1R6U Ligase date Oct 16, 2003
title Crystal Structure Of An Active Fragment Of Human Tryptophany Synthetase With Cytokine Activity
authors X.L.Yang, F.J.Otero, R.J.Skene, D.E.Mcree, L.Ribas De Pouplana, P.Schimmel
compound source
Molecule: Tryptophanyl-Trna Synthetase
Chain: A, B
Synonym: Tryptophan-Trna Ligase, Trprs, Ifp53, Hwrs
Ec: 6.1.1.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Wars
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet20b+
symmetry Space Group: C 1 2 1
R_factor 0.254 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.658 96.460 97.132 90.00 129.90 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand GOL, MSE, TYM enzyme Ligase E.C.6.1.1.2 BRENDA
related structures by homologous chain: 1R6T
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceFunctional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase., Yang XL, Guo M, Kapoor M, Ewalt KL, Otero FJ, Skene RJ, McRee DE, Schimmel P, Structure. 2007 Jul;15(7):793-805. PMID:17637340
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (1r6u.pdb1.gz) 126 Kb
  • LPC: Ligand-Protein Contacts for 1R6U
  • CSU: Contacts of Structural Units for 1R6U
  • Likely Quarternary Molecular Structure file(s) for 1R6U
  • Structure Factors (1703 Kb)
  • Retrieve 1R6U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R6U from S2C, [Save to disk]
  • Re-refined 1r6u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1R6U 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 1R6U
  • 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 1R6U, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r6ua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1r6ub_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1r6u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r6u_A] [1r6u_B] [1r6u]
  • SWISS-PROT database: [P23381]
  • Domain organization of [SYWC_HUMAN] by SWISSPFAM
  • Other resources with information on 1R6U
  • Community annotation for 1R6U 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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