data_6Y3B # _model_server_result.job_id na90rIhaNp1rE3tPJMg35Q _model_server_result.datetime_utc '2024-11-08 20:47:18' _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 6y3b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 6Y3B # _exptl.entry_id 6Y3B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 630.782 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(8~{R},15~{S},18~{S})-15,18-bis(4-azanylbutyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine _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 90 _cell.entry_id 6Y3B _cell.length_a 48.626 _cell.length_b 60.493 _cell.length_c 83.139 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y3B _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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,F,G _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C30 H50 N10 O5' _chem_comp.formula_weight 630.782 _chem_comp.id O7N _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(8~{R},15~{S},18~{S})-15,18-bis(4-azanylbutyl)-4,7,14,17,20-pentakis(oxidanylidene)-3,6,13,16,19-pentazabicyclo[20.3.1]hexacosa-1(25),22(26),23-trien-8-yl]guanidine _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 C17 O7N sing 250 n n C17 C16 O7N sing 251 n n C11 N4 O7N sing 252 n n C11 C10 O7N sing 253 n n C9 C10 O7N sing 254 n n C9 C8 O7N sing 255 n n C19 C20 O7N sing 256 n n C19 C18 O7N sing 257 n n C21 C22 O7N doub 258 n y C21 C20 O7N sing 259 n y C22 C23 O7N sing 260 n y C20 C25 O7N doub 261 n y C16 C15 O7N sing 262 n n C25 C24 O7N sing 263 n y C23 C24 O7N doub 264 n y C24 C26 O7N sing 265 n n C15 C14 O7N sing 266 n n C8 C7 O7N sing 267 n n N7 C18 O7N sing 268 n n N7 C13 O7N sing 269 n n C26 N8 O7N sing 270 n n C18 O2 O7N doub 271 n n C14 C13 O7N sing 272 n n O3 C27 O7N doub 273 n n C13 C12 O7N sing 274 n n N5 C7 O7N sing 275 n n N5 C12 O7N sing 276 n n C7 C6 O7N sing 277 n n N8 C27 O7N sing 278 n n C27 C28 O7N sing 279 n n C12 O1 O7N doub 280 n n O C6 O7N doub 281 n n O4 C29 O7N doub 282 n n C6 N3 O7N sing 283 n n N C O7N doub 284 n n C28 N9 O7N sing 285 n n C29 N9 O7N sing 286 n n C29 C1 O7N sing 287 n n N3 C5 O7N sing 288 n n C1 N2 O7N sing 289 n n C1 C2 O7N sing 290 n n C N2 O7N sing 291 n n C N1 O7N sing 292 n n C3 C2 O7N sing 293 n n C3 C4 O7N sing 294 n n C5 C4 O7N sing 295 n n C4 H1 O7N sing 296 n n C4 H2 O7N sing 297 n n C5 H3 O7N sing 298 n n C5 H4 O7N sing 299 n n N1 H5 O7N sing 300 n n N1 H6 O7N sing 301 n n C7 H7 O7N sing 302 n n C8 H8 O7N sing 303 n n C8 H9 O7N sing 304 n n N2 H10 O7N sing 305 n n C9 H11 O7N sing 306 n n C9 H12 O7N sing 307 n n C10 H13 O7N sing 308 n n C10 H14 O7N sing 309 n n C11 H15 O7N sing 310 n n C11 H16 O7N sing 311 n n N3 H17 O7N sing 312 n n C13 H18 O7N sing 313 n n C14 H19 O7N sing 314 n n C14 H20 O7N sing 315 n n C15 H21 O7N sing 316 n n C15 H22 O7N sing 317 n n N4 H23 O7N sing 318 n n N4 H24 O7N sing 319 n n N H26 O7N sing 320 n n C1 H27 O7N sing 321 n n C16 H28 O7N sing 322 n n C16 H29 O7N sing 323 n n C17 H30 O7N sing 324 n n C17 H31 O7N sing 325 n n C19 H32 O7N sing 326 n n C19 H33 O7N sing 327 n n C2 H34 O7N sing 328 n n C2 H35 O7N sing 329 n n C21 H36 O7N sing 330 n n C22 H37 O7N sing 331 n n C23 H38 O7N sing 332 n n C25 H39 O7N sing 333 n n C26 H40 O7N sing 334 n n C26 H41 O7N sing 335 n n C28 H42 O7N sing 336 n n C28 H43 O7N sing 337 n n C3 H44 O7N sing 338 n n C3 H45 O7N sing 339 n n N5 H46 O7N sing 340 n n N6 H47 O7N sing 341 n n N6 H48 O7N sing 342 n n N7 H50 O7N sing 343 n n N8 H51 O7N sing 344 n n N9 H52 O7N sing 345 n n # _atom_sites.entry_id 6Y3B _atom_sites.fract_transf_matrix[1][1] 0.020565 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016531 _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] 0.012028 _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 GOL B 1 201 1 GOL GOL . D 4 O7N B 1 202 1 O7N XXX . E 5 SO4 B 1 203 1 SO4 SO4 . F 6 HOH A 1 101 182 HOH HOH . F 6 HOH A 2 102 112 HOH HOH . F 6 HOH A 3 103 141 HOH HOH . F 6 HOH A 4 104 78 HOH HOH . F 6 HOH A 5 105 97 HOH HOH . F 6 HOH A 6 106 77 HOH HOH . F 6 HOH A 7 107 84 HOH HOH . F 6 HOH A 8 108 15 HOH HOH . F 6 HOH A 9 109 127 HOH HOH . F 6 HOH A 10 110 29 HOH HOH . F 6 HOH A 11 111 82 HOH HOH . F 6 HOH A 12 112 133 HOH HOH . F 6 HOH A 13 113 10 HOH HOH . F 6 HOH A 14 114 192 HOH HOH . F 6 HOH A 15 115 163 HOH HOH . F 6 HOH A 16 116 28 HOH HOH . F 6 HOH A 17 117 18 HOH HOH . F 6 HOH A 18 118 19 HOH HOH . F 6 HOH A 19 119 186 HOH HOH . F 6 HOH A 20 120 59 HOH HOH . F 6 HOH A 21 121 193 HOH HOH . F 6 HOH A 22 122 94 HOH HOH . F 6 HOH A 23 123 136 HOH HOH . F 6 HOH A 24 124 45 HOH HOH . F 6 HOH A 25 125 91 HOH HOH . F 6 HOH A 26 126 178 HOH HOH . F 6 HOH A 27 127 155 HOH HOH . F 6 HOH A 28 128 171 HOH HOH . G 6 HOH B 1 301 108 HOH HOH . G 6 HOH B 2 302 144 HOH HOH . G 6 HOH B 3 303 115 HOH HOH . G 6 HOH B 4 304 38 HOH HOH . G 6 HOH B 5 305 67 HOH HOH . G 6 HOH B 6 306 113 HOH HOH . G 6 HOH B 7 307 31 HOH HOH . G 6 HOH B 8 308 74 HOH HOH . G 6 HOH B 9 309 85 HOH HOH . G 6 HOH B 10 310 64 HOH HOH . G 6 HOH B 11 311 69 HOH HOH . G 6 HOH B 12 312 30 HOH HOH . G 6 HOH B 13 313 89 HOH HOH . G 6 HOH B 14 314 90 HOH HOH . G 6 HOH B 15 315 151 HOH HOH . G 6 HOH B 16 316 25 HOH HOH . G 6 HOH B 17 317 167 HOH HOH . G 6 HOH B 18 318 150 HOH HOH . G 6 HOH B 19 319 11 HOH HOH . G 6 HOH B 20 320 116 HOH HOH . G 6 HOH B 21 321 130 HOH HOH . G 6 HOH B 22 322 107 HOH HOH . G 6 HOH B 23 323 22 HOH HOH . G 6 HOH B 24 324 76 HOH HOH . G 6 HOH B 25 325 9 HOH HOH . G 6 HOH B 26 326 50 HOH HOH . G 6 HOH B 27 327 7 HOH HOH . G 6 HOH B 28 328 96 HOH HOH . G 6 HOH B 29 329 174 HOH HOH . G 6 HOH B 30 330 104 HOH HOH . G 6 HOH B 31 331 2 HOH HOH . G 6 HOH B 32 332 106 HOH HOH . G 6 HOH B 33 333 48 HOH HOH . G 6 HOH B 34 334 26 HOH HOH . G 6 HOH B 35 335 12 HOH HOH . G 6 HOH B 36 336 194 HOH HOH . G 6 HOH B 37 337 40 HOH HOH . G 6 HOH B 38 338 81 HOH HOH . G 6 HOH B 39 339 66 HOH HOH . G 6 HOH B 40 340 54 HOH HOH . G 6 HOH B 41 341 52 HOH HOH . G 6 HOH B 42 342 177 HOH HOH . G 6 HOH B 43 343 143 HOH HOH . G 6 HOH B 44 344 181 HOH HOH . G 6 HOH B 45 345 6 HOH HOH . G 6 HOH B 46 346 41 HOH HOH . G 6 HOH B 47 347 121 HOH HOH . G 6 HOH B 48 348 36 HOH HOH . G 6 HOH B 49 349 14 HOH HOH . G 6 HOH B 50 350 21 HOH HOH . G 6 HOH B 51 351 148 HOH HOH . G 6 HOH B 52 352 170 HOH HOH . G 6 HOH B 53 353 34 HOH HOH . G 6 HOH B 54 354 110 HOH HOH . G 6 HOH B 55 355 17 HOH HOH . G 6 HOH B 56 356 131 HOH HOH . G 6 HOH B 57 357 111 HOH HOH . G 6 HOH B 58 358 27 HOH HOH . G 6 HOH B 59 359 183 HOH HOH . G 6 HOH B 60 360 189 HOH HOH . G 6 HOH B 61 361 160 HOH HOH . G 6 HOH B 62 362 98 HOH HOH . G 6 HOH B 63 363 24 HOH HOH . G 6 HOH B 64 364 187 HOH HOH . G 6 HOH B 65 365 46 HOH HOH . G 6 HOH B 66 366 190 HOH HOH . G 6 HOH B 67 367 55 HOH HOH . G 6 HOH B 68 368 20 HOH HOH . G 6 HOH B 69 369 16 HOH HOH . G 6 HOH B 70 370 117 HOH HOH . G 6 HOH B 71 371 152 HOH HOH . G 6 HOH B 72 372 32 HOH HOH . G 6 HOH B 73 373 125 HOH HOH . G 6 HOH B 74 374 147 HOH HOH . G 6 HOH B 75 375 201 HOH HOH . G 6 HOH B 76 376 200 HOH HOH . G 6 HOH B 77 377 149 HOH HOH . G 6 HOH B 78 378 83 HOH HOH . G 6 HOH B 79 379 126 HOH HOH . G 6 HOH B 80 380 191 HOH HOH . G 6 HOH B 81 381 157 HOH HOH . G 6 HOH B 82 382 161 HOH HOH . G 6 HOH B 83 383 198 HOH HOH . G 6 HOH B 84 384 158 HOH HOH . G 6 HOH B 85 385 123 HOH HOH . G 6 HOH B 86 386 75 HOH HOH . G 6 HOH B 87 387 145 HOH HOH . G 6 HOH B 88 388 173 HOH HOH . G 6 HOH B 89 389 164 HOH HOH . G 6 HOH B 90 390 176 HOH HOH . G 6 HOH B 91 391 122 HOH HOH . G 6 HOH B 92 392 51 HOH HOH . G 6 HOH B 93 393 195 HOH HOH . G 6 HOH B 94 394 87 HOH HOH . G 6 HOH B 95 395 105 HOH HOH . G 6 HOH B 96 396 140 HOH HOH . G 6 HOH B 97 397 180 HOH HOH . G 6 HOH B 98 398 188 HOH HOH . G 6 HOH B 99 399 60 HOH HOH . G 6 HOH B 100 400 68 HOH HOH . G 6 HOH B 101 401 184 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 O O3 O7N . . . D 4 10.27 -16.541 2.451 1 21.71 ? O3 O7N 202 B 1 HETATM 2 C C4 O7N . . . D 4 4.003 -15.006 7.069 1 19.07 ? C4 O7N 202 B 1 HETATM 3 C C5 O7N . . . D 4 2.803 -15.679 6.413 1 18.74 ? C5 O7N 202 B 1 HETATM 4 O O4 O7N . . . D 4 7.405 -14.782 3.88 1 18.25 ? O4 O7N 202 B 1 HETATM 5 C C6 O7N . . . D 4 2.411 -14.917 4.119 1 19.8 ? C6 O7N 202 B 1 HETATM 6 N N1 O7N . . . D 4 10.01 -11.068 6.853 1 19.78 ? N1 O7N 202 B 1 HETATM 7 C C7 O7N . . . D 4 1.779 -13.84 3.247 1 19.07 ? C7 O7N 202 B 1 HETATM 8 C C8 O7N . . . D 4 1.247 -14.448 1.951 1 18.69 ? C8 O7N 202 B 1 HETATM 9 N N2 O7N . . . D 4 8.294 -12.568 6.537 1 17.61 ? N2 O7N 202 B 1 HETATM 10 C C9 O7N . . . D 4 0.659 -13.411 1.006 1 20.25 ? C9 O7N 202 B 1 HETATM 11 C C10 O7N . . . D 4 -0.627 -12.749 1.489 1 22.16 ? C10 O7N 202 B 1 HETATM 12 C C11 O7N . . . D 4 -1.085 -11.688 0.504 1 23.3 ? C11 O7N 202 B 1 HETATM 13 C C12 O7N . . . D 4 2.676 -11.564 3.414 1 19.26 ? C12 O7N 202 B 1 HETATM 14 N N3 O7N . . . D 4 2.183 -14.803 5.426 1 18.96 ? N3 O7N 202 B 1 HETATM 15 C C13 O7N . . . D 4 3.721 -10.573 2.911 1 17.94 ? C13 O7N 202 B 1 HETATM 16 C C14 O7N . . . D 4 2.978 -9.385 2.289 1 25.9 ? C14 O7N 202 B 1 HETATM 17 C C15 O7N . . . D 4 3.876 -8.284 1.753 1 29.51 ? C15 O7N 202 B 1 HETATM 18 N N4 O7N . . . D 4 -2.47 -11.214 0.713 1 21.96 ? N4 O7N 202 B 1 HETATM 19 N N O7N . . . D 4 8.965 -11.24 4.671 1 18.3 ? N O7N 202 B 1 HETATM 20 C C O7N . . . D 4 9.101 -11.586 5.945 1 18.48 ? C O7N 202 B 1 HETATM 21 O O O7N . . . D 4 3.111 -15.811 3.616 1 20.93 ? O O7N 202 B 1 HETATM 22 C C1 O7N . . . D 4 7.307 -13.315 5.777 1 16.58 ? C1 O7N 202 B 1 HETATM 23 C C16 O7N . . . D 4 3.117 -7.02 1.333 1 24.64 ? C16 O7N 202 B 1 HETATM 24 C C17 O7N . . . D 4 2.199 -7.19 0.14 1 25.49 ? C17 O7N 202 B 1 HETATM 25 C C18 O7N . . . D 4 5.936 -11.39 2.231 1 16.79 ? C18 O7N 202 B 1 HETATM 26 C C19 O7N . . . D 4 6.763 -11.779 1.022 1 20.17 ? C19 O7N 202 B 1 HETATM 27 C C2 O7N . . . D 4 6.243 -13.855 6.74 1 19.48 ? C2 O7N 202 B 1 HETATM 28 C C20 O7N . . . D 4 8.251 -11.645 1.231 1 17.95 ? C20 O7N 202 B 1 HETATM 29 C C21 O7N . . . D 4 8.89 -10.428 1.058 1 18.34 ? C21 O7N 202 B 1 HETATM 30 C C22 O7N . . . D 4 10.258 -10.323 1.228 1 19.15 ? C22 O7N 202 B 1 HETATM 31 C C23 O7N . . . D 4 11.005 -11.443 1.557 1 18.63 ? C23 O7N 202 B 1 HETATM 32 C C24 O7N . . . D 4 10.393 -12.679 1.707 1 19.38 ? C24 O7N 202 B 1 HETATM 33 C C25 O7N . . . D 4 9.016 -12.764 1.542 1 18.24 ? C25 O7N 202 B 1 HETATM 34 C C26 O7N . . . D 4 11.185 -13.912 2.068 1 18.9 ? C26 O7N 202 B 1 HETATM 35 C C27 O7N . . . D 4 10.226 -15.737 3.384 1 21.79 ? C27 O7N 202 B 1 HETATM 36 C C28 O7N . . . D 4 9.621 -16.131 4.721 1 18.89 ? C28 O7N 202 B 1 HETATM 37 C C29 O7N . . . D 4 7.911 -14.448 4.945 1 18.09 ? C29 O7N 202 B 1 HETATM 38 C C3 O7N . . . D 4 5.084 -14.563 6.055 1 18.8 ? C3 O7N 202 B 1 HETATM 39 N N5 O7N . . . D 4 2.782 -12.821 2.964 1 18.48 ? N5 O7N 202 B 1 HETATM 40 N N6 O7N . . . D 4 1.781 -5.836 -0.342 1 22.32 ? N6 O7N 202 B 1 HETATM 41 N N7 O7N . . . D 4 4.644 -11.177 1.957 1 18.52 ? N7 O7N 202 B 1 HETATM 42 N N8 O7N . . . D 4 10.71 -14.496 3.316 1 18.97 ? N8 O7N 202 B 1 HETATM 43 N N9 O7N . . . D 4 9.011 -15.027 5.424 1 20.18 ? N9 O7N 202 B 1 HETATM 44 O O1 O7N . . . D 4 1.795 -11.193 4.198 1 18.86 ? O1 O7N 202 B 1 HETATM 45 O O2 O7N . . . D 4 6.429 -11.246 3.347 1 19.3 ? O2 O7N 202 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #