2WFD Ligase date Apr 03, 2009
title Structure Of The Human Cytosolic Leucyl-Trna Synthetase Editing Domain
authors E.Seiradake, W.Mao, V.Hernandez, S.J.Baker, J.J.Plattner, M.R.K.Alley, S.Cusack
compound source
Molecule: Leucyl-Trna Synthetase, Cytoplasmic
Chain: A, B
Fragment: Editing Or Cp1 Domain, Residues 260-509
Synonym: Leucine--Trna Ligase, Leurs
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pproex Htb
symmetry Space Group: P 65
R_factor 0.202 R_Free 0.240
length a length b length c angle alpha angle beta angle gamma
94.540 94.540 148.820 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.25 Å
ligand MSE enzyme Ligase E.C. BRENDA
A, B

Primary referenceCrystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles., Seiradake E, Mao W, Hernandez V, Baker SJ, Plattner JJ, Alley MR, Cusack S, J Mol Biol. 2009 May 6. PMID:19426743
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (2wfd.pdb1.gz) 166 Kb
  • LPC: Ligand-Protein Contacts for 2WFD
  • CSU: Contacts of Structural Units for 2WFD
  • Likely Quarternary Molecular Structure file(s) for 2WFD
  • Structure Factors (95 Kb)
  • Retrieve 2WFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WFD from S2C, [Save to disk]
  • Re-refined 2wfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2WFD 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 2WFD
  • 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 2WFD, from MSDmotif at EBI
  • Fold representative 2wfd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2wfd_A] [2wfd] [2wfd_B]
  • SWISS-PROT database: [Q9P2J5]
  • Domain organization of [SYLC_HUMAN] by SWISSPFAM
  • Other resources with information on 2WFD
  • Community annotation for 2WFD 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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