3C2Y Transferase date Jan 26, 2008
title Trna-Guanine Transglycosylase (Tgt) In Complex With 6-Amino- 1,7-Dihydro-Imidazo[4,5-G]Quinazolin-8-One
authors T.Ritschel, A.Heine, G.Klebe
compound source
Molecule: Queuine Trna-Ribosyltransferase
Chain: A
Synonym: Trna-Guanine Transglycosylase, Guanine Insertion E Tgt;
Ec: 2.4.2.29
Engineered: Yes
 Organism_scientific: Zymomonas Mobilis
Organism_taxid: 542
Gene: Tgt
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet9d
symmetry Space Group: C 1 2 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.300 64.800 70.300 90.00 96.00 90.00
method X-Ray Diffractionresolution 1.78 Å
ligand GOL, S60, ZN BindingDB enzyme Transferase E.C.2.4.2.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT., Ritschel T, Hoertner S, Heine A, Diederich F, Klebe G, Chembiochem. 2009 Mar 2;10(4):716-27. PMID:19199329
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3c2y.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 3C2Y
  • CSU: Contacts of Structural Units for 3C2Y
  • Likely Quarternary Molecular Structure file(s) for 3C2Y
  • Structure Factors (289 Kb)
  • Retrieve 3C2Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C2Y from S2C, [Save to disk]
  • Re-refined 3c2y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3C2Y 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 3C2Y
  • 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 3C2Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c2y] [3c2y_A]
  • SWISS-PROT database: [P28720]
  • Domain organization of [TGT_ZYMMO] by SWISSPFAM
    • Other resources with information on 3C2Y
  • Community annotation for 3C2Y 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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