0.02899 0.00000 0.00000 0.00000 0.02591 0.00000 0.00000 0.00000 0.02123 0.00000 0.00000 0.00000 Kielkopf, C.L. Bremer, R.E. White, S. Baird, E.E. Dervan, P.B. Rees, D.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 34.493 38.593 47.112 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 H2 O 18.015 WATER non-polymer C31 H42 N11 O5 1 648.736 IMIDAZOLE-PYRROLE POLYAMIDE IMIDAZOLE-PYRROLE-PYRROLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C 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 H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N O N 145 N H N 146 N H Y 147 N C Y 148 N C Y 149 N C N 150 N C Y 151 N C N 152 N C Y 153 N C Y 154 N C N 155 N C Y 156 N C N 157 N C Y 158 N C Y 159 N C Y 160 N C N 161 N C Y 162 N C N 163 N C N 164 N C N 165 N C N 166 N C N 167 N C N 168 N C N 169 N C Y 170 N C Y 171 N C Y 172 N C N 173 N C N 174 N C N 175 N C N 176 N C Y 177 N C N 178 N O N 179 N O N 180 N O N 181 N O N 182 N O Y 183 N N N 184 N N Y 185 N N N 186 N N Y 187 N N N 188 N N N 189 N N N 190 N N Y 191 N N Y 192 N N N 193 N N 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 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing 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 doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub 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 N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub 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 sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing Y 152 N doub Y 153 N sing N 154 N sing Y 155 N sing Y 156 N doub N 157 N sing Y 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing Y 165 N doub Y 166 N sing N 167 N doub N 168 N sing Y 169 N doub N 170 N sing Y 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing Y 178 N sing N 179 N doub N 180 N sing Y 181 N sing Y 182 N doub N 183 N sing Y 184 N doub N 185 N sing Y 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 Y 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 sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N doub N 213 N sing N 214 N sing N 215 N doub N 216 N sing Y 217 N sing Y 218 N doub Y 219 N doub Y 220 N sing N 221 N sing Y 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N doub N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 295 557 567 10.1006/jmbi.1999.3364 10623546 Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove. 2000 10.2210/pdb1cvy/pdb pdb_00001cvy 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 103 1 IMAGE PLATE RIGAKU RAXIS IV SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU 3045.004 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3' 2 syn polymer 648.736 IMIDAZOLE-PYRROLE POLYAMIDE 2 syn non-polymer 18.015 water 52 nat water no no (DC)(DC)(DA)(DG)(DA)(DT)(DC)(DT)(DG)(DG) CCAGATCTGG A,B polydeoxyribonucleotide n n n n n n n n n n 1 2.47 50.22 VAPOR DIFFUSION, SITTING DROP 8.1 CALCIUM ACETATE, TRIS, MPD, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K 277.0 CALCIUM ACETATE 1 TRIS 1 MPD 1 MPD 2 -6.256 1 19 A 1 B 10 0.952 A_DC1:DG10_B 1 -27.964 -0.626 0.127 0.142 -10.405 1 19 A 2 B 9 0.096 A_DC2:DG9_B 2 -9.515 0.211 0.362 -0.192 -0.879 1 20 A 3 B 8 3.554 A_DA3:DT8_B 3 -6.611 -0.185 0.344 -0.236 -4.465 1 19 A 4 B 7 -1.101 A_DG4:DC7_B 4 -11.442 0.000 0.313 -0.269 -4.843 1 20 A 5 B 6 -12.831 A_DA5:DT6_B 5 -17.575 -0.289 0.160 0.058 1.535 1 20 A 6 B 5 -10.747 A_DT6:DA5_B 6 -18.954 0.148 0.481 0.114 2.826 1 19 A 7 B 4 1.110 A_DC7:DG4_B 7 -2.919 0.760 0.159 -0.396 0.333 1 20 A 8 B 3 4.598 A_DT8:DA3_B 8 -0.906 0.510 0.188 -0.242 2.769 1 19 A 9 B 2 1.639 A_DG9:DC2_B 9 -8.626 0.025 0.098 -0.168 8.015 1 19 A 10 B 1 4.152 A_DG10:DC1_B 10 -29.570 -0.155 0.110 -0.269 3.548 37.339 A A 1 2 15.401 B B 10 9 3.579 9.752 -0.112 0.332 AA_DC1DC2:DG9DG10_BB 1 -1.210 1.910 36.067 -0.910 -0.002 3.204 40.098 A A 2 3 2.051 B B 9 8 3.164 1.405 -0.014 1.405 AA_DC2DA3:DT8DG9_BB 2 -2.741 4.002 39.984 1.893 -0.285 3.276 31.902 A A 3 4 27.312 B B 8 7 3.514 14.465 -0.972 0.122 AA_DA3DG4:DC7DT8_BB 3 -3.057 5.771 28.349 -2.678 1.156 3.449 37.899 A A 4 5 -0.696 B B 7 6 3.253 -0.450 -1.661 1.020 AA_DG4DA5:DT6DC7_BB 4 -5.729 8.853 37.477 1.629 1.802 3.005 38.070 A A 5 6 -16.519 B B 6 5 3.132 -10.642 0.202 0.027 AA_DA5DT6:DA5DT6_BB 5 -0.562 0.872 36.601 1.335 -0.379 3.507 42.514 A A 6 7 1.586 B B 5 4 3.233 1.144 1.668 1.230 AA_DT6DC7:DG4DA5_BB 6 7.835 -10.863 41.804 1.576 -1.476 3.263 29.070 A A 7 8 30.701 B B 4 3 3.483 14.672 0.733 0.357 AA_DC7DT8:DA3DG4_BB 7 4.032 -8.437 24.843 -2.883 -0.472 3.235 42.105 A A 8 9 -1.885 B B 3 2 3.314 -1.353 0.004 2.268 AA_DT8DG9:DC2DA3_BB 8 2.964 -4.130 41.984 3.298 0.301 3.121 30.581 A A 9 10 24.796 B B 2 1 3.138 12.694 0.265 0.604 AA_DG9DG10:DC1DC2_BB 9 1.600 -3.125 27.834 -1.381 -0.185 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Structure summary Data collection Database references Derived calculations 1 0 2000-01-15 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-02-01 1 4 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id HYDROXYPYRROLE COUNTERPART RCSB Y RCSB 1999-08-24 REL IPY IMIDAZOLE-PYRROLE POLYAMIDE HOH water IPY 12 2 IPY IPY 12 A IPY 11 2 IPY IPY 11 B HOH 23 3 HOH HOH 23 A HOH 25 3 HOH HOH 25 A HOH 26 3 HOH HOH 26 A HOH 27 3 HOH HOH 27 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 30 3 HOH HOH 30 A HOH 31 3 HOH HOH 31 A HOH 32 3 HOH HOH 32 A HOH 33 3 HOH HOH 33 A HOH 36 3 HOH HOH 36 A HOH 37 3 HOH HOH 37 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 42 3 HOH HOH 42 A HOH 48 3 HOH HOH 48 A HOH 51 3 HOH HOH 51 A HOH 54 3 HOH HOH 54 A HOH 55 3 HOH HOH 55 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 58 3 HOH HOH 58 A HOH 59 3 HOH HOH 59 A HOH 60 3 HOH HOH 60 A HOH 62 3 HOH HOH 62 A HOH 63 3 HOH HOH 63 A HOH 64 3 HOH HOH 64 A HOH 67 3 HOH HOH 67 A HOH 68 3 HOH HOH 68 A HOH 69 3 HOH HOH 69 A HOH 74 3 HOH HOH 74 A HOH 24 3 HOH HOH 24 B HOH 34 3 HOH HOH 34 B HOH 35 3 HOH HOH 35 B HOH 40 3 HOH HOH 40 B HOH 41 3 HOH HOH 41 B HOH 43 3 HOH HOH 43 B HOH 44 3 HOH HOH 44 B HOH 45 3 HOH HOH 45 B HOH 46 3 HOH HOH 46 B HOH 47 3 HOH HOH 47 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 52 3 HOH HOH 52 B HOH 53 3 HOH HOH 53 B HOH 61 3 HOH HOH 61 B HOH 65 3 HOH HOH 65 B HOH 66 3 HOH HOH 66 B HOH 70 3 HOH HOH 70 B HOH 71 3 HOH HOH 71 B HOH 72 3 HOH HOH 72 B HOH 73 3 HOH HOH 73 B 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 A 5 n 5 DA 5 A T 6 n 6 DT 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A C 1 n 1 DC 1 B C 2 n 2 DC 2 B A 3 n 3 DA 3 B G 4 n 4 DG 4 B A 5 n 5 DA 5 B T 6 n 6 DT 6 B C 7 n 7 DC 7 B T 8 n 8 DT 8 B G 9 n 9 DG 9 B G 10 n 10 DG 10 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 A O O HOH HOH 25 69 2.08 1 A A N3 O DG HOH 10 67 2.12 1 A A O O HOH HOH 25 68 2.13 1 A DA 5 0.080 SIDE CHAIN 1 B DA 5 0.076 SIDE CHAIN 1 2.21 0.30 108.30 110.51 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 -4.83 0.80 102.40 97.57 A A A C3' C2' C1' DG DG DG 10 10 10 N 1 3.89 0.30 108.30 112.19 B B B O4' C1' N1 DC DC DC 2 2 2 N 1 6.86 1.10 110.50 117.36 B B B O3' P OP1 DT DC DC 6 7 7 Y 1 A A N9 C4 DA DA 3 3 0.036 0.006 1.374 1.410 N 1 A A N3 C4 DC DC 7 7 -0.043 0.007 1.335 1.292 N 1 A A O3' C3' DG DG 9 9 -0.047 0.006 1.419 1.372 N 0.2290000 0.2290000 0.2290000 2.15 17.0 144 3618 3618 5 97.2 RANDOM 1 THROUGHOUT 0 0 2.15 17.0 52 550 94 404 0 0.02 2.1 2.15 17.0 1CVY 3618 3618 0 0.0410000 1 33.8 5.9 97.2 0.0740000 2.15 2.25 1 94.2 phasing AMoRE refinement CNS data reduction DENZO data scaling SCALEPACK CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 9 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 9 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 9 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 7 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 7 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 7 B N4 DC 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 6 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 6 B O4 DT 6 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 1 B N4 DC 1 1_555 DNA IMIDAZOLE-PYRROLE POLYAMIDE, DOUBLE DRUG IN MINOR GROOVE, MINOR GROOVE RECOGNITION, DNA 1CVY PDB 1 1CVY 1 10 1CVY 1 10 1CVY A 1 1 10 1 10 1CVY 1 10 1CVY B 1 1 10 BINDING SITE FOR RESIDUE IPY B 11 B IPY 11 Software 14 BINDING SITE FOR RESIDUE IPY A 12 A IPY 12 Software 15 A DG 4 A DG 4 14 1_555 A DT 6 A DT 6 14 4_565 A IPY 12 C IPY 14 1_555 A HOH 54 E HOH 14 1_555 A HOH 59 E HOH 14 2_574 B DG 4 B DG 4 14 1_555 B DA 5 B DA 5 14 1_555 B DT 6 B DT 6 14 1_555 B DC 7 B DC 7 14 1_555 B DT 8 B DT 8 14 1_555 B DG 9 B DG 9 14 1_555 B HOH 41 F HOH 14 1_655 B HOH 52 F HOH 14 1_555 B HOH 53 F HOH 14 1_555 A DG 4 A DG 4 15 1_555 A DA 5 A DA 5 15 1_555 A DT 6 A DT 6 15 1_555 A DC 7 A DC 7 15 1_555 A DT 8 A DT 8 15 1_555 A DG 9 A DG 9 15 1_555 A HOH 28 E HOH 15 1_555 A HOH 54 E HOH 15 1_555 A HOH 63 E HOH 15 1_555 A HOH 64 E HOH 15 1_555 A HOH 67 E HOH 15 1_555 B DG 4 B DG 4 15 1_555 B DT 6 B DT 6 15 4_475 B IPY 11 D IPY 15 1_555 B HOH 53 F HOH 15 1_555 19 orthorhombic P 21 21 21