3ZGZ Ligase Rna date Dec 19, 2012
title Ternary Complex Of E. Coli Leucyl-Trna Synthetase, Trna(Leu) Moiety From Agrocin 84 (Tm84) In Aminoacylation-Like Confor
authors S.Chopra, A.Palencia, C.Virus, A.Tripathy, B.R.Temple, A.Velazque S.Cusack, J.S.Reader
compound source
Molecule: Leucine--Trna Ligase
Chain: A, D
Synonym: Leucyl-Trna Synthetase, Leurs
Ec: 6.1.1.4
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b

Molecule: Trna-Leu Uaa Isoacceptor
Chain: B, E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
symmetry Space Group: C 1 2 1
R_factor 0.187 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
158.580 68.190 226.220 90.00 105.53 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 84T, MG, ZN enzyme Ligase E.C.6.1.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D
  • aminoacyl-tRNA editing activ...


  • Primary referencePlant tumour biocontrol agent employs a tRNA-dependent mechanism to inhibit leucyl-tRNA synthetase., Chopra S, Palencia A, Virus C, Tripathy A, Temple BR, Velazquez-Campoy A, Cusack S, Reader JS, Nat Commun. 2013 Jan 29;4:1417. doi: 10.1038/ncomms2421. PMID:23361008
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (720 Kb) [Save to disk]
  • Biological Unit Coordinates (3zgz.pdb1.gz) 358 Kb
  • Biological Unit Coordinates (3zgz.pdb2.gz) 359 Kb
  • LPC: Ligand-Protein Contacts for 3ZGZ
  • CSU: Contacts of Structural Units for 3ZGZ
  • Structure Factors (658 Kb)
  • Retrieve 3ZGZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZGZ from S2C, [Save to disk]
  • Re-refined 3zgz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZGZ 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 3ZGZ
  • 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 3ZGZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zgz_B] [3zgz_E] [3zgz_A] [3zgz_D] [3zgz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3ZGZ
  • Community annotation for 3ZGZ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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