1Q11 Ligase date Jul 18, 2003
title Crystal Structure Of An Active Fragment Of Human Tyrosyl-Trn Synthetase With Tyrosinol
authors X.L.Yang, P.Schimmel, L.Ribas De Pouplana
compound source
Molecule: Tyrosyl-Trna Synthetase
Chain: A
Fragment: Mini Tyrrs
Synonym: Tyrosyl--Trna Ligase, Tyrrs
Ec: 6.1.1.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet20b
symmetry Space Group: P 21 21 2
R_factor 0.197 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.825 162.989 35.267 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand GOL, K, PO4, TYE enzyme Ligase E.C.6.1.1.1 BRENDA
related structures by homologous chain: 1N3L
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structures that suggest late development of genetic code components for differentiating aromatic side chains., Yang XL, Otero FJ, Skene RJ, McRee DE, Schimmel P, de Pouplana LR, Proc Natl Acad Sci U S A 2003 Dec 23;100(26):15376-80. Epub 2003 Dec 11. PMID:14671330
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (1q11.pdb1.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 1Q11
  • CSU: Contacts of Structural Units for 1Q11
  • Likely Quarternary Molecular Structure file(s) for 1Q11
  • Structure Factors (783 Kb)
  • Retrieve 1Q11 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q11 from S2C, [Save to disk]
  • Re-refined 1q11 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q11 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 1Q11
  • 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 1Q11, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q11a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1q11 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: [1q11_A] [1q11]
  • SWISS-PROT database: [P54577]
  • Domain organization of [SYYC_HUMAN] by SWISSPFAM
  • Other resources with information on 1Q11
  • Community annotation for 1Q11 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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