5EKD Ligase Antibiotic date Nov 03, 2015
title Human Mitochondrial Tryptophanyl-Trna Synthetase Bound By In And Mnatp.
authors T.L.Williams, C.W.Carter Jr.
compound source
Molecule: Tryptophan--Trna Ligase, Mitochondrial
Chain: A, B
Synonym: (Mt)Trprs,Tryptophanyl-Trna Synthetase,Trprs
Ec: 6.1.1.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Wars2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet28
symmetry Space Group: C 1 2 1
R_factor 0.170 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.289 78.087 153.996 90.00 96.55 90.00
method X-Ray Diffractionresolution 1.82 Å
ligand 5BX, ATP, GOL, MN enzyme Ligase E.C.6.1.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (225 Kb) [Save to disk]
  • Biological Unit Coordinates (5ekd.pdb1.gz) 218 Kb
  • LPC: Ligand-Protein Contacts for 5EKD
  • CSU: Contacts of Structural Units for 5EKD
  • Structure Factors (3524 Kb)
  • Retrieve 5EKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EKD from S2C, [Save to disk]
  • Re-refined 5ekd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EKD 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 5EKD
  • 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
  • Fold representative 5ekd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ekd] [5ekd_A] [5ekd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EKD
  • Community annotation for 5EKD at PDBWiki (http://pdbwiki.org)

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