5VL1 Ligase date Apr 24, 2017
title Crystal Structure Of Lysyl-Trna Synthetase From Mycobacteriu Complexed With L-Lysine
authors Seattle Structural Genomics Center For Infectious Disease (S
compound source
Molecule: Lysine--Trna Ligase
Chain: A, B, C, D
Fragment: Myula.00612.A.B1
Synonym: Lysyl-Trna Synthetase,Lysrs
Ec: 6.1.1.6
Engineered: Yes
 Organism_scientific: Mycobacterium Ulcerans (Strain Agy99)
Organism_taxid: 362242
Strain: Agy99
Gene: Lyss, Mul_4181
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Myula.00612.A.B1
symmetry Space Group: P 1
R_factor 0.177 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.040 96.690 105.560 90.38 104.84 117.15
method X-Ray Diffractionresolution 2.70 Å
ligand LYS, PEG, PGE enzyme Ligase E.C.6.1.1.6 BRENDA
Gene MUL
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (637 Kb) [Save to disk]
  • Biological Unit Coordinates (5vl1.pdb1.gz) 160 Kb
  • Biological Unit Coordinates (5vl1.pdb2.gz) 160 Kb
  • Biological Unit Coordinates (5vl1.pdb3.gz) 161 Kb
  • Biological Unit Coordinates (5vl1.pdb4.gz) 159 Kb
  • Biological Unit Coordinates (5vl1.pdb5.gz) 316 Kb
  • Biological Unit Coordinates (5vl1.pdb6.gz) 316 Kb
  • LPC: Ligand-Protein Contacts for 5VL1
  • CSU: Contacts of Structural Units for 5VL1
  • Structure Factors (1936 Kb)
  • Retrieve 5VL1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VL1 from S2C, [Save to disk]
  • Re-refined 5vl1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5VL1 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 5VL1
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vl1] [5vl1_D] [5vl1_A] [5vl1_C] [5vl1_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VL1
  • Community annotation for 5VL1 at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science