5INO Hydrolase Dna date Mar 07, 2016
title Human Tdp2 Reaction Product (5'-Phosphorylated Dna)-Mg2+ Com
authors M.J.Schellenberg, R.S.Williams
compound source
Molecule: Tyrosyl-Dna Phosphodiesterase 2
Chain: A, B
Fragment: Unp Residues 138-392
Synonym: Htdp2,5'-Tyrosyl-Dna Phosphodiesterase,5'-Tyr-Dna Phosphodiesterase,Ets1-Associated Protein 2,Ets1-Associated II,Eapii,Traf And Tnf Receptor-Associated Protein,Tyrosyl-R Phosphodiesterase,Vpg Unlinkase;
Ec: 3.1.4.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdp2, Eap2, Ttrap, Ad-022
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'-D(Pcpcpgpapaptptpcpg)-3')
Chain: D, C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 31
R_factor 0.214 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
69.663 69.663 120.677 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.21 Å
ligand SO4 enzyme Hydrolase E.C.3.1.4 BRENDA
Primary referenceReversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2., Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS, Nucleic Acids Res. 2016 May 5;44(8):3829-44. doi: 10.1093/nar/gkw228. Epub 2016, Apr 8. PMID:27060144
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (5ino.pdb1.gz) 193 Kb
  • LPC: Ligand-Protein Contacts for 5INO
  • CSU: Contacts of Structural Units for 5INO
  • Structure Factors (131 Kb)
  • Retrieve 5INO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5INO from S2C, [Save to disk]
  • Re-refined 5ino structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5INO 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 5INO
  • 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 5ino from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ino_C] [5ino_B] [5ino_A] [5ino] [5ino_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5INO
  • Community annotation for 5INO at PDBWiki (http://pdbwiki.org)

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