5T40 Hydrolase date Aug 27, 2016
title A Novel Domain In Human Exog Converts Apoptotic Endonuclease Repair Enzyme
authors M.R.Szymanski, W.Y.Yin
compound source
Molecule: Nuclease Exog, Mitochondrial
Chain: A, B
Fragment: Unp Residues 59-368
Synonym: Endonuclease G-Like 1,Endo G-Like 1
Ec: 3.1.30.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exog, Endogl1, Endogl2, Engl
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.162 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.368 83.732 74.999 90.00 113.54 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand MG, SO4 enzyme Hydrolase E.C.3.1.30 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease., Szymanski MR, Yu W, Gmyrek AM, White MA, Molineux IJ, Lee JC, Yin YW, Nat Commun. 2017 May 3;8:14959. doi: 10.1038/ncomms14959. PMID:28466855
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (304 Kb) [Save to disk]
  • Biological Unit Coordinates (5t40.pdb1.gz) 297 Kb
  • LPC: Ligand-Protein Contacts for 5T40
  • CSU: Contacts of Structural Units for 5T40
  • Structure Factors (1455 Kb)
  • Retrieve 5T40 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5T40 from S2C, [Save to disk]
  • Re-refined 5t40 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5T40 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 5T40
  • 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: [5t40_A] [5t40_B] [5t40]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5T40
  • Community annotation for 5T40 at PDBWiki (http://pdbwiki.org)

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