1WYW Hydrolase date Feb 17, 2005
title Crystal Structure Of Sumo1-Conjugated Thymine Dna Glycosylase
authors D.Baba, N.Maita, J.G.Jee, Y.Uchimura, H.Saitoh, K.Sugasawa, F.Hanaoka, 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 Smt3c
Chain: B
Synonym: Ubiquitin-Homology Domain Protein Pic1, Ubiquitin- Like Protein Ubl1, Ubiquitin-Related Protein Sumo-1, Gap Modifying Protein 1, Gmp1, Sentrin, Oksw-Cl.43;
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-E1e2s1
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.212 70.420 106.434 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CL, MG, NA enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 2BF8
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceCrystal structure of thymine DNA glycosylase conjugated to SUMO-1., Baba D, Maita N, Jee JG, Uchimura Y, Saitoh H, Sugasawa K, Hanaoka F, Tochio H, Hiroaki H, Shirakawa M, Nature. 2005 Jun 16;435(7044):979-82. PMID:15959518
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (1wyw.pdb1.gz) 52 Kb
  • LPC: Ligand-Protein Contacts for 1WYW
  • CSU: Contacts of Structural Units for 1WYW
  • Likely Quarternary Molecular Structure file(s) for 1WYW
  • Structure Factors (154 Kb)
  • Retrieve 1WYW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WYW from S2C, [Save to disk]
  • Re-refined 1wyw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1WYW 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 1WYW
  • 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
  • 3D motif for 1WYW, from MSDmotif at EBI
  • Fold representative 1wyw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wyw] [1wyw_B] [1wyw_A]
  • SWISS-PROT database: [P63165] [Q13569]
  • Domain organization of [SUMO1_HUMAN] [TDG_HUMAN] by SWISSPFAM
  • Domains found in 1WYW: [UBQ] [UDG] [UreE_C ] by SMART
  • Other resources with information on 1WYW
  • Community annotation for 1WYW 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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