1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Volk, D.E. Yang, X. Fennewald, S.M. King, D.J. Bassett, S.E. Venkitachalam, S. Herzog, N. Luxon, B.A. Gorenstein, D.G. 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 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 Bioorg.Chem. BOCMBM 0368 0045-2068 30 396 419 10.1016/S0045-2068(02)00510-2 12642125 Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB 2002 10.2210/pdb1k8j/pdb pdb_00001k8j 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 4249.781 FIRST STRAND OF CK14 DNA DUPLEX 1 syn polymer CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 4311.802 SECOND STRAND OF CK14 DNA DUPLEX 1 syn polymer no no (DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DC) CCAGGAGATTCCAC A polydeoxyribonucleotide no no (DG)(DT)(DG)(DG)(DA)(DA)(DT)(DC)(DT)(DC)(DC)(DT)(DG)(DG) GTGGAATCTCCTGG 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 n n 17.458 1 19 A 1 B 28 -1.057 A_DC1:DG28_B 1 -15.057 0.392 -0.019 -0.196 2.782 1 19 A 2 B 27 -0.647 A_DC2:DG27_B 2 -10.959 0.375 0.188 -0.230 -2.199 1 20 A 3 B 26 -3.296 A_DA3:DT26_B 3 -6.685 0.165 -0.139 -0.099 6.144 1 19 A 4 B 25 -0.926 A_DG4:DC25_B 4 -2.578 -0.320 0.278 -0.209 -4.831 1 19 A 5 B 24 -0.864 A_DG5:DC24_B 5 -11.270 -0.423 -0.200 -0.247 -5.359 1 20 A 6 B 23 -3.526 A_DA6:DT23_B 6 -9.673 0.272 -0.215 -0.066 -0.472 1 19 A 7 B 22 -0.511 A_DG7:DC22_B 7 -15.897 -0.405 0.121 -0.239 -6.342 1 20 A 8 B 21 -3.096 A_DA8:DT21_B 8 -9.385 0.192 0.000 -0.079 -7.378 1 20 A 9 B 20 -4.384 A_DT9:DA20_B 9 -11.127 -0.168 0.176 -0.089 -8.022 1 20 A 10 B 19 -2.260 A_DT10:DA19_B 10 -14.229 -0.169 -0.153 -0.103 -11.268 1 19 A 11 B 18 -1.552 A_DC11:DG18_B 11 -2.066 0.315 0.160 -0.188 -7.739 1 19 A 12 B 17 -0.220 A_DC12:DG17_B 12 4.468 0.353 0.063 -0.204 0.826 1 20 A 13 B 16 -3.164 A_DA13:DT16_B 13 -4.719 0.270 0.057 -0.078 7.011 1 19 A 14 B 15 -0.077 A_DC14:DG15_B 14 -4.395 0.478 0.114 -0.229 3.466 42.002 A A 1 2 5.095 B B 28 27 3.572 3.643 -0.258 -1.235 AA_DC1DC2:DG27DG28_BB 1 -3.755 5.251 41.689 -2.132 -0.061 2.769 30.115 A A 2 3 18.830 B B 27 26 3.229 9.618 -0.744 -0.865 AA_DC2DA3:DT26DG27_BB 2 1.075 -2.105 28.552 -3.517 1.638 2.963 33.231 A A 3 4 0.286 B B 26 25 3.023 0.163 0.291 -0.649 AA_DA3DG4:DC25DT26_BB 3 -4.119 7.220 32.982 -1.160 -1.143 3.409 36.701 A A 4 5 7.402 B B 25 24 3.528 4.634 0.453 -0.995 AA_DG4DG5:DC24DC25_BB 4 5.237 -8.365 36.051 -2.259 0.047 3.250 40.565 A A 5 6 4.002 B B 24 23 3.248 2.772 -0.883 -0.341 AA_DG5DA6:DT23DC24_BB 5 -1.591 2.296 40.444 -0.799 1.097 3.004 30.063 A A 6 7 6.210 B B 23 22 3.163 3.208 0.554 -0.562 AA_DA6DG7:DC22DT23_BB 6 -3.480 6.736 29.697 -1.708 -1.745 3.303 37.582 A A 7 8 2.045 B B 22 21 3.326 1.317 -0.773 -0.898 AA_DG7DA8:DT21DC22_BB 7 -0.467 0.725 37.557 -1.567 1.138 3.296 31.396 A A 8 9 -0.662 B B 21 20 3.281 -0.358 -0.228 -1.009 AA_DA8DT9:DA20DT21_BB 8 -0.655 1.210 31.387 -1.797 0.297 3.166 38.334 A A 9 10 -0.383 B B 20 19 3.169 -0.251 0.104 -0.369 AA_DT9DT10:DA19DA20_BB 9 3.946 -6.020 38.137 -0.532 0.321 3.376 37.720 A A 10 11 3.000 B B 19 18 3.414 1.939 0.775 -0.347 AA_DT10DC11:DG18DA19_BB 10 -0.812 1.257 37.663 -0.797 -1.308 3.320 41.520 A A 11 12 -2.429 B B 18 17 3.302 -1.721 0.527 -0.045 AA_DC11DC12:DG17DG18_BB 11 1.820 -2.569 41.448 0.122 -0.548 3.126 31.723 A A 12 13 -2.413 B B 17 16 3.069 -1.318 -1.743 0.038 AA_DC12DA13:DT16DG17_BB 12 -1.178 2.156 31.675 0.300 2.984 3.197 36.078 A A 13 14 -3.521 B B 16 15 3.197 -2.179 0.852 -0.757 AA_DA13DC14:DG15DT16_BB 13 -1.570 2.537 35.982 -0.920 -1.594 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-04-15 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name NMR Structure of CK14, an analog with 6 phosphorodithioates NMR Structure of CK14, an analog with 2 phosphorodithioates RCSB Y RCSB 2001-10-24 REL REL This structure was determined using standard 2D homonuclear techniques. Proton resonances were assigned using COSY, TOCSY, and NOESY data. structures with the lowest energy 10 1 2D NOESY 2D NOESY 100 mM 6.7 ambient 278 K 100 mM 6.7 ambient 288 K Distance restraints were derived by MORASS 2.5 using a total relaxation matrix approach. The deposited structure represents the average of 10 final structures. molecular dynamics 1 minimized average structure 2 mM DNA DUPLEX; 12 mM Na2HPO4; 8 mM NaH2PO4; 56 mM NaCl; 50 uM NaN3 90% H2O/10% D2O 2 mM DNA DUPLEX; 12 mM Na2HPO4; 8 mM NaH2PO4; 56 mM NaCl; 50 uM NaN3 99.96% D2O Gorenstein iterative matrix relaxation MORASS 2.5 Case and Kollman refinement Amber 5 750 Varian UNITYPLUS 600 Varian UNITYPLUS C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A G 5 n 5 DG 5 A A 6 n 6 DA 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A T 9 n 9 DT 9 A T 10 n 10 DT 10 A C 11 n 11 DC 11 A C 12 n 12 DC 12 A A 13 n 13 DA 13 A C 14 n 14 DC 14 A G 15 n 1 DG 15 B T 16 n 2 DT 16 B G 17 n 3 DG 17 B G 18 n 4 DG 18 B A 19 n 5 DA 19 B A 20 n 6 DA 20 B T 21 n 7 DT 21 B C 22 n 8 DC 22 B T 23 n 9 DT 23 B C 24 n 10 DC 24 B C 25 n 11 DC 25 B T 26 n 12 DT 26 B G 27 n 13 DG 27 B G 28 n 14 DG 28 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 2.67 0.30 108.30 110.97 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 2.32 0.30 108.30 110.62 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 2.83 0.30 108.30 111.13 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DC DC DC 11 11 11 N 1 2.31 0.30 108.30 110.61 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 4.82 0.30 108.30 113.12 B B B O4' C1' N9 DG DG DG 17 17 17 N 1 3.01 0.50 117.70 120.71 B B B C5 C6 N1 DA DA DA 20 20 20 N 1 -3.72 0.60 122.90 119.18 B B B C6 C5 C7 DT DT DT 21 21 21 N 1 3.77 0.30 108.30 112.07 B B B O4' C1' N1 DC DC DC 22 22 22 N 1 4.02 0.30 108.30 112.32 B B B O4' C1' N9 DG DG DG 27 27 27 N minimized average NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1 1 N N 2 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 28 B N1 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 28 B O6 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 28 B N2 DG 14 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 27 B N1 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 27 B O6 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 27 B N2 DG 13 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 26 B N3 DT 12 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 26 B O4 DT 12 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 25 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 25 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 25 B N4 DC 11 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B DC 24 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B DC 24 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B DC 24 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 23 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 23 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 22 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 22 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 22 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 21 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 21 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 20 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 20 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 19 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 19 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 18 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 18 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 18 B N2 DG 4 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 17 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 17 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 17 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 13 A N1 DA 13 1_555 B DT 16 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 13 A N6 DA 13 1_555 B DT 16 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 14 A N3 DC 14 1_555 B DG 15 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A N4 DC 14 1_555 B DG 15 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A O2 DC 14 1_555 B DG 15 B N2 DG 1 1_555 DNA DNA DUPLEX, CK14, CK1, NF-KB, DNA 1K8J PDB 1 1K8J 1K8J PDB 2 1K8J 1 14 1K8J 1 14 1K8J A 1 1 14 15 28 1K8J 15 28 1K8J B 2 1 14