1MB2 Ligase date Aug 02, 2002
title Crystal Structure Of Tryptophanyl-Trna Synthetase Complexed Tryptophan In An Open Conformation
authors P.Retailleau, X.Huang, Y.Yin, M.Hu, V.Weinreb, P.Vachette, C.Vonrh G.Bricogne, P.Roversi, V.Ilyin, C.W.Carter Jr.
compound source
Molecule: Tryptophan-Trna Ligase
Chain: A, B, C, D, E, F
Synonym: Tryptophanyl-Trna Synthetase
Ec: 6.1.1.2
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.220 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
228.730 92.240 157.590 90.00 132.71 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand TRP enzyme Ligase E.C.6.1.1.2 BRENDA
related structures by homologous chain: 1D2R, 1M83
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceInterconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations., Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW Jr, J Mol Biol 2003 Jan 3;325(1):39-63. PMID:12473451
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (310 Kb) [Save to disk]
  • Biological Unit Coordinates (1mb2.pdb1.gz) 104 Kb
  • Biological Unit Coordinates (1mb2.pdb2.gz) 103 Kb
  • Biological Unit Coordinates (1mb2.pdb3.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 1MB2
  • CSU: Contacts of Structural Units for 1MB2
  • Likely Quarternary Molecular Structure file(s) for 1MB2
  • Structure Factors (536 Kb)
  • Retrieve 1MB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MB2 from S2C, [Save to disk]
  • Re-refined 1mb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1MB2 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 1MB2
  • 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 1MB2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mb2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1mb2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1s1mb2, region B:1-266 [Jmol] [rasmolscript] [script source]
        - Domain d1m1mb2, region B:186-333 [Jmol] [rasmolscript] [script source]
        - Domain d1v1mb2, region B:205-342 [Jmol] [rasmolscript] [script source]
        - Domain d1n1mb2, region B:509-766 [Jmol] [rasmolscript] [script source]
        - Domain d1w1mb2, region B:6-273 [Jmol] [rasmolscript] [script source]
        - Domain d1mb2c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1mb2d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1mb2e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1mb2f_, region F [Jmol] [rasmolscript] [script source]
  • 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: [1mb2_C] [1mb2_A] [1mb2_D] [1mb2_B] [1mb2] [1mb2_F] [1mb2_E]
  • SWISS-PROT database: [P00953]
  • Domain organization of [SYW_BACST] by SWISSPFAM
  • Other resources with information on 1MB2
  • Community annotation for 1MB2 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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