data_8CNC # _model_server_result.job_id 0Y44mVqEsdSeickTcif-ug _model_server_result.datetime_utc '2024-11-13 18:55:17' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8cnc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 8CNC # _exptl.entry_id 8CNC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 424.455 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8CNC _cell.length_a 110.344 _cell.length_b 110.344 _cell.length_c 129.875 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CNC _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C17 H28 N8 O5' _chem_comp.formula_weight 424.455 _chem_comp.id 6D6 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N6 C15 6D6 sing 1 n n C15 N7 6D6 doub 2 n y C15 C9 6D6 sing 3 n y N5 C9 6D6 sing 4 n y N5 C8 6D6 doub 5 n y N7 C16 6D6 sing 6 n y C9 C17 6D6 doub 7 n y C8 N4 6D6 sing 8 n y C16 N8 6D6 doub 9 n y C17 N4 6D6 sing 10 n y C17 N8 6D6 sing 11 n y N4 C13 6D6 sing 12 n n N1 C1 6D6 sing 13 n n C13 C14 6D6 sing 14 n n C13 O3 6D6 sing 15 n n C14 O4 6D6 sing 16 n n C14 C7 6D6 sing 17 n n O3 C12 6D6 sing 18 n n C1 C2 6D6 sing 19 n n C2 C3 6D6 sing 20 n n C6 C12 6D6 sing 21 n n C6 N2 6D6 sing 22 n n C7 C12 6D6 sing 23 n n C7 O5 6D6 sing 24 n n C3 N2 6D6 sing 25 n n N2 C4 6D6 sing 26 n n C4 C10 6D6 sing 27 n n C10 C5 6D6 sing 28 n n N3 C5 6D6 sing 29 n n C5 C11 6D6 sing 30 n n O1 C11 6D6 doub 31 n n C11 O2 6D6 sing 32 n n C1 H1 6D6 sing 33 n n C1 H2 6D6 sing 34 n n C2 H3 6D6 sing 35 n n C2 H4 6D6 sing 36 n n C3 H5 6D6 sing 37 n n C3 H6 6D6 sing 38 n n C4 H7 6D6 sing 39 n n C4 H8 6D6 sing 40 n n C5 H9 6D6 sing 41 n n C6 H10 6D6 sing 42 n n C6 H11 6D6 sing 43 n n C7 H12 6D6 sing 44 n n C8 H13 6D6 sing 45 n n N1 H14 6D6 sing 46 n n N1 H15 6D6 sing 47 n n C10 H18 6D6 sing 48 n n C10 H19 6D6 sing 49 n n N3 H20 6D6 sing 50 n n N3 H21 6D6 sing 51 n n O2 H23 6D6 sing 52 n n C12 H24 6D6 sing 53 n n C13 H25 6D6 sing 54 n n C14 H26 6D6 sing 55 n n O4 H27 6D6 sing 56 n n O5 H28 6D6 sing 57 n n N6 H29 6D6 sing 58 n n N6 H30 6D6 sing 59 n n C16 H31 6D6 sing 60 n n # _atom_sites.entry_id 8CNC _atom_sites.fract_transf_matrix[1][1] 0.009063 _atom_sites.fract_transf_matrix[1][2] 0.005232 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010465 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.0077 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 6D6 A 1 301 301 6D6 K21 . D 4 HOH A 1 401 124 HOH HOH . D 4 HOH A 2 402 174 HOH HOH . D 4 HOH A 3 403 90 HOH HOH . D 4 HOH A 4 404 116 HOH HOH . D 4 HOH A 5 405 117 HOH HOH . D 4 HOH A 6 406 43 HOH HOH . D 4 HOH A 7 407 155 HOH HOH . D 4 HOH A 8 408 62 HOH HOH . D 4 HOH A 9 409 153 HOH HOH . D 4 HOH A 10 410 178 HOH HOH . D 4 HOH A 11 411 125 HOH HOH . D 4 HOH A 12 412 167 HOH HOH . D 4 HOH A 13 413 95 HOH HOH . D 4 HOH A 14 414 161 HOH HOH . D 4 HOH A 15 415 123 HOH HOH . D 4 HOH A 16 416 162 HOH HOH . D 4 HOH A 17 417 127 HOH HOH . D 4 HOH A 18 418 19 HOH HOH . D 4 HOH A 19 419 42 HOH HOH . D 4 HOH A 20 420 80 HOH HOH . D 4 HOH A 21 421 24 HOH HOH . D 4 HOH A 22 422 64 HOH HOH . D 4 HOH A 23 423 66 HOH HOH . D 4 HOH A 24 424 21 HOH HOH . D 4 HOH A 25 425 50 HOH HOH . D 4 HOH A 26 426 68 HOH HOH . D 4 HOH A 27 427 16 HOH HOH . D 4 HOH A 28 428 140 HOH HOH . D 4 HOH A 29 429 146 HOH HOH . D 4 HOH A 30 430 14 HOH HOH . D 4 HOH A 31 431 73 HOH HOH . D 4 HOH A 32 432 48 HOH HOH . D 4 HOH A 33 433 111 HOH HOH . D 4 HOH A 34 434 135 HOH HOH . D 4 HOH A 35 435 61 HOH HOH . D 4 HOH A 36 436 41 HOH HOH . D 4 HOH A 37 437 3 HOH HOH . D 4 HOH A 38 438 84 HOH HOH . D 4 HOH A 39 439 55 HOH HOH . D 4 HOH A 40 440 177 HOH HOH . D 4 HOH A 41 441 170 HOH HOH . D 4 HOH A 42 442 1 HOH HOH . D 4 HOH A 43 443 171 HOH HOH . D 4 HOH A 44 444 11 HOH HOH . D 4 HOH A 45 445 5 HOH HOH . D 4 HOH A 46 446 72 HOH HOH . D 4 HOH A 47 447 23 HOH HOH . D 4 HOH A 48 448 31 HOH HOH . D 4 HOH A 49 449 172 HOH HOH . D 4 HOH A 50 450 131 HOH HOH . D 4 HOH A 51 451 180 HOH HOH . D 4 HOH A 52 452 75 HOH HOH . D 4 HOH A 53 453 32 HOH HOH . D 4 HOH A 54 454 148 HOH HOH . D 4 HOH A 55 455 52 HOH HOH . D 4 HOH A 56 456 126 HOH HOH . D 4 HOH A 57 457 109 HOH HOH . D 4 HOH A 58 458 70 HOH HOH . D 4 HOH A 59 459 138 HOH HOH . D 4 HOH A 60 460 26 HOH HOH . D 4 HOH A 61 461 6 HOH HOH . D 4 HOH A 62 462 100 HOH HOH . D 4 HOH A 63 463 154 HOH HOH . D 4 HOH A 64 464 29 HOH HOH . D 4 HOH A 65 465 101 HOH HOH . D 4 HOH A 66 466 98 HOH HOH . D 4 HOH A 67 467 181 HOH HOH . D 4 HOH A 68 468 118 HOH HOH . D 4 HOH A 69 469 69 HOH HOH . D 4 HOH A 70 470 88 HOH HOH . D 4 HOH A 71 471 92 HOH HOH . D 4 HOH A 72 472 99 HOH HOH . D 4 HOH A 73 473 113 HOH HOH . D 4 HOH A 74 474 76 HOH HOH . D 4 HOH A 75 475 163 HOH HOH . D 4 HOH A 76 476 54 HOH HOH . D 4 HOH A 77 477 10 HOH HOH . D 4 HOH A 78 478 34 HOH HOH . D 4 HOH A 79 479 151 HOH HOH . D 4 HOH A 80 480 39 HOH HOH . D 4 HOH A 81 481 169 HOH HOH . D 4 HOH A 82 482 106 HOH HOH . D 4 HOH A 83 483 149 HOH HOH . D 4 HOH A 84 484 168 HOH HOH . D 4 HOH A 85 485 147 HOH HOH . D 4 HOH A 86 486 133 HOH HOH . D 4 HOH A 87 487 137 HOH HOH . D 4 HOH A 88 488 27 HOH HOH . D 4 HOH A 89 489 128 HOH HOH . D 4 HOH A 90 490 143 HOH HOH . D 4 HOH A 91 491 165 HOH HOH . D 4 HOH A 92 492 59 HOH HOH . D 4 HOH A 93 493 74 HOH HOH . D 4 HOH A 94 494 182 HOH HOH . D 4 HOH A 95 495 110 HOH HOH . D 4 HOH A 96 496 112 HOH HOH . E 4 HOH B 1 201 176 HOH HOH . E 4 HOH B 2 202 186 HOH HOH . E 4 HOH B 3 203 129 HOH HOH . E 4 HOH B 4 204 9 HOH HOH . E 4 HOH B 5 205 122 HOH HOH . E 4 HOH B 6 206 183 HOH HOH . E 4 HOH B 7 207 38 HOH HOH . E 4 HOH B 8 208 119 HOH HOH . E 4 HOH B 9 209 157 HOH HOH . E 4 HOH B 10 210 107 HOH HOH . E 4 HOH B 11 211 77 HOH HOH . E 4 HOH B 12 212 7 HOH HOH . E 4 HOH B 13 213 156 HOH HOH . E 4 HOH B 14 214 12 HOH HOH . E 4 HOH B 15 215 20 HOH HOH . E 4 HOH B 16 216 96 HOH HOH . E 4 HOH B 17 217 150 HOH HOH . E 4 HOH B 18 218 2 HOH HOH . E 4 HOH B 19 219 36 HOH HOH . E 4 HOH B 20 220 136 HOH HOH . E 4 HOH B 21 221 33 HOH HOH . E 4 HOH B 22 222 25 HOH HOH . E 4 HOH B 23 223 79 HOH HOH . E 4 HOH B 24 224 65 HOH HOH . E 4 HOH B 25 225 166 HOH HOH . E 4 HOH B 26 226 8 HOH HOH . E 4 HOH B 27 227 57 HOH HOH . E 4 HOH B 28 228 121 HOH HOH . E 4 HOH B 29 229 83 HOH HOH . E 4 HOH B 30 230 46 HOH HOH . E 4 HOH B 31 231 82 HOH HOH . E 4 HOH B 32 232 89 HOH HOH . E 4 HOH B 33 233 49 HOH HOH . E 4 HOH B 34 234 30 HOH HOH . E 4 HOH B 35 235 15 HOH HOH . E 4 HOH B 36 236 22 HOH HOH . E 4 HOH B 37 237 173 HOH HOH . E 4 HOH B 38 238 184 HOH HOH . E 4 HOH B 39 239 35 HOH HOH . E 4 HOH B 40 240 53 HOH HOH . E 4 HOH B 41 241 145 HOH HOH . E 4 HOH B 42 242 18 HOH HOH . E 4 HOH B 43 243 4 HOH HOH . E 4 HOH B 44 244 86 HOH HOH . E 4 HOH B 45 245 71 HOH HOH . E 4 HOH B 46 246 45 HOH HOH . E 4 HOH B 47 247 141 HOH HOH . E 4 HOH B 48 248 104 HOH HOH . E 4 HOH B 49 249 51 HOH HOH . E 4 HOH B 50 250 17 HOH HOH . E 4 HOH B 51 251 185 HOH HOH . E 4 HOH B 52 252 103 HOH HOH . E 4 HOH B 53 253 47 HOH HOH . E 4 HOH B 54 254 28 HOH HOH . E 4 HOH B 55 255 13 HOH HOH . E 4 HOH B 56 256 94 HOH HOH . E 4 HOH B 57 257 37 HOH HOH . E 4 HOH B 58 258 108 HOH HOH . E 4 HOH B 59 259 81 HOH HOH . E 4 HOH B 60 260 130 HOH HOH . E 4 HOH B 61 261 159 HOH HOH . E 4 HOH B 62 262 67 HOH HOH . E 4 HOH B 63 263 60 HOH HOH . E 4 HOH B 64 264 40 HOH HOH . E 4 HOH B 65 265 87 HOH HOH . E 4 HOH B 66 266 114 HOH HOH . E 4 HOH B 67 267 134 HOH HOH . E 4 HOH B 68 268 179 HOH HOH . E 4 HOH B 69 269 120 HOH HOH . E 4 HOH B 70 270 164 HOH HOH . E 4 HOH B 71 271 93 HOH HOH . E 4 HOH B 72 272 144 HOH HOH . E 4 HOH B 73 273 142 HOH HOH . E 4 HOH B 74 274 91 HOH HOH . E 4 HOH B 75 275 63 HOH HOH . E 4 HOH B 76 276 175 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 6D6 . . . C 3 -34.915 -1.463 -15.621 1 27.25 ? C1 6D6 301 A 1 HETATM 2 C C2 6D6 . . . C 3 -35.16 -2.759 -15.291 1 20.92 ? C2 6D6 301 A 1 HETATM 3 C C3 6D6 . . . C 3 -34.574 -3.156 -13.828 1 18.03 ? C3 6D6 301 A 1 HETATM 4 C C4 6D6 . . . C 3 -36.648 -4.1 -12.946 1 14.2 ? C4 6D6 301 A 1 HETATM 5 C C5 6D6 . . . C 3 -38.141 -3.749 -10.874 1 13.52 ? C5 6D6 301 A 1 HETATM 6 C C6 6D6 . . . C 3 -35.08 -5.508 -14.194 1 13.24 ? C6 6D6 301 A 1 HETATM 7 C C7 6D6 . . . C 3 -33.719 -6.885 -12.476 1 13.32 ? C7 6D6 301 A 1 HETATM 8 C C8 6D6 . . . C 3 -32.727 -9.45 -15.823 1 14.62 ? C8 6D6 301 A 1 HETATM 9 C C9 6D6 . . . C 3 -33.546 -11.386 -16.261 1 13.74 ? C9 6D6 301 A 1 HETATM 10 N N1 6D6 . . . C 3 -35.551 -1.141 -16.874 1 16.49 ? N1 6D6 301 A 1 HETATM 11 N N2 6D6 . . . C 3 -35.254 -4.339 -13.341 1 14.72 ? N2 6D6 301 A 1 HETATM 12 C C10 6D6 . . . C 3 -36.771 -4.138 -11.42 1 13.29 ? C10 6D6 301 A 1 HETATM 13 N N3 6D6 . . . C 3 -39.201 -4.635 -11.46 1 13.03 ? N3 6D6 301 A 1 HETATM 14 C C11 6D6 . . . C 3 -38.459 -2.285 -11.177 1 15.23 ? C11 6D6 301 A 1 HETATM 15 O O1 6D6 . . . C 3 -39.33 -2.066 -12.028 1 13.81 ? O1 6D6 301 A 1 HETATM 16 O O2 6D6 . . . C 3 -37.775 -1.44 -10.568 1 14.99 ? O2 6D6 301 A 1 HETATM 17 C C12 6D6 . . . C 3 -34.951 -6.769 -13.374 1 13.02 ? C12 6D6 301 A 1 HETATM 18 O O3 6D6 . . . C 3 -34.906 -7.895 -14.287 1 13.37 ? O3 6D6 301 A 1 HETATM 19 C C13 6D6 . . . C 3 -34.02 -8.839 -13.735 1 13.67 ? C13 6D6 301 A 1 HETATM 20 C C14 6D6 . . . C 3 -32.906 -8.015 -13.123 1 12.65 ? C14 6D6 301 A 1 HETATM 21 O O4 6D6 . . . C 3 -32.093 -8.765 -12.246 1 14.25 ? O4 6D6 301 A 1 HETATM 22 O O5 6D6 . . . C 3 -34.059 -7.088 -11.107 1 13.32 ? O5 6D6 301 A 1 HETATM 23 N N4 6D6 . . . C 3 -33.603 -9.715 -14.813 1 12.91 ? N4 6D6 301 A 1 HETATM 24 N N5 6D6 . . . C 3 -32.663 -10.42 -16.723 1 15.36 ? N5 6D6 301 A 1 HETATM 25 C C15 6D6 . . . C 3 -33.902 -12.653 -16.739 1 15.18 ? C15 6D6 301 A 1 HETATM 26 N N6 6D6 . . . C 3 -33.397 -13.217 -17.835 1 15 ? N6 6D6 301 A 1 HETATM 27 N N7 6D6 . . . C 3 -34.801 -13.361 -16.022 1 14.11 ? N7 6D6 301 A 1 HETATM 28 C C16 6D6 . . . C 3 -35.331 -12.795 -14.922 1 14.34 ? C16 6D6 301 A 1 HETATM 29 N N8 6D6 . . . C 3 -35.052 -11.623 -14.351 1 14.13 ? N8 6D6 301 A 1 HETATM 30 C C17 6D6 . . . C 3 -34.156 -10.948 -15.095 1 13.32 ? C17 6D6 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #