5J3S Hydrolase date Mar 31, 2016
title Crystal Structure Of The Catalytic Domain Of Human Tyrosyl D Phosphodiesterase 2 In Complex With A Small Molecule Inhibi
authors P.Hornyak, L.H.Pearl, K.W.Caldecott, A.W.Oliver
compound source
Molecule: Tyrosyl-Dna Phosphodiesterase 2
Chain: A
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: B834(De3)
symmetry Space Group: P 65 2 2
R_factor 0.254 R_Free 0.273
length a length b length c angle alpha angle beta angle gamma
68.516 68.516 209.505 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.40 Å
ligand 6FQ 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] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (5j3s.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 5J3S
  • CSU: Contacts of Structural Units for 5J3S
  • Structure Factors (87 Kb)
  • Retrieve 5J3S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J3S from S2C, [Save to disk]
  • Re-refined 5j3s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J3S 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 5J3S
  • 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 5j3s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j3s] [5j3s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5J3S
  • Community annotation for 5J3S at PDBWiki (http://pdbwiki.org)

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