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 C9 H14 N3 O5 P S2 339.328 n CYTIDINE-5'-DITHIOPHOSPHORATE DNA linking 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 C10 H14 N5 O5 P S2 379.352 n GUANOSINE-5'-DITHIOPHOSPHORATE DNA linking C10 H15 N2 O6 P S2 354.340 n THYMIDINE-5'-DITHIOPHOSPHORATE 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/pdb1k8l/pdb pdb_00001k8l 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 4314.044 FIRST STRAND OF CK14 DNA DUPLEX DITHIOATED AT T10, C11 DITHIOATED AT T10, C11 1 syn polymer CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 4440.326 SECOND STRAND OF CK14 DNA DUPLEX DITHIOATED AT G17, C22, C24, G27 DITHIOATED AT G17, C22, C24, G27 1 syn polymer no yes (DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(T2S)(C2S)(DC)(DA)(DC) CCAGGAGATTCCAC A polydeoxyribonucleotide no yes (DG)(DT)(G2S)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(G2S)(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 3.476 1 19 A 1 B 28 0.320 A_DC1:DG28_B 1 -9.454 0.459 0.198 -0.213 0.468 1 19 A 2 B 27 -0.838 A_DC2:G2S27_B 2 -11.881 0.215 -0.004 -0.199 4.025 1 20 A 3 B 26 -4.832 A_DA3:DT26_B 3 -1.795 0.210 -0.151 -0.069 8.173 1 19 A 4 B 25 -0.672 A_DG4:DC25_B 4 -0.256 -0.381 0.097 -0.208 -1.859 1 19 A 5 B 24 -0.540 A_DG5:C2S24_B 5 -6.693 -0.492 -0.177 -0.260 -5.788 1 20 A 6 B 23 -1.340 A_DA6:DT23_B 6 -7.764 0.163 -0.159 -0.094 -2.788 1 19 A 7 B 22 -1.133 A_DG7:C2S22_B 7 -5.687 -0.365 -0.003 -0.218 -0.340 1 20 A 8 B 21 -0.130 A_DA8:DT21_B 8 -10.564 0.077 -0.208 -0.114 -5.511 1 20 A 9 B 20 -0.441 A_DT9:DA20_B 9 -10.748 -0.090 -0.110 -0.120 -0.595 1 20 A 10 B 19 -2.384 A_T2S10:DA19_B 10 -10.870 -0.102 -0.452 -0.140 -5.916 1 19 A 11 B 18 -0.676 A_C2S11:DG18_B 11 -2.151 0.398 0.139 -0.221 -3.966 1 19 A 12 B 17 -0.624 A_DC12:G2S17_B 12 0.539 0.379 0.218 -0.223 -2.233 1 20 A 13 B 16 -1.896 A_DA13:DT16_B 13 -6.055 0.193 -0.123 -0.106 -3.382 1 19 A 14 B 15 -0.164 A_DC14:DG15_B 14 0.805 0.453 0.265 -0.227 3.320 41.593 A A 1 2 -3.290 B B 28 27 3.347 -2.333 -0.089 0.129 AA_DC1DC2:G2S27DG28_BB 1 3.163 -4.461 41.415 0.433 0.468 2.564 29.499 A A 2 3 28.995 B B 27 26 3.174 14.176 -0.934 -0.445 AA_DC2DA3:DT26G2S27_BB 2 0.724 -1.481 25.926 -3.704 1.979 3.019 28.608 A A 3 4 2.561 B B 26 25 3.167 1.263 0.658 -1.430 AA_DA3DG4:DC25DT26_BB 3 -2.970 6.023 28.429 -3.165 -1.970 3.355 37.548 A A 4 5 5.761 B B 25 24 3.494 3.701 0.063 -1.282 AA_DG4DG5:C2S24DC25_BB 4 1.954 -3.041 37.323 -2.499 0.169 3.240 38.555 A A 5 6 6.843 B B 24 23 3.342 4.508 -0.531 -0.863 AA_DG5DA6:DT23C2S24_BB 5 -1.376 2.089 38.276 -1.870 0.632 2.667 24.314 A A 6 7 14.434 B B 23 22 3.169 6.018 0.647 -1.669 AA_DA6DG7:C2S22DT23_BB 6 0.053 -0.126 23.568 -5.678 -1.520 3.082 41.160 A A 7 8 15.396 B B 22 21 3.296 10.709 -0.234 -0.418 AA_DG7DA8:DT21C2S22_BB 7 0.954 -1.371 39.790 -1.745 0.435 3.292 26.102 A A 8 9 5.362 B B 21 20 3.426 2.418 -0.197 -1.334 AA_DA8DT9:DA20DT21_BB 8 -0.297 0.658 25.990 -3.633 0.354 3.072 40.685 A A 9 10 10.321 B B 20 19 3.060 7.114 0.555 0.047 AA_DT9T2S10:DA19DA20_BB 9 6.368 -9.238 39.595 -0.682 -0.127 3.130 32.160 A A 10 11 10.796 B B 19 18 3.457 5.935 0.364 -1.152 AA_T2S10C2S11:DG18DA19_BB 10 -3.707 6.742 31.409 -3.162 -1.332 3.269 39.638 A A 11 12 -0.633 B B 18 17 3.259 -0.429 -0.080 -0.941 AA_C2S11DC12:G2S17DG18_BB 11 -0.386 0.569 39.634 -1.338 0.073 3.032 31.959 A A 12 13 3.550 B B 17 16 3.165 1.951 -0.699 -0.811 AA_DC12DA13:DT16G2S17_BB 12 3.091 -5.626 31.754 -1.808 1.801 3.405 40.840 A A 13 14 -4.164 B B 16 15 3.412 -2.896 0.234 -0.812 AA_DA13DC14:DG15DT16_BB 13 -5.238 7.531 40.418 -0.830 -0.939 chem_comp database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn pdbx_struct_mod_residue repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Derived calculations 1 0 2003-04-15 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 1 4 2022-06-22 _chem_comp.type _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag _pdbx_struct_mod_residue.parent_comp_id NMR Structure of CK14, the non-thioated analog of XBY6 NMR Structure of CK14, an analog with 2 phosphorodithioates RCSB Y RCSB 2001-10-24 REL REL SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY sample SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY sample 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 DQF-COSY 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. AMBER 5 was used for MD and minimization. The deposited structure represents the average of ten final structures molecular dynamics 1 minimized average structure 1 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3 90% H2O/10% D2O 1 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56mM NaCl, 50 uM NaN3 99.96% D2O Gorenstein iterative matrix relaxation MORASS 2.5 Case,Kollman, et al structure solution Amber 5 Case,Kollman, et al 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 T2S 10 n 10 T2S 10 A C2S 11 n 11 C2S 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 G2S 17 n 3 G2S 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 C2S 22 n 8 C2S 22 B T 23 n 9 DT 23 B C2S 24 n 10 C2S 24 B C 25 n 11 DC 25 B T 26 n 12 DT 26 B G2S 27 n 13 G2S 27 B G 28 n 14 DG 28 B author_defined_assembly 2 dimeric A T2S 10 THYMIDINE-5'-DITHIOPHOSPHORATE A T2S 10 DT A C2S 11 CYTIDINE-5'-DITHIOPHOSPHORATE A C2S 11 DC B G2S 17 GUANOSINE-5'-DITHIOPHOSPHORATE B G2S 3 DG B C2S 22 CYTIDINE-5'-DITHIOPHOSPHORATE B C2S 8 DC B C2S 24 CYTIDINE-5'-DITHIOPHOSPHORATE B C2S 10 DC B G2S 27 GUANOSINE-5'-DITHIOPHOSPHORATE B G2S 13 DG 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 A HO5' OP2 DC DC 1 2 1.40 1 -6.51 1.00 110.10 103.59 A A A C1' O4' C4' DC DC DC 1 1 1 N 1 -5.21 0.80 102.40 97.19 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 -5.46 0.80 105.90 100.44 A A A O4' C1' C2' DC DC DC 1 1 1 N 1 6.83 0.30 108.30 115.13 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -4.25 0.70 121.90 117.65 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 3.97 0.30 108.30 112.27 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.22 0.50 117.70 120.92 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 2.87 0.30 108.30 111.17 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DG DG DG 5 5 5 N 1 3.84 0.30 108.30 112.14 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 4.00 0.30 108.30 112.30 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 -3.74 0.60 122.90 119.16 A A A C6 C5 C7 DT DT DT 9 9 9 N 1 2.83 0.30 108.30 111.13 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 2.32 0.30 108.30 110.62 B B B O4' C1' N9 DA DA DA 19 19 19 N 1 4.80 0.30 108.30 113.10 B B B O4' C1' N1 DT DT DT 21 21 21 N 1 -3.81 0.60 122.90 119.09 B B B C6 C5 C7 DT DT DT 21 21 21 N 1 1.86 0.30 108.30 110.16 B B B O4' C1' N1 DT DT DT 23 23 23 N 1 -4.00 0.60 122.90 118.90 B B B C6 C5 C7 DT DT DT 23 23 23 N 1 2.06 0.30 108.30 110.36 B B B O4' C1' N9 DG DG DG 28 28 28 N minimized average XBY6: An analog of CK14 containing 6 dithiophosphate groups 1 N N 2 N N covale 1.623 both A DT 9 A O3' DT 9 1_555 A T2S 10 A P T2S 10 1_555 covale 1.618 both A T2S 10 A O3' T2S 10 1_555 A C2S 11 A P C2S 11 1_555 covale 1.618 both A C2S 11 A O3' C2S 11 1_555 A DC 12 A P DC 12 1_555 covale 1.617 both B DT 16 B O3' DT 2 1_555 B G2S 17 B P G2S 3 1_555 covale 1.616 both B G2S 17 B O3' G2S 3 1_555 B DG 18 B P DG 4 1_555 covale 1.622 both B DT 21 B O3' DT 7 1_555 B C2S 22 B P C2S 8 1_555 covale 1.616 both B C2S 22 B O3' C2S 8 1_555 B DT 23 B P DT 9 1_555 covale 1.620 both B DT 23 B O3' DT 9 1_555 B C2S 24 B P C2S 10 1_555 covale 1.617 both B C2S 24 B O3' C2S 10 1_555 B DC 25 B P DC 11 1_555 covale 1.617 both B DT 26 B O3' DT 12 1_555 B G2S 27 B P G2S 13 1_555 covale 1.611 both B G2S 27 B O3' G2S 13 1_555 B DG 28 B P DG 14 1_555 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 G2S 27 B N1 G2S 13 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B G2S 27 B O6 G2S 13 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B G2S 27 B N2 G2S 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 C2S 24 B N3 C2S 10 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B C2S 24 B O2 C2S 10 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B C2S 24 B N4 C2S 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 C2S 22 B N3 C2S 8 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B C2S 22 B O2 C2S 8 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B C2S 22 B N4 C2S 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 T2S 10 A N3 T2S 10 1_555 B DA 19 B N1 DA 5 1_555 hydrog WATSON-CRICK A T2S 10 A O4 T2S 10 1_555 B DA 19 B N6 DA 5 1_555 hydrog WATSON-CRICK A C2S 11 A N3 C2S 11 1_555 B DG 18 B N1 DG 4 1_555 hydrog WATSON-CRICK A C2S 11 A N4 C2S 11 1_555 B DG 18 B O6 DG 4 1_555 hydrog WATSON-CRICK A C2S 11 A O2 C2S 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 G2S 17 B N1 G2S 3 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B G2S 17 B O6 G2S 3 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B G2S 17 B N2 G2S 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 XBY6, CK14, CK1, PHOSPHORODITHIOATE, NF-KB, DNA 1K8L PDB 1 1K8L 1K8L PDB 2 1K8L 1 14 1K8L 1 14 1K8L A 1 1 14 15 28 1K8L 15 28 1K8L B 2 1 14