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(-) Description

Title :  CRYSTAL STRUCTURE OF M2HTDP2-CAT IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
 
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 :  1.70
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
    ChainsA, B
    EC Number3.1.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid562
    Expression System VariantPLYSS
    FragmentUNP RESIDUES 118-370
    GeneTDP2, TTRAP
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymM2HTDP2-CAT, TYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- ASSOCIATED PROTEIN

 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  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
16FV2Ligand/Ion10-(4-HYDROXYPHENYL)-2,4-DIOXO-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MN2Ligand/IonMANGANESE (II) ION
5TLA6Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
16FV1Ligand/Ion10-(4-HYDROXYPHENYL)-2,4-DIOXO-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
16FV1Ligand/Ion10-(4-HYDROXYPHENYL)-2,4-DIOXO-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5TLA4Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:240 , ARG A:241 , ARG A:276 , CYS A:321 , LEU A:323 , TLA A:402 , HOH A:528 , HOH A:539 , HOH A:541 , HOH A:582 , ILE B:317 , PRO B:318 , 6FV B:401 , TLA B:405binding site for residue 6FV A 401
02AC2SOFTWARETHR A:240 , ARG A:241 , GLY A:242 , 6FV A:401 , HOH A:521 , HOH A:534 , HOH A:716 , HOH A:720 , ALA B:319 , ALA B:320 , HOH B:591binding site for residue TLA A 402
03AC3SOFTWAREASP A:132 , LEU A:134 , GLU A:162 , ARG A:216 , HIS A:236 , SER A:239 , MN A:406 , HOH A:528 , HOH A:530 , HOH A:536 , HOH A:601 , HOH A:616 , HOH A:625 , HOH A:642 , ARG B:316binding site for residue TLA A 403
04AC4SOFTWARELYS A:252 , LEU A:255 , GLY A:256 , GLN A:259 , GLY A:285 , PRO A:287 , HOH A:501 , HOH A:502 , HOH A:503 , HOH A:666binding site for residue GOL A 404
05AC5SOFTWAREARG A:276 , ASP A:277 , LEU A:323 , ARG A:327 , HOH A:506 , HOH A:533 , HOH A:604 , HOH A:615binding site for residue EDO A 405
06AC6SOFTWAREASP A:132 , GLU A:162 , TLA A:403 , HOH A:530 , HOH A:613binding site for residue MN A 406
07AC7SOFTWAREILE A:317 , PRO A:318 , 6FV A:401 , THR B:240 , ARG B:241 , ARG B:276 , ARG B:278 , TRP B:307 , CYS B:321 , TLA B:402 , TLA B:405 , HOH B:510 , HOH B:533 , HOH B:583binding site for residue 6FV B 401
08AC8SOFTWAREPRO A:318 , ALA A:319 , ALA A:320 , HOH A:566 , THR B:240 , ARG B:241 , GLY B:242 , 6FV B:401 , HOH B:505 , HOH B:506 , HOH B:512 , HOH B:632 , HOH B:725binding site for residue TLA B 402
09AC9SOFTWAREARG A:316 , ASP B:132 , LEU B:134 , GLU B:162 , ARG B:216 , HIS B:236 , SER B:239 , MN B:408 , HOH B:510 , HOH B:547 , HOH B:559 , HOH B:594 , HOH B:606 , HOH B:647 , HOH B:659binding site for residue TLA B 403
10AD1SOFTWAREARG B:276 , ASP B:277 , TYR B:305 , LEU B:323 , HOH B:504 , HOH B:517 , HOH B:602 , HOH B:617 , HOH B:640 , HOH B:644binding site for residue TLA B 404
11AD2SOFTWAREARG A:241 , ALA A:319 , 6FV A:401 , ARG B:241 , ALA B:319 , 6FV B:401 , HOH B:501 , HOH B:512 , HOH B:632 , HOH B:639binding site for residue TLA B 405
12AD3SOFTWAREPHE B:209 , PRO B:210 , ASN B:211 , GLU B:246 , ARG B:249 , THR B:253 , HOH B:624binding site for residue GOL B 406
13AD4SOFTWARELYS B:301 , GLN B:304 , TYR B:305 , ASP B:308 , LEU B:344 , TRP B:360 , HOH B:609binding site for residue EDO B 407
14AD5SOFTWAREARG A:316 , ASP B:132 , GLU B:162 , TLA B:403 , HOH B:553 , HOH B:647binding site for residue MN B 408

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:137 -B:137

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5J42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J42)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J42)

(-) Exons   (0, 0)

(no "Exon" information available for 5J42)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhh......eeehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j42 A 123 TISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTRGHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDREVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAACKLRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        

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....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh......eehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j42 B 122 STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTRGHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDREVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAACKLRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 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         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5J42)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J42)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J42)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        TYDP2_MOUSE | Q9JJX74gyz 4gz0 4gz1 4gz2 4puq 5ht2 5ink 5inl 5inm 5inn 5inp 5inq 5j3z

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