A
Synonym: Phenylalanyl-Trna Synthetase, Phers, Phenylalanine Ligase Alpha Chain;
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Phenylalanyl-Trna Synthetase Beta Chain
Chain: B
Synonym: Phenylalanyl-Trna Synthetase, Phers, Phenylalanine Ligase Beta Chain;

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Trnaphe
Chain: T

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 32 2 1
R_factor 0.238 R_Free 0.299
length a length b length c angle alpha angle beta angle gamma
173.400 173.400 139.400 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand FYA, MG enzyme Ligase E.C. BRENDA


Primary referenceThe crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end., Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M, Biochemistry. 2006 Sep 5;45(35):10572-83. PMID:16939209
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (216 Kb) [Save to disk]
  • Biological Unit Coordinates (2iy5.pdb1.gz) 416 Kb
  • LPC: Ligand-Protein Contacts for 2IY5
  • CSU: Contacts of Structural Units for 2IY5
  • Likely Quarternary Molecular Structure file(s) for 2IY5
  • Structure Factors (313 Kb)
  • Retrieve 2IY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IY5 from S2C, [Save to disk]
  • Re-refined 2iy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IY5 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 2IY5
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2IY5, from MSDmotif at EBI
  • Fold representative 2iy5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2iy5] [2iy5_B] [2iy5_T] [2iy5_A]
  • SWISS-PROT database: [P27001] [P27002]
  • Domain organization of [SYFA_THETH] [SYFB_THETH] by SWISSPFAM
  • Domains found in 2IY5: [B3_4] [B5] [FDX-ACB ] by SMART
  • Other resources with information on 2IY5
  • Community annotation for 2IY5 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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