3UFJ Hydrolase Dna date Nov 01, 2011
title Human Thymine Dna Glycosylase Bound To Substrate Analog 2'-F Deoxyuridine
authors E.Pozharski, A.Maiti, A.C.Drohat
compound source
Molecule: Gt Mismatch-Specific Thymine Dna Glycosylase
Chain: A, B
Fragment: Core Domain (Unp Residues 111-308)
Synonym: Thymine-Dna Glycosylase
Ec: 3.2.2.29
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdg
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28

Molecule: 5'-D(Cpapgpcptpcptpgptpapcpgptpgpa Gptpgpgpa)-3';
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Cpcpapcptpgpcptpcpap(Uf2) Pgptpapcpapgpapgpcptpgpt)-3';
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 65
R_factor 0.263 R_Free 0.304
crystal
cell
length a length b length c angle alpha angle beta angle gamma
162.537 162.537 54.959 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.97 Å
ligand UF2 enzyme Hydrolase E.C.3.2.2.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA., Maiti A, Noon MS, Mackerell AD Jr, Pozharski E, Drohat AC, Proc Natl Acad Sci U S A. 2012 May 9. PMID:22573813
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (3ufj.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (3ufj.pdb2.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 3UFJ
  • CSU: Contacts of Structural Units for 3UFJ
  • Structure Factors (127 Kb)
  • Retrieve 3UFJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UFJ from S2C, [Save to disk]
  • Re-refined 3ufj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UFJ 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 3UFJ
  • 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 3UFJ, from MSDmotif at EBI
  • Fold representative 3ufj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ufj_A] [3ufj] [3ufj_F] [3ufj_B] [3ufj_D] [3ufj_E] [3ufj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3UFJ: [UDG] [UreE_C ] by SMART
  • Other resources with information on 3UFJ
  • Community annotation for 3UFJ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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