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(-) Description

Title :  HUMAN TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-MG2+ COMPLEX
 
Authors :  M. J. Schellenberg, R. S. Williams
Date :  07 Mar 16  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
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 138-392
    Gene: TDP2, EAP2, TTRAP, AD-022
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HTDP2,5'-TYROSYL-DNA PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,ETS1-ASSOCIATED PROTEIN 2,ETS1-ASSOCIATED PROTEIN II,EAPII,TRAF AND TNF RECEPTOR-ASSOCIATED PROTEIN,TYROSYL-RNA PHOSPHODIESTERASE,VPG UNLINKASE
 
Molecule 2 - DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
    Chains: D, C
    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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:127 , LYS A:242 , ARG A:346binding site for residue SO4 A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5INO)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.......eehhhhh.........ee.............ee..eeeeee......eeeeeeeee...............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ino A 108 QENGSMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRCGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEGHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDII 361
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      |328       338       348       358   
                                                                                                                                                                                                                                                  324|                                   
                                                                                                                                                                                                                                                   326                                   


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.......eehhhhh.........ee.............ee..eeeeee......eeeeeeee...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ino B 111 GSMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRCGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAEGHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDI 360
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  ||   332       342       352        
                                                                                                                                                                                                                                              323|                                  
                                                                                                                                                                                                                                               326                                  


Chain C from PDB  Type:DNA  Length:9
                                         
                 5ino C   1 CCGAATTCG   9


Chain D from PDB  Type:DNA  Length:9
                                         
                 5ino D   1 CCGAATTCG   9
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 5INO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP2_HUMAN | O95551: 5j3p 5j3s

(-) Related Entries Specified in the PDB File

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5inq 4GZ1 HAS THE MOUSE HOMOLOG OF TDP2 BOUND TO THE SAME DNA