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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 :  1.80
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 BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2 PLYSS
    Fragment: UNP RESIDUES 118-370
    Gene: TDP2, TTRAP
    Mutation: YES
    Organism Common: HOUSE 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

 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, 29)

Asymmetric Unit (5, 29)
No.NameCountTypeFull Name
16FQ2Ligand/Ion2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2ACT6Ligand/IonACETATE ION
3EDO15Ligand/Ion1,2-ETHANEDIOL
4GOL4Ligand/IonGLYCEROL
5MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
16FQ1Ligand/Ion2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2ACT1Ligand/IonACETATE ION
3EDO11Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
16FQ1Ligand/Ion2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2ACT5Ligand/IonACETATE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:240 , ARG A:241 , ARG A:276 , ILE A:317 , CYS A:321 , LEU A:323 , HOH A:534 , HOH A:625 , HOH A:648 , ILE B:317 , PRO B:318 , 6FQ B:401binding site for residue 6FQ A 401
02AC2SOFTWAREASP A:132 , GLU A:162 , HOH A:501 , HOH A:502 , HOH A:510 , HOH A:535 , HOH A:715 , ARG B:316binding site for residue MG A 402
03AC3SOFTWARETRP A:307 , ASP A:358 , HIS A:359 , EDO A:409 , HOH A:502 , HOH A:535 , HOH A:563 , HOH A:679 , PRO B:318 , HOH B:572binding site for residue GOL A 403
04AC4SOFTWAREGLY A:256 , GLN A:259 , PRO A:287 , HOH A:657binding site for residue GOL A 404
05AC5SOFTWAREVAL A:199 , LYS A:200 , PHE A:201 , HOH A:569 , HOH A:583binding site for residue EDO A 405
06AC6SOFTWARELYS A:301 , HIS A:302 , GLN A:304 , TYR A:305 , ASP A:308 , LEU A:344 , TRP A:360 , HOH A:550binding site for residue EDO A 406
07AC7SOFTWAREASN A:184 , GLU A:186 , TYR A:188 , PHE A:189 , MET A:214 , MET A:215 , HOH A:522 , HOH A:605 , HOH A:699binding site for residue EDO A 407
08AC8SOFTWAREASP A:156 , ARG A:198 , EDO A:410 , EDO A:411 , HOH A:514 , HOH A:562binding site for residue EDO A 408
09AC9SOFTWAREASN A:130 , GLU A:162 , HIS A:236 , SER A:239 , ASP A:272 , ASN A:274 , HIS A:359 , GOL A:403 , HOH A:579binding site for residue EDO A 409
10AD1SOFTWARETHR A:123 , ASP A:156 , GLY A:226 , EDO A:408 , HOH A:612binding site for residue EDO A 410
11AD2SOFTWAREEDO A:408 , HOH A:606 , HOH A:669binding site for residue EDO A 411
12AD3SOFTWAREHOH A:515 , HOH A:539 , HOH A:551binding site for residue EDO A 412
13AD4SOFTWAREARG A:241 , SER A:244 , ASP A:277 , GLU A:279binding site for residue EDO A 413
14AD5SOFTWAREHIS A:302 , SER A:341 , LEU A:342 , ASP A:343 , HOH A:548 , HOH A:559binding site for residue EDO A 414
15AD6SOFTWAREASN A:289 , PHE A:291 , ALA A:332 , GLU A:334binding site for residue EDO A 415
16AD7SOFTWARELEU A:152 , HOH A:529binding site for residue ACT A 416
17AD8SOFTWAREILE A:317 , PRO A:318 , ALA A:319 , 6FQ A:401 , THR B:240 , ARG B:241 , ARG B:276 , ARG B:278 , ILE B:317 , CYS B:321 , LEU B:323 , HOH B:610 , HOH B:624binding site for residue 6FQ B 401
18AD9SOFTWAREASP B:132 , GLU B:162 , HOH B:508 , HOH B:531 , HOH B:669binding site for residue MG B 402
19AE1SOFTWAREASN B:211 , ARG B:249 , GOL B:404 , HOH B:517 , HOH B:539binding site for residue GOL B 403
20AE2SOFTWAREPHE B:209 , PRO B:210 , ASN B:211 , GLU B:246 , ARG B:249 , THR B:253 , GOL B:403 , HOH B:540binding site for residue GOL B 404
21AE3SOFTWARELYS B:301 , HIS B:302 , GLN B:304 , TYR B:305 , ASP B:308 , LEU B:344 , TRP B:360 , HOH B:695binding site for residue EDO B 405
22AE4SOFTWARECYS B:149 , TYR B:153 , GLY B:346 , LEU B:347 , HOH B:576binding site for residue EDO B 406
23AE5SOFTWARELYS B:257 , GLU B:260 , HOH B:646binding site for residue EDO B 407
24AE6SOFTWAREASP B:277 , TRP B:294 , GLN B:304 , TYR B:305 , ARG B:324 , HOH B:536 , HOH B:567binding site for residue EDO B 408
25AE7SOFTWAREGLY B:197 , VAL B:199 , HOH B:522 , HOH B:574binding site for residue ACT B 409
26AE8SOFTWAREILE B:180 , ILE B:181 , THR B:182 , GLU B:185 , HOH B:501 , HOH B:598binding site for residue ACT B 410
27AE9SOFTWAREGLY B:197 , HOH B:603 , HOH B:687binding site for residue ACT B 411
28AF1SOFTWARETRP B:307 , ASP B:358 , HIS B:359 , HOH B:504binding site for residue ACT B 412
29AF2SOFTWARETYR B:170binding site for residue ACT B 413

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:137 -B:137
2A:220 -A:231

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:335 -His B:336

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3Z)

(-) 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: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.....hhhhhhh......eehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3z A 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         


Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhh.....eeehhhhh..hhhhh..ee.............ee..eeeeee...eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3z B 121 SSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTRGHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDREVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAACKLRFDRIFFRAGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 ||    342       352       362        
                                                                                                                                                                                                                                             332|                                   
                                                                                                                                                                                                                                              335
   Legend:   → Mismatch (orange background)
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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 5J3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3Z)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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        TYDP2_MOUSE | Q9JJX7: 4gyz 4gz0 4gz1 4gz2 4puq 5ht2 5ink 5inl 5inm 5inn 5inp 5inq 5j42

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