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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN TYROSYL DNA PHOSPHODIESTERASE 2
 
Authors :  P. Hornyak, L. H. Pearl, K. W. Caldecott, A. W. Oliver
Date :  31 Mar 16  (Deposition) - 04 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tyrosyl, Dna Phosphodiesterase 2, Catalytic Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Hornyak, T. Askwith, S. Walker, E. Komulainen, M. Paradowski, L. E. Pennicott, E. J. Bartlett, N. C. Brissett, A. Raoof, M. Watson, A. M. Jordan, D. J. Ogilvie, S. E. Ward, J. R. Atack, L. H. Pearl, K. W. Caldecott, A. W. Oliver
Mode Of Action Of Dna-Competitive Small Molecule Inhibitors Of Tyrosyl Dna Phosphodiesterase 2.
Biochem. J. V. 473 1869 2016
PubMed-ID: 27099339  |  Reference-DOI: 10.1042/BCJ20160180

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 2
    Chains: A, B
    EC Number: 3.1.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B832(DE3)
    Expression System Taxid: 562
    Gene: TDP2, EAP2, TTRAP, AD-022
    Mutation: YES
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:122 , GLU A:152 , HOH A:501binding site for residue MG A 401
2AC2SOFTWARELEU B:142binding site for residue GOL B 401
3AC3SOFTWAREASP B:122 , GLU B:152 , ASP B:350 , HOH B:501binding site for residue MG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3P)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3P)

(-) Sequences/Alignments

Asymmetric 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee........hhhhhhhhhhhhhhhhhh.....eeeeeee.....hhhhhh.......eehhhhh.........ee.............ee..eeeeee...eeeeeeeee...............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j3p A 112 HMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRSGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDII 361
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321 ||    335       345       355      
                                                                                                                                                                                                                                             323|                                 
                                                                                                                                                                                                                                              328                                 


Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh.....eeeeeee...............hhhhhh.........ee.......ee..eeee..eeeeeeeee...............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3p B 112 HMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLREVTRSLPNNIVDVWEFLGKPKHCQYTWDTQMNSNCKLRFDRIFFHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDII 361
                                   121       131       141       151       161       171       181       191       201       211       221     ||235       245       255       265||   ||279       289       299    || 315    || 332       342       352         
                                                                                                                                             227|                               266| 273|                         304|      320|                                 
                                                                                                                                              232                                269  276                          311       328
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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 5J3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3P)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        TYDP2_HUMAN | O95551: 5ino 5j3s

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