1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Yang, X.-L. Hubbard IV, R.B. Lee, M. Tao, Z.-F. Sugiyama, H. Wang, A.H.-J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C20 H28 N11 O4 1 486.508 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM TRI-IMIDAZOLE DNA MINOR GROOVE BINDER; AR-1-144 non-polymer 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 N 1 N C N 2 N O N 3 N N Y 4 N C Y 5 N N Y 6 N C Y 7 N N N 8 N C Y 9 N C N 10 N C N 11 N O N 12 N N Y 13 N C Y 14 N N Y 15 N C Y 16 N N N 17 N C Y 18 N C N 19 N C N 20 N O N 21 N N Y 22 N C Y 23 N N Y 24 N C Y 25 N N N 26 N C Y 27 N C N 28 N C N 29 N O N 30 N N N 31 N C N 32 N C N 33 N N N 34 N C N 35 N C N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N O N 65 N P N 66 N O N 67 N O N 68 N O N 69 N C N 70 R C N 71 N O N 72 S C N 73 N O N 74 N C N 75 R C Y 76 N N Y 77 N C Y 78 N N Y 79 N C Y 80 N C N 81 N N Y 82 N N Y 83 N C Y 84 N N Y 85 N C N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N O N 101 N P N 102 N O N 103 N O N 104 N O N 105 N C N 106 R C N 107 N O N 108 S C N 109 N O N 110 N C N 111 R C N 112 N N N 113 N C N 114 N O N 115 N N N 116 N C N 117 N N N 118 N C N 119 N C N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N O N 135 N P N 136 N O N 137 N O N 138 N O N 139 N C N 140 R C N 141 N O N 142 S C N 143 N O N 144 N C N 145 R C Y 146 N N Y 147 N C Y 148 N N Y 149 N C N 150 N C N 151 N O N 152 N N N 153 N C N 154 N N N 155 N N Y 156 N C N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N O N 172 N P N 173 N O N 174 N O N 175 N O N 176 N C N 177 R C N 178 N O N 179 S C N 180 N O N 181 N C N 182 R C N 183 N N N 184 N C N 185 N O N 186 N N N 187 N C N 188 N O N 189 N C N 190 N C N 191 N C N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing Y 6 N sing Y 7 N doub Y 8 N doub Y 9 N sing N 10 N sing N 11 N sing Y 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N doub N 18 N sing N 19 N sing N 20 N sing Y 21 N sing Y 22 N doub Y 23 N doub Y 24 N sing N 25 N sing N 26 N sing Y 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N doub N 33 N sing N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub Y 38 N doub Y 39 N sing N 40 N sing N 41 N sing Y 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N doub N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing Y 89 N sing Y 90 N sing Y 91 N doub N 92 N sing Y 93 N sing Y 94 N sing Y 95 N doub N 96 N sing Y 97 N doub N 98 N sing N 99 N sing Y 100 N sing Y 101 N doub N 102 N sing Y 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N doub N 130 N sing N 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N doub N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N doub N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing Y 162 N sing Y 163 N sing Y 164 N doub N 165 N sing Y 166 N sing N 167 N sing Y 168 N doub N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N doub N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub N 204 N sing N 205 N sing N 206 N sing N 207 N doub N 208 N sing N 209 N sing N 210 N doub N 211 N sing N 212 N sing N 213 N sing N 214 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 27 4183 4190 10.1093/nar/27.21.4183 10518609 Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs 1999 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 263 646 655 10.1046/j.1432-1327.1999.00515.x Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy 1999 10.2210/pdb1cyz/pdb pdb_00001cyz 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3060.016 5'-D(*GP*AP*AP*CP*TP*GP*GP*TP*TP*C)-3' 2 syn polymer 486.508 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM 2 syn non-polymer no no (DG)(DA)(DA)(DC)(DT)(DG)(DG)(DT)(DT)(DC) GAACTGGTTC A,B polydeoxyribonucleotide n n n n n n n n n n -18.277 1 19 A 1 B 25 2.396 A_DG1:DC25_B 1 -2.432 -0.477 -0.557 -0.029 -16.527 1 20 A 2 B 24 3.147 A_DA2:DT24_B 2 13.974 -0.244 0.025 -0.089 -6.924 1 20 A 3 B 23 6.155 A_DA3:DT23_B 3 -3.205 -0.338 -0.072 -0.139 -7.131 1 19 A 4 B 22 -6.604 A_DC4:DG22_B 4 -18.137 -0.112 0.330 -0.207 5.619 28 A 5 B 21 -3.995 A_DT5:DG21_B 5 -4.908 2.349 0.142 -0.450 -5.421 28 A 6 B 20 -4.016 A_DG6:DT20_B 6 -4.973 -2.334 0.143 -0.461 7.286 1 19 A 7 B 19 -6.619 A_DG7:DC19_B 7 -18.264 0.112 0.333 -0.231 6.917 1 20 A 8 B 18 6.150 A_DT8:DA18_B 8 -3.389 0.314 -0.060 -0.158 16.441 1 20 A 9 B 17 3.135 A_DT9:DA17_B 9 13.795 0.201 0.027 -0.088 18.071 1 19 A 10 B 16 2.398 A_DC10:DG16_B 10 -2.502 0.437 -0.551 0.007 3.439 36.309 A A 1 2 -5.556 B B 25 24 3.355 -3.454 -0.074 -1.113 AA_DG1DA2:DT24DC25_BB 1 -2.960 4.762 36.033 -1.283 -0.312 2.523 33.436 A A 2 3 28.178 B B 24 23 3.306 15.614 0.809 -0.927 AA_DA2DA3:DT23DT24_BB 2 0.200 -0.361 29.658 -4.058 -1.374 3.329 39.289 A A 3 4 -19.813 B B 23 22 3.260 -13.064 -2.033 -0.175 AA_DA3DC4:DG22DT23_BB 3 -4.056 6.152 36.919 1.360 2.521 3.002 34.456 A A 4 5 2.094 B B 22 21 2.981 1.240 0.491 0.513 AA_DC4DT5:DG21DG22_BB 4 0.360 -0.609 34.432 0.690 -0.777 3.009 33.787 A A 5 6 -13.060 B B 21 20 3.363 -7.530 0.000 1.265 AA_DT5DG6:DT20DG21_BB 5 -0.005 0.009 32.961 3.379 0.000 3.002 34.456 A A 6 7 2.084 B B 20 19 2.981 1.234 -0.491 0.513 AA_DG6DG7:DC19DT20_BB 6 -0.364 0.614 34.433 0.690 0.777 3.331 39.297 A A 7 8 -19.812 B B 19 18 3.262 -13.065 2.033 -0.175 AA_DG7DT8:DA18DC19_BB 7 4.058 -6.153 36.928 1.360 -2.520 2.523 33.434 A A 8 9 28.157 B B 18 17 3.305 15.602 -0.808 -0.927 AA_DT8DT9:DA17DA18_BB 8 -0.202 0.364 29.662 -4.056 1.374 3.439 36.308 A A 9 10 -5.544 B B 17 16 3.356 -3.446 0.074 -1.114 AA_DT9DC10:DG16DA17_BB 9 2.962 -4.764 36.032 -1.285 0.312 chem_comp database_2 entity pdbx_entity_nonpoly pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_site chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Structure summary Data collection 1 0 1999-09-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-05-22 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_nmr_software.name _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id 1B0S CONTAINS THE NMR STRUCTURE OF GAACCGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX RCSB Y RCSB 1999-08-31 REL REL AR1 (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES WITH BACK NOE CALCULATION REFINED AVERAGE STRUCTURE 11 1 2D NOESY TOCSY NO ADDITIONAL SALT 7 AMBIENT 275 K NOE-RESTRAINED CONJUGATE GRADIENT REFINEMENT IN X-PLOR; FULL MATRIX RELAXATION 1 refined average structure 1.5 MM DNA DUPLEX; 20 MM PHOSPHATE BUFFER; 100% D2O OR 90% H2O, 10% D2O MSI data analysis Felix 1.1 AND 98 BRUNGER refinement X-PLOR 3.851 750 Varian INOVA AR1 12 2 AR1 AR1 12 A AR1 26 2 AR1 AR1 26 B G 1 n 1 DG 1 A A 2 n 2 DA 2 A A 3 n 3 DA 3 A C 4 n 4 DC 4 A T 5 n 5 DT 5 A G 6 n 6 DG 6 A G 7 n 7 DG 7 A T 8 n 8 DT 8 A T 9 n 9 DT 9 A C 10 n 10 DC 10 A G 16 n 1 DG 16 B A 17 n 2 DA 17 B A 18 n 3 DA 18 B C 19 n 4 DC 19 B T 20 n 5 DT 20 B G 21 n 6 DG 21 B G 22 n 7 DG 22 B T 23 n 8 DT 23 B T 24 n 9 DT 24 B C 25 n 10 DC 25 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 6.65 0.30 108.30 114.95 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 3.16 0.30 108.30 111.46 A A A O4' C1' N9 DA DA DA 2 2 2 N 1 -4.99 0.80 105.90 100.91 A A A O4' C1' C2' DA DA DA 3 3 3 N 1 4.15 0.30 108.30 112.45 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 4.61 0.60 106.00 110.61 A A A O4' C4' C3' DG DG DG 7 7 7 N 1 -5.30 0.80 105.90 100.60 A A A O4' C1' C2' DG DG DG 7 7 7 N 1 9.17 0.30 108.30 117.47 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -4.36 0.60 122.90 118.54 A A A C6 C5 C7 DT DT DT 9 9 9 N 1 6.66 0.30 108.30 114.96 B B B O4' C1' N9 DG DG DG 16 16 16 N 1 3.18 0.30 108.30 111.48 B B B O4' C1' N9 DA DA DA 17 17 17 N 1 -5.02 0.80 105.90 100.88 B B B O4' C1' C2' DA DA DA 18 18 18 N 1 4.13 0.30 108.30 112.43 B B B O4' C1' N1 DT DT DT 20 20 20 N 1 4.65 0.60 106.00 110.65 B B B O4' C4' C3' DG DG DG 22 22 22 N 1 -5.34 0.80 105.90 100.56 B B B O4' C1' C2' DG DG DG 22 22 22 N 1 9.18 0.30 108.30 117.48 B B B O4' C1' N1 DT DT DT 23 23 23 N 1 -4.37 0.60 122.90 118.53 B B B C6 C5 C7 DT DT DT 24 24 24 N 1 A A C5' C4' DG DG 1 1 0.043 0.007 1.512 1.555 N 1 A A C5 C7 DT DT 5 5 0.044 0.006 1.496 1.540 N 1 B B C5' C4' DG DG 16 16 0.044 0.007 1.512 1.556 N 1 B B C5 C7 DT DT 20 20 0.044 0.006 1.496 1.540 N NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX 1 N N 1 N N 2 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 25 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 25 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 25 B N4 DC 10 1_555 hydrog WATSON-CRICK A DA 2 A N1 DA 2 1_555 B DT 24 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 2 A N6 DA 2 1_555 B DT 24 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 23 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 23 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 B DG 22 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 B DG 22 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 B DG 22 B N2 DG 7 1_555 hydrog TYPE_28_PAIR A DT 5 A N3 DT 5 1_555 B DG 21 B O6 DG 6 1_555 hydrog TYPE_28_PAIR A DT 5 A O2 DT 5 1_555 B DG 21 B N1 DG 6 1_555 hydrog TYPE_28_PAIR A DG 6 A N1 DG 6 1_555 B DT 20 B O2 DT 5 1_555 hydrog TYPE_28_PAIR A DG 6 A O6 DG 6 1_555 B DT 20 B N3 DT 5 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 19 B N3 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 19 B O2 DC 4 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 19 B N4 DC 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 18 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 18 B N6 DA 3 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 17 B N1 DA 2 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 17 B N6 DA 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 16 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 16 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 16 B N2 DG 1 1_555 DNA T:G RECOGNIZED BY IM/IM PAIR IN THE DNA MINOR GROOVE, DNA 1CYZ PDB 1 1CYZ 1 10 1CYZ 1 10 1CYZ A 1 1 10 16 25 1CYZ 16 25 1CYZ B 1 1 10 BINDING SITE FOR RESIDUE AR1 A 12 A AR1 12 Software 10 BINDING SITE FOR RESIDUE AR1 B 26 B AR1 26 Software 10 A DC 4 A DC 4 10 1_555 A DT 5 A DT 5 10 1_555 A DG 6 A DG 6 10 1_555 A DG 7 A DG 7 10 1_555 A DT 8 A DT 8 10 1_555 A DT 9 A DT 9 10 1_555 B DC 19 B DC 4 10 1_555 B DG 21 B DG 6 10 1_555 B DG 22 B DG 7 10 1_555 B AR1 26 D AR1 10 1_555 A DC 4 A DC 4 10 1_555 A DG 6 A DG 6 10 1_555 A DG 7 A DG 7 10 1_555 A AR1 12 C AR1 10 1_555 B DC 19 B DC 4 10 1_555 B DT 20 B DT 5 10 1_555 B DG 21 B DG 6 10 1_555 B DG 22 B DG 7 10 1_555 B DT 23 B DT 8 10 1_555 B DT 24 B DT 9 10 1_555 1 P 1