4Z7Z Hydrolase Dna date Apr 08, 2015
title Structure Of The Enzyme-Product Complex Resulting From Tdg A Gt Mismatch In The Presence Of Excess Base
authors E.Pozharski, S.S.Malik, A.C.Drohat
compound source
Molecule: Gt Mismatch-Specific Thymine Dna Glycosylase
Chain: A
Fragment: Unp Residues 111-308
Synonym: Thymine-Dna Glycosylase,Htdg
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: 562

Molecule: Dna (28-Mer)
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (28-Mer)
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.193 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.729 53.460 82.033 90.00 95.54 90.00
method X-Ray Diffractionresolution 1.83 Å
ligand ACY, EDO, ORP enzyme Hydrolase E.C.3.2.2.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA., Malik SS, Coey CT, Varney KM, Pozharski E, Drohat AC, Nucleic Acids Res. 2015 Sep 10. pii: gkv890. PMID:26358812
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (128 Kb) [Save to disk]
  • Biological Unit Coordinates (4z7z.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 4Z7Z
  • CSU: Contacts of Structural Units for 4Z7Z
  • Structure Factors (833 Kb)
  • Retrieve 4Z7Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Z7Z from S2C, [Save to disk]
  • Re-refined 4z7z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Z7Z 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 4Z7Z
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 4z7z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4z7z] [4z7z_A] [4z7z_D] [4z7z_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Z7Z: [UDG] [UreE_C ] by SMART
  • Other resources with information on 4Z7Z
  • Community annotation for 4Z7Z at PDBWiki (http://pdbwiki.org)

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