2D07 Hydrolase date Jul 26, 2005
title Crystal Structure Of Sumo-3-Modified Thymine-Dna Glycosylase
authors D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hana H.Tochio, H.Hiroaki, M.Shirakawa
compound source
Molecule: Gt Mismatch-Specific Thymine Dna Glycosylase
Chain: A
Fragment: Central Region
Synonym: Tdg
Ec: 3.2.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t-3

Molecule: Ubiquitin-Like Protein Smt3b
Chain: B
Synonym: Sentrin-2, Ubiquitin-Related Protein Sumo-3, Hsmt3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt-E1e2s2
symmetry Space Group: C 1 2 1
R_factor 0.208 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.481 75.931 50.527 90.00 114.98 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand
enzyme Hydrolase E.C.3.2.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceCrystal structure of SUMO-3-modified thymine-DNA glycosylase., Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M, J Mol Biol. 2006 May 26;359(1):137-47. Epub 2006 Mar 31. PMID:16626738
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (2d07.pdb1.gz) 48 Kb
  • CSU: Contacts of Structural Units for 2D07
  • Likely Quarternary Molecular Structure file(s) for 2D07
  • Structure Factors (168 Kb)
  • Retrieve 2D07 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D07 from S2C, [Save to disk]
  • Re-refined 2d07 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D07 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 2D07
  • 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 2D07, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d07_B] [2d07] [2d07_A]
  • SWISS-PROT database: [P61956] [Q13569]
  • Domain organization of [SUMO2_HUMAN] [TDG_HUMAN] by SWISSPFAM
  • Domains found in 2D07: [UBQ] [UDG] [UreE_C ] by SMART
  • Other resources with information on 2D07
  • Community annotation for 2D07 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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