1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hwang, G.S. Jones, G.B. Goldberg, I.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C31 H31 N O7 529.580 SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) non-polymer C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking US Biochemistry BICHAW 0033 0006-2960 42 8472 8483 10.1021/bi030072d 12859193 Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA 2003 10.2210/pdb1p96/pdb pdb_00001p96 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 4265.780 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3' 1 syn polymer 3694.402 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3' 1 syn polymer 529.580 SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) 1 syn non-polymer no no (DC)(DA)(DC)(DG)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DG)(DA)(DC) CACGCAGTTCGGAC A polydeoxyribonucleotide no no (DG)(DT)(DC)(DC)(DG)(DA)(DT)(DG)(DC)(DG)(DT)(DG) GTCCGATGCGTG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n -4.621 1 19 A 1 B 12 2.782 A_DC1:DG12_B 1 18.115 0.274 0.713 -0.043 21.060 1 20 A 2 B 11 0.902 A_DA2:DT11_B 2 15.436 -0.185 1.407 -0.293 -14.788 1 19 A 3 B 10 -4.544 A_DC3:DG10_B 3 9.927 0.342 -0.016 -0.031 16.739 1 19 A 4 B 9 -4.336 A_DG4:DC9_B 4 8.890 -0.324 0.127 -0.015 -16.767 1 19 A 5 B 8 -3.863 A_DC5:DG8_B 5 24.556 0.285 0.227 -0.061 4.308 A 6 B 7 -23.263 A_DA6:DT7_B 6 36.893 0.013 0.409 0.597 -13.078 A 9 B 6 8.034 A_DT9:DA6_B 7 -3.940 0.253 -0.441 0.321 -31.018 1 19 A 10 B 5 -7.150 A_DC10:DG5_B 8 9.511 0.061 1.820 -0.481 8.820 1 19 A 11 B 4 -1.719 A_DG11:DC4_B 9 12.094 -0.319 0.769 -0.146 8.609 1 19 A 12 B 3 -5.043 A_DG12:DC3_B 10 12.246 -0.309 -0.120 -0.060 24.966 1 20 A 13 B 2 -6.049 A_DA13:DT2_B 11 6.230 -0.006 1.362 -0.194 3.070 1 19 A 14 B 1 -14.169 A_DC14:DG1_B 12 18.967 0.452 -1.074 -0.474 3.122 37.641 A A 1 2 -20.213 B B 12 11 3.327 -12.772 -0.343 0.111 AA_DC1DA2:DT11DG12_BB 1 -4.280 6.773 35.230 1.867 -0.037 5.764 37.601 A A 2 3 -6.446 B B 11 10 5.976 -4.130 -0.884 -0.322 AA_DA2DC3:DG10DT11_BB 2 6.096 -9.515 36.898 0.475 2.810 2.537 35.882 A A 3 4 -20.271 B B 10 9 2.721 -12.252 -0.060 0.092 AA_DC3DG4:DC9DG10_BB 3 -0.716 1.185 33.783 1.606 0.012 4.170 38.479 A A 4 5 19.559 B B 9 8 4.880 12.655 0.523 -1.276 AA_DG4DC5:DG8DC9_BB 4 -2.875 4.443 36.303 -4.180 -1.304 4.019 28.646 A A 5 6 -1.839 B B 8 7 4.119 -0.909 -1.867 0.199 AA_DC5DA6:DT7DG8_BB 5 1.378 -2.787 28.599 0.658 4.161 5.068 43.872 A A 9 10 3.570 B B 6 5 4.846 2.615 -1.464 0.353 AA_DT9DC10:DG5DA6_BB 6 -15.334 20.937 41.149 0.082 -0.326 2.399 32.232 A A 10 11 -8.445 B B 5 4 2.409 -4.667 0.258 -0.007 AA_DC10DG11:DC4DG5_BB 7 2.885 -5.220 31.774 0.603 -0.085 3.821 36.874 A A 11 12 12.838 B B 4 3 3.913 8.031 -0.056 0.218 AA_DG11DG12:DC3DC4_BB 8 5.490 -8.777 35.611 -0.965 0.985 3.198 37.208 A A 12 13 -4.079 B B 3 2 3.261 -2.592 0.241 -0.154 AA_DG12DA13:DT2DC3_BB 9 -5.390 8.481 36.741 0.101 -1.090 4.843 43.687 A A 13 14 -27.407 B B 2 1 5.545 -19.617 -0.397 -0.005 AA_DA13DC14:DG1DT2_BB 10 7.789 -10.882 38.470 3.192 1.804 database_2 pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_oper_list struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-08-26 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_spectrometer.model _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id The complexed structure of the bulge DNA and natural product with a similar aglycone structure. RCSB Y RCSB 2003-05-09 REL DDI SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI) This sequence was synthesized by DNA synthesizer. sample This sequence was synthesized by DNA synthesizer. sample This structure was determined using 2D homonuclear and heteronuclear techniques. all calculated structures submitted 10 10 2D NOESY 2D TOCSY DQF-COSY H-P COSY COSY-45 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA 6.5 ambient 298 K The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints. distance geometry sinulated annealing 1 all calculated structures submited have the least restraint violation and the lowst energy. 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 90% H20/10% D20; 99.96% D20 Delaglio, F. processing NMRPipe 2002.044.17.08 Goddard, T.D. and Kneller, D.G. data analysis Sparky 3.106 Brunger, A.T. et al refinement CNS 1.0 600 Bruker AVANCE 750 Varian INOVA 500 Varian INOVA DDI 1 3 DDI DDI 21 A CYT 1 n 1 DC 1 A ADE 2 n 2 DA 2 A CYT 3 n 3 DC 3 A GUA 4 n 4 DG 4 A CYT 5 n 5 DC 5 A ADE 6 n 6 DA 6 A GUA 7 n 7 DG 7 A THY 8 n 8 DT 8 A THY 9 n 9 DT 9 A CYT 10 n 10 DC 10 A GUA 11 n 11 DG 11 A GUA 12 n 12 DG 12 A ADE 13 n 13 DA 13 A CYT 14 n 14 DC 14 A GUA 1 n 1 DG 1 B THY 2 n 2 DT 2 B CYT 3 n 3 DC 3 B CYT 4 n 4 DC 4 B GUA 5 n 5 DG 5 B ADE 6 n 6 DA 6 B THY 7 n 7 DT 7 B GUA 8 n 8 DG 8 B CYT 9 n 9 DC 9 B GUA 10 n 10 DG 10 B THY 11 n 11 DT 11 B GUA 12 n 12 DG 12 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A C27 DDI 21 WRONG HAND 1 A C28 DDI 21 WRONG HAND 1 A C29 DDI 21 WRONG HAND 1 A C30 DDI 21 WRONG HAND 1 A C26 DDI 21 WRONG HAND 1 A C25 DDI 21 WRONG HAND 1 A C12 DDI 21 WRONG HAND 1 A C11 DDI 21 WRONG HAND 1 A C9 DDI 21 WRONG HAND 2 A C27 DDI 21 WRONG HAND 2 A C28 DDI 21 WRONG HAND 2 A C29 DDI 21 WRONG HAND 2 A C30 DDI 21 WRONG HAND 2 A C26 DDI 21 WRONG HAND 2 A C25 DDI 21 WRONG HAND 2 A C12 DDI 21 WRONG HAND 2 A C11 DDI 21 WRONG HAND 2 A C9 DDI 21 WRONG HAND 3 A C27 DDI 21 WRONG HAND 3 A C28 DDI 21 WRONG HAND 3 A C29 DDI 21 WRONG HAND 3 A C30 DDI 21 WRONG HAND 3 A C26 DDI 21 WRONG HAND 3 A C25 DDI 21 WRONG HAND 3 A C12 DDI 21 WRONG HAND 3 A C11 DDI 21 WRONG HAND 3 A C9 DDI 21 WRONG HAND 4 A C27 DDI 21 WRONG HAND 4 A C28 DDI 21 WRONG HAND 4 A C29 DDI 21 WRONG HAND 4 A C30 DDI 21 WRONG HAND 4 A C26 DDI 21 WRONG HAND 4 A C25 DDI 21 WRONG HAND 4 A C12 DDI 21 WRONG HAND 4 A C11 DDI 21 WRONG HAND 4 A C9 DDI 21 WRONG HAND 5 A C27 DDI 21 WRONG HAND 5 A C28 DDI 21 WRONG HAND 5 A C29 DDI 21 WRONG HAND 5 A C30 DDI 21 WRONG HAND 5 A C26 DDI 21 WRONG HAND 5 A C25 DDI 21 WRONG HAND 5 A C12 DDI 21 WRONG HAND 5 A C11 DDI 21 WRONG HAND 5 A C9 DDI 21 WRONG HAND 6 A C27 DDI 21 WRONG HAND 6 A C28 DDI 21 WRONG HAND 6 A C29 DDI 21 WRONG HAND 6 A C30 DDI 21 WRONG HAND 6 A C26 DDI 21 WRONG HAND 6 A C25 DDI 21 WRONG HAND 6 A C12 DDI 21 WRONG HAND 6 A C11 DDI 21 WRONG HAND 6 A C9 DDI 21 WRONG HAND 7 A C27 DDI 21 WRONG HAND 7 A C28 DDI 21 WRONG HAND 7 A C29 DDI 21 WRONG HAND 7 A C30 DDI 21 WRONG HAND 7 A C26 DDI 21 WRONG HAND 7 A C25 DDI 21 WRONG HAND 7 A C12 DDI 21 WRONG HAND 7 A C11 DDI 21 WRONG HAND 7 A C9 DDI 21 WRONG HAND 8 A C27 DDI 21 WRONG HAND 8 A C28 DDI 21 WRONG HAND 8 A C29 DDI 21 WRONG HAND 8 A C30 DDI 21 WRONG HAND 8 A C26 DDI 21 WRONG HAND 8 A C25 DDI 21 WRONG HAND 8 A C12 DDI 21 WRONG HAND 8 A C11 DDI 21 WRONG HAND 8 A C9 DDI 21 WRONG HAND 9 A C27 DDI 21 WRONG HAND 9 A C28 DDI 21 WRONG HAND 9 A C29 DDI 21 WRONG HAND 9 A C30 DDI 21 WRONG HAND 9 A C26 DDI 21 WRONG HAND 9 A C25 DDI 21 WRONG HAND 9 A C12 DDI 21 WRONG HAND 9 A C11 DDI 21 WRONG HAND 9 A C9 DDI 21 WRONG HAND 10 A C27 DDI 21 WRONG HAND 10 A C28 DDI 21 WRONG HAND 10 A C29 DDI 21 WRONG HAND 10 A C30 DDI 21 WRONG HAND 10 A C26 DDI 21 WRONG HAND 10 A C25 DDI 21 WRONG HAND 10 A C12 DDI 21 WRONG HAND 10 A C11 DDI 21 WRONG HAND 10 A C9 DDI 21 WRONG HAND Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA 1 N N 2 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 12 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 DG 12 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 11 B N3 DT 11 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 11 B O4 DT 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 9 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 9 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 8 B N1 DG 8 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 8 B O6 DG 8 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 8 B N2 DG 8 1_555 hydrog DA-DT PAIR A DA 6 A N6 DA 6 1_555 B DT 7 B O4 DT 7 1_555 hydrog DT-DA PAIR A DT 9 A N3 DT 9 1_555 B DA 6 B N1 DA 6 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 5 B N1 DG 5 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 5 B O6 DG 5 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 5 B N2 DG 5 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 4 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 4 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 4 B N4 DC 4 1_555 hydrog WATSON-CRICK A DG 12 A N1 DG 12 1_555 B DC 3 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 12 A N2 DG 12 1_555 B DC 3 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 12 A O6 DG 12 1_555 B DC 3 B N4 DC 3 1_555 hydrog WATSON-CRICK A DA 13 A N1 DA 13 1_555 B DT 2 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 13 A N6 DA 13 1_555 B DT 2 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 14 A N3 DC 14 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A N4 DC 14 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A O2 DC 14 1_555 B DG 1 B N2 DG 1 1_555 DNA Wedge-shaped synthetic drug-bulged DNA complex, DNA 1P96 PDB 1 1P96 1P96 PDB 2 1P96 1 14 1P96 1 14 1P96 A 1 1 14 1 12 1P96 1 12 1P96 B 2 1 12 BINDING SITE FOR RESIDUE DDI A 21 A DDI 21 Software 4 A DA 6 A DA 6 4 1_555 A DG 7 A DG 7 4 1_555 A DT 9 A DT 9 4 1_555 B DT 7 B DT 7 4 1_555