1D2R Ligase date Sep 27, 1999
title 2.9 A Crystal Structure Of Ligand-Free Tryptophanyl-Trna Syn Domain Movements Fragment The Adenine Nucleotide Binding Si
authors V.A.Ilyin, C.W.Carter Jr.
compound source
Molecule: Protein (Tryptophanyl Trna Synthetase)
Chain: A, B, C, D, E, F
Synonym: Trprs
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
symmetry Space Group: C 1 2 1
R_factor 0.237 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
226.760 91.660 156.970 90.00 132.66 90.00
method X-Ray Diffractionresolution 2.90 Å
enzyme Ligase E.C. BRENDA
related structures by homologous chain: 1MAW, 1MB2
F, A, D, C, E, B

Primary reference2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site., Ilyin VA, Temple B, Hu M, Li G, Yin Y, Vachette P, Carter CW Jr, Protein Sci 2000 Feb;9(2):218-31. PMID:10716174
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (314 Kb) [Save to disk]
  • Biological Unit Coordinates (1d2r.pdb1.gz) 106 Kb
  • Biological Unit Coordinates (1d2r.pdb2.gz) 105 Kb
  • Biological Unit Coordinates (1d2r.pdb3.gz) 106 Kb
  • CSU: Contacts of Structural Units for 1D2R
  • Likely Quarternary Molecular Structure file(s) for 1D2R
  • Structure Factors (323 Kb)
  • Retrieve 1D2R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D2R from S2C, [Save to disk]
  • Re-refined 1d2r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D2R 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 1D2R
  • 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 1D2R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d2ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1d2rb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1d2rc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1d2rd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1d2re_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1d2rf_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1d2r 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: [1d2r_E] [1d2r_A] [1d2r_D] [1d2r] [1d2r_C] [1d2r_F] [1d2r_B]
  • SWISS-PROT database: [P00953]
  • Domain organization of [SYW_BACST] by SWISSPFAM
  • Other resources with information on 1D2R
  • Community annotation for 1D2R 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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