1EIY Ligase Rna date Feb 29, 2000
title The Crystal Structure Of Phenylalanyl-Trna Synthetase From T Thermophilus Complexed With Cognate Trnaphe
authors Y.Goldgur, L.Mosyak, L.Reshetnikova, V.Ankilova, M.Safro
compound source
Molecule: Trna(Phe)
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Phenylalanyl-Trna Synthetase
Chain: A
Fragment: Alpha Chain
Synonym: Phenylalanine--Trna Ligase Alpha Chain, Phers
Ec: 6.1.1.20

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8

Molecule: Phenylalanyl-Trna Synthetase
Chain: B
Fragment: Beta Chain
Synonym: Phenylalanine--Trna Ligase Beta Chain, Phers
Ec: 6.1.1.20

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
symmetry Space Group: P 32 2 1
R_factor 0.221 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
175.000 175.000 140.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand
enzyme Ligase E.C.6.1.1.20 BRENDA
note 1EIY (Molecule of the Month:pdb16)
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceThe crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe., Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M, Structure 1997 Jan 15;5(1):59-68. PMID:9016717
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (212 Kb) [Save to disk]
  • Biological Unit Coordinates (1eiy.pdb1.gz) 411 Kb
  • CSU: Contacts of Structural Units for 1EIY
  • Likely Quarternary Molecular Structure file(s) for 1EIY
  • Structure Factors (187 Kb)
  • Retrieve 1EIY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EIY from S2C, [Save to disk]
  • Re-refined 1eiy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1EIY 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 1EIY
  • 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 1EIY, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1eiya1, region A:6-84 [Jmol] [rasmolscript] [script source]
        - Domain d1eiya2, region A:85-350 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb1, region B:1-38,B:152-190 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb6, region B:191-399 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb3, region B:39-151 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb2, region B:400-474 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb5, region B:475-681 [Jmol] [rasmolscript] [script source]
        - Domain d1eiyb4, region B:682-785 [Jmol] [rasmolscript] [script source]
  • Fold representative 1eiy from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1eiy_B] [1eiy_A] [1eiy] [1eiy_C]
  • SWISS-PROT database: [Q5SGX2] [Q5SGX1]
  • Domain organization of [SYFA_THET8] [SYFB_THET8] by SWISSPFAM
  • Domains found in 1EIY: [B3_4] [B5] [FDX-ACB ] by SMART
  • Other resources with information on 1EIY
  • Community annotation for 1EIY 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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