5KN8 Hydrolase Dna date Jun 27, 2016
title Muty N-Terminal Domain In Complex With Undamaged Dna
authors L.Wang, S.Chakravarthy, G.L.Verdine
compound source
Molecule: Adenine Dna Glycosylase
Chain: A
Fragment: Unp Residues 1-229
Synonym: Oxog:A-Specific Adenine Glycosylase
Ec: 3.2.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Muty
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Aptpcpcptpgptpgpcpt)-3')
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422

Molecule: Dna (5'-D(Apgpcpapcpapgpgpapt)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.200 38.618 83.796 90.00 104.00 90.00
method X-Ray Diffractionresolution 1.81 Å
ligand CA, SF4 enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Basis for the Lesion-scanning Mechanism of the Bacterial MutY DNA Glycosylase., Wang L, Chakravarthy S, Verdine GL, J Biol Chem. 2017 Jan 27. pii: jbc.M116.757039. doi: 10.1074/jbc.M116.757039. PMID:28130451
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (5kn8.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 5KN8
  • CSU: Contacts of Structural Units for 5KN8
  • Structure Factors (1807 Kb)
  • Retrieve 5KN8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KN8 from S2C, [Save to disk]
  • Re-refined 5kn8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5KN8 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 5KN8
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5kn8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5kn8_D] [5kn8] [5kn8_C] [5kn8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5KN8
  • Community annotation for 5KN8 at PDBWiki (http://pdbwiki.org)

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