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(-) Description

Title :  MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MG2+ COMPLEX WITH DEOXYADENOSINE
 
Authors :  M. J. Schellenberg, C. K. Vilas, R. S. Williams
Date :  07 Mar 16  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase/Dna, Dna Repair, Endonuclease/Exonuclease/Phosphatase (Eep) Domain, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Schellenberg, L. Perera, C. N. Strom, C. A. Waters, B. Monian, C. D. Appel, C. K. Vilas, J. G. Williams, D. A. Ramsden, R. S. Williams
Reversal Of Dna Damage Induced Topoisomerase 2 Dna-Protein Crosslinks By Tdp2.
Nucleic Acids Res. V. 44 3829 2016
PubMed-ID: 27060144  |  Reference-DOI: 10.1093/NAR/GKW228

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 118-370
    Gene: TDP2, TTRAP
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- ASSOCIATED PROTEIN
 
Molecule 2 - DNA (5'-D(P*AP*CP*GP*AP*AP*TP*TP*CP*G)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MG3Ligand/IonMAGNESIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:162 , HOH A:519 , HOH A:523 , HOH A:550 , DA D:1 , HOH D:117binding site for residue MG A 401
2AC2SOFTWAREGLU B:162 , HOH B:527 , HOH B:533 , HOH B:556 , DA C:1 , HOH C:120binding site for residue MG B 401
3AC3SOFTWARECYS B:149 , LEU B:152 , TYR B:153 , VAL B:345 , GLY B:346 , LEU B:347 , GLU B:348 , HOH B:687binding site for residue EPE B 402
4AC4SOFTWAREILE B:180 , HOH B:510 , HOH B:600binding site for residue PEG B 403
5AC5SOFTWAREHOH A:535 , GLN B:340 , HOH B:585 , HOH B:704 , HOH B:754binding site for residue MG B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5INL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5INL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5INL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5INL)

(-) Exons   (0, 0)

(no "Exon" information available for 5INL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5inl A 115 SKGLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       335       345       355       365     
                                                                                                                                                                                                                                                   332|                                    
                                                                                                                                                                                                                                                    334                                    


Chain B from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhhh......eehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5inl B 122 STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361         


Chain C from PDB  Type:DNA  Length:9
                                         
                 5inl C   1 ACGAATTCG   9


Chain D from PDB  Type:DNA  Length:9
                                         
                 5inl D   1 ACGAATTCG   9
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5INL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5INL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5INL)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  TYDP2_MOUSE | Q9JJX7
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  3.1.4.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TYDP2_MOUSE | Q9JJX7: 4gyz 4gz0 4gz1 4gz2 4puq 5ht2 5ink 5inm 5inn 5inp 5inq 5j3z 5j42

(-) Related Entries Specified in the PDB File

5ink 5inm 5inn 5ino 5inp 5inq