5UUG Hydrolase Dna Antibiotic date Feb 16, 2017
title Bacillus Cereus Dna Glycosylase Alkd Bound To A Yatakemycin- Nucleobase Adduct And Dna Containing An Abasic Site (9-Mer Complex)
authors E.A.Mullins, B.F.Eichman
compound source
Molecule: Dna-7-Methylguanine Glycosylase
Chain: A
Synonym: Alkd
Engineered: Yes
 Organism_scientific: Bacillus Cereus
Organism_taxid: 1396
Atcc: 14579
Gene: Bcere0015_46090
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
Expression_system_strain: Hms174(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbg103

Molecule: Dna (5'-D(Apgpgpcpap(Orp)Papgpc)-3')
Chain: B
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Tpgpcptptptpgpcpc)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.136 R_Free 0.177
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.715 55.661 47.991 90.00 112.20 90.00
method X-Ray Diffractionresolution 1.71 Å
ligand CA, ORP, YTA enzyme
Primary referenceToxicity and repair of DNA adducts produced by the natural product yatakemycin., Mullins EA, Shi R, Eichman BF, Nat Chem Biol. 2017 Jul 24. doi: 10.1038/nchembio.2439. PMID:28759018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (5uug.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 5UUG
  • CSU: Contacts of Structural Units for 5UUG
  • Structure Factors (230 Kb)
  • Retrieve 5UUG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UUG from S2C, [Save to disk]
  • Re-refined 5uug structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5UUG 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 5UUG
  • 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: [5uug_C] [5uug_A] [5uug_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5UUG
  • Community annotation for 5UUG at PDBWiki (http://pdbwiki.org)

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