3UBY Hydrolase Dna date Oct 25, 2011
title Crystal Structure Of Human Alklyadenine Dna Glycosylase In A Higher-Affinity Complex With Dna
authors J.W.Setser, G.M.Lingaraju, C.A.Davis, L.D.Samson, C.L.Drennan
compound source
Molecule: Dna-3-Methyladenine Glycosylase
Chain: A, B
Fragment: Delta79aag
Synonym: 3-Alkyladenine Dna Glycosylase, 3-Methyladenine Dn Glycosidase, Adpg, N-Methylpurine-Dna Glycosylase;
Ec: 3.2.2.21
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mpg, Aag, Anpg, Mid1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Gpapcpaptpgp(Edc)Ptptpgpcpc
Chain: C, D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43
R_factor 0.219 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.168 41.168 262.546 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EDC enzyme Hydrolase E.C.3.2.2.21 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceSearching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase., Setser JW, Lingaraju GM, Davis CA, Samson LD, Drennan CL, Biochemistry. 2011 Dec 20. PMID:22148158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (145 Kb) [Save to disk]
  • Biological Unit Coordinates (3uby.pdb1.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 3UBY
  • CSU: Contacts of Structural Units for 3UBY
  • Structure Factors (421 Kb)
  • Retrieve 3UBY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UBY from S2C, [Save to disk]
  • Re-refined 3uby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UBY 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 3UBY
  • 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
  • 3D motif for 3UBY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3uby_B] [3uby_A] [3uby_C] [3uby_D] [3uby]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3UBY
  • Community annotation for 3UBY at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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