5TT5 Ligase date Nov 01, 2016
title Escherichia Coli Liga (K115m) In Complex With Nad+
authors Y.Goldgur, M.C.Unciuleac, S.H.Shuman
compound source
Molecule: Dna Ligase
Chain: A
Fragment: Residues 1-586
Synonym: Polydeoxyribonucleotide Synthase [Nad(+)]
Ec: 6.5.1.2
Engineered: Yes
Mutation: Yes
 Organism_scientific: Escherichia Coli (Strain K12)
Organism_taxid: 83333
Strain: K12
Gene: Liga, Dnal, Lig, Lop, Pdec, B2411, Jw2403
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.907 94.312 150.927 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.55 Å
ligand MG, NAD, ZN enzyme Ligase E.C.6.5.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTwo-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD+-dependent polynucleotide ligases., Unciuleac MC, Goldgur Y, Shuman S, Proc Natl Acad Sci U S A. 2017 Feb 21. pii: 201619220. doi:, 10.1073/pnas.1619220114. PMID:28223499
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (5tt5.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 5TT5
  • CSU: Contacts of Structural Units for 5TT5
  • Structure Factors (1754 Kb)
  • Retrieve 5TT5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TT5 from S2C, [Save to disk]
  • Re-refined 5tt5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5TT5 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 5TT5
  • 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: [5tt5] [5tt5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5TT5
  • Community annotation for 5TT5 at PDBWiki (http://pdbwiki.org)

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