5INK	Hydrolase Dna	date	Mar 07, 2016
title	Mouse Tdp2 Reaction Product (5'-Phosphorylated Dna)-Abasict Complex
authors	M.J.Schellenberg, R.S.Williams
compound		source
Molecule: Tyrosyl-Dna Phosphodiesterase 2 Chain: A, B Fragment: Unp Residues 118-370 Synonym: Tyr-Dna Phosphodiesterase 2,5'-Tyrosyl-Dna Phosphodiesterase,5'-Tyr-Dna Phosphodiesterase,Traf And Tnf Associated Protein; Ec: 3.1.4.- Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Gene: Tdp2, Ttrap Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pmcsg9
Molecule: Dna (5'-D(P(3dr)Pcpgpapaptptpcpg)-3') Chain: C, D Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_taxid: 9606
symmetry	Space Group: P 21 21 21	R_factor 0.165 R_Free 0.201
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.615 67.662 166.745 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.15 Å
ligand	3DR, EPE, GOL, MG, PEG	enzyme	Hydrolase E.C.3.1.4 BRENDA
Primary reference	Reversal 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] (194 Kb) [Save to disk] Biological Unit Coordinates (5ink.pdb1.gz) 189 Kb LPC: Ligand-Protein Contacts for 5INK CSU: Contacts of Structural Units for 5INK Structure Factors (390 Kb) Retrieve 5INK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5INK from S2C, [Save to disk] Re-refined 5ink structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5INK 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 5INK

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5ink_C] [5ink] [5ink_A] [5ink_B] [5ink_D] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5INK

Community annotation for 5INK at PDBWiki (http://pdbwiki.org)

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