5J3P Hydrolase date Mar 31, 2016
title Crystal Structure Of The Catalytic Domain Of Human Tyrosyl D Phosphodiesterase 2
authors P.Hornyak, L.H.Pearl, K.W.Caldecott, A.W.Oliver
compound source
Molecule: Tyrosyl-Dna Phosphodiesterase 2
Chain: A, B
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
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tdp2, Eap2, Ttrap, Ad-022
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B832(De3)
symmetry Space Group: P 31 2 1
R_factor 0.256 R_Free 0.291
length a length b length c angle alpha angle beta angle gamma
92.545 92.545 119.075 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand GOL, MG enzyme Hydrolase E.C.3.1.4 BRENDA
Primary referenceMode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2., Hornyak P, Askwith T, Walker S, Komulainen E, Paradowski M, Pennicott LE, Bartlett EJ, Brissett NC, Raoof A, Watson M, Jordan AM, Ogilvie DJ, Ward SE, Atack JR, Pearl LH, Caldecott KW, Oliver AW, Biochem J. 2016 Apr 20. pii: BCJ20160180. PMID:27099339
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (5j3p.pdb1.gz) 80 Kb
  • Biological Unit Coordinates (5j3p.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5J3P
  • CSU: Contacts of Structural Units for 5J3P
  • Structure Factors (696 Kb)
  • Retrieve 5J3P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J3P from S2C, [Save to disk]
  • Re-refined 5j3p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J3P 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 5J3P
  • 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
  • Fold representative 5j3p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j3p_A] [5j3p_B] [5j3p]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5J3P
  • Community annotation for 5J3P at PDBWiki (http://pdbwiki.org)

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