5LPG Hydrolase date Aug 12, 2016
title Structure Of Nudt15 In Complex With 6-Thio-Gmp
authors G.Masuyer, M.Carter, D.Rehling, P.Stenmark, T.Helleday, A.S.Jemt N.C.K.Valerie, E.Homan, P.Herr, L.Bevc, B.D.G.Page, A.Hagenkort
compound source
Molecule: Probable 8-Oxo-Dgtp Diphosphatase Nudt15
Chain: A, B
Synonym: 8-Oxo-Dgtpase Nudt15,7,8-Dihydro-8-Oxoguanine-Trip Nudt15,Mutt Homolog 2,Mth2,Nucleoside Diphosphate-Linked Mo Motif 15,Nudix Motif 15;
Ec: 3.6.1.55
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nudt15, Mth2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a(+)
symmetry Space Group: P 21 21 21
R_factor 0.216 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.502 49.050 135.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand 71V, MG enzyme Hydrolase E.C.3.6.1.55 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceNUDT15 hydrolyzes 6-thio-deoxyGTP to mediate the anticancer efficacy of 6-thioguanine., Valerie NC, Hagenkort A, Page BD, Masuyer G, Rehling D, Carter M, Bevc L, Herr P, Homan E, Sheppard NG, Stenmark P, Jemth AS, Helleday T, Cancer Res. 2016 Aug 16. pii: canres.0584.2016. PMID:27530327
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (5lpg.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 5LPG
  • CSU: Contacts of Structural Units for 5LPG
  • Structure Factors (2238 Kb)
  • Retrieve 5LPG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LPG from S2C, [Save to disk]
  • Re-refined 5lpg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LPG 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 5LPG
  • 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: [5lpg_A] [5lpg] [5lpg_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LPG
  • Community annotation for 5LPG at PDBWiki (http://pdbwiki.org)

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