data_3TYX # _model_server_result.job_id CBWN0BifsLdwPMkowVvrEQ _model_server_result.datetime_utc '2024-11-28 12:13:42' _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 3tyx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 3TYX # _exptl.entry_id 3TYX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 2 _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 3TYX _cell.length_a 118.23 _cell.length_b 118.23 _cell.length_c 54.839 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TYX _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 3TYX _atom_sites.fract_transf_matrix[1][1] 0.008458 _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] 0.008458 _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] 0.018235 _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 2 AMP A 1 401 401 AMP AMP . D 2 AMP B 1 401 401 AMP AMP . E 3 HOH A 1 334 1 HOH HOH . E 3 HOH A 2 335 4 HOH HOH . E 3 HOH A 3 336 5 HOH HOH . E 3 HOH A 4 337 6 HOH HOH . E 3 HOH A 5 338 7 HOH HOH . E 3 HOH A 6 339 8 HOH HOH . E 3 HOH A 7 340 10 HOH HOH . E 3 HOH A 8 341 11 HOH HOH . E 3 HOH A 9 342 12 HOH HOH . E 3 HOH A 10 343 15 HOH HOH . E 3 HOH A 11 344 16 HOH HOH . E 3 HOH A 12 345 19 HOH HOH . E 3 HOH A 13 346 22 HOH HOH . E 3 HOH A 14 347 23 HOH HOH . E 3 HOH A 15 348 26 HOH HOH . E 3 HOH A 16 349 27 HOH HOH . E 3 HOH A 17 350 29 HOH HOH . E 3 HOH A 18 351 30 HOH HOH . E 3 HOH A 19 352 35 HOH HOH . E 3 HOH A 20 353 36 HOH HOH . E 3 HOH A 21 354 38 HOH HOH . E 3 HOH A 22 355 39 HOH HOH . E 3 HOH A 23 356 41 HOH HOH . E 3 HOH A 24 357 42 HOH HOH . E 3 HOH A 25 358 47 HOH HOH . E 3 HOH A 26 359 49 HOH HOH . E 3 HOH A 27 360 51 HOH HOH . E 3 HOH A 28 361 57 HOH HOH . E 3 HOH A 29 362 59 HOH HOH . E 3 HOH A 30 363 61 HOH HOH . E 3 HOH A 31 364 62 HOH HOH . E 3 HOH A 32 365 63 HOH HOH . E 3 HOH A 33 366 64 HOH HOH . E 3 HOH A 34 367 65 HOH HOH . E 3 HOH A 35 368 68 HOH HOH . E 3 HOH A 36 369 69 HOH HOH . E 3 HOH A 37 370 70 HOH HOH . E 3 HOH A 38 371 71 HOH HOH . E 3 HOH A 39 372 72 HOH HOH . E 3 HOH A 40 373 73 HOH HOH . E 3 HOH A 41 374 74 HOH HOH . E 3 HOH A 42 375 76 HOH HOH . E 3 HOH A 43 376 78 HOH HOH . E 3 HOH A 44 377 79 HOH HOH . E 3 HOH A 45 378 81 HOH HOH . E 3 HOH A 46 379 82 HOH HOH . E 3 HOH A 47 380 85 HOH HOH . E 3 HOH A 48 381 87 HOH HOH . E 3 HOH A 49 382 89 HOH HOH . E 3 HOH A 50 383 93 HOH HOH . E 3 HOH A 51 384 94 HOH HOH . E 3 HOH A 52 385 95 HOH HOH . E 3 HOH A 53 386 96 HOH HOH . E 3 HOH A 54 387 97 HOH HOH . E 3 HOH A 55 388 98 HOH HOH . E 3 HOH A 56 389 100 HOH HOH . E 3 HOH A 57 390 102 HOH HOH . E 3 HOH A 58 391 107 HOH HOH . E 3 HOH A 59 392 108 HOH HOH . E 3 HOH A 60 393 109 HOH HOH . E 3 HOH A 61 394 112 HOH HOH . E 3 HOH A 62 395 116 HOH HOH . E 3 HOH A 63 396 117 HOH HOH . E 3 HOH A 64 397 118 HOH HOH . E 3 HOH A 65 398 120 HOH HOH . E 3 HOH A 66 399 122 HOH HOH . E 3 HOH A 67 400 126 HOH HOH . E 3 HOH A 68 402 131 HOH HOH . E 3 HOH A 69 403 133 HOH HOH . E 3 HOH A 70 404 138 HOH HOH . E 3 HOH A 71 405 139 HOH HOH . E 3 HOH A 72 406 146 HOH HOH . E 3 HOH A 73 407 147 HOH HOH . E 3 HOH A 74 408 148 HOH HOH . E 3 HOH A 75 409 150 HOH HOH . E 3 HOH A 76 410 152 HOH HOH . E 3 HOH A 77 411 153 HOH HOH . E 3 HOH A 78 412 159 HOH HOH . E 3 HOH A 79 413 160 HOH HOH . E 3 HOH A 80 414 161 HOH HOH . E 3 HOH A 81 415 163 HOH HOH . E 3 HOH A 82 416 170 HOH HOH . E 3 HOH A 83 417 171 HOH HOH . E 3 HOH A 84 418 174 HOH HOH . E 3 HOH A 85 419 175 HOH HOH . E 3 HOH A 86 420 178 HOH HOH . E 3 HOH A 87 421 181 HOH HOH . E 3 HOH A 88 422 182 HOH HOH . E 3 HOH A 89 423 183 HOH HOH . E 3 HOH A 90 424 184 HOH HOH . E 3 HOH A 91 425 185 HOH HOH . E 3 HOH A 92 426 186 HOH HOH . E 3 HOH A 93 427 188 HOH HOH . E 3 HOH A 94 428 194 HOH HOH . E 3 HOH A 95 429 196 HOH HOH . E 3 HOH A 96 430 197 HOH HOH . E 3 HOH A 97 431 198 HOH HOH . E 3 HOH A 98 432 199 HOH HOH . E 3 HOH A 99 433 200 HOH HOH . E 3 HOH A 100 434 202 HOH HOH . E 3 HOH A 101 435 203 HOH HOH . E 3 HOH A 102 436 205 HOH HOH . E 3 HOH A 103 437 206 HOH HOH . E 3 HOH A 104 438 207 HOH HOH . E 3 HOH A 105 439 210 HOH HOH . E 3 HOH A 106 440 211 HOH HOH . E 3 HOH A 107 441 214 HOH HOH . E 3 HOH A 108 442 224 HOH HOH . E 3 HOH A 109 443 227 HOH HOH . E 3 HOH A 110 444 231 HOH HOH . E 3 HOH A 111 445 233 HOH HOH . E 3 HOH A 112 446 236 HOH HOH . E 3 HOH A 113 447 237 HOH HOH . E 3 HOH A 114 448 242 HOH HOH . E 3 HOH A 115 449 244 HOH HOH . E 3 HOH A 116 450 245 HOH HOH . E 3 HOH A 117 451 252 HOH HOH . E 3 HOH A 118 452 253 HOH HOH . E 3 HOH A 119 453 254 HOH HOH . E 3 HOH A 120 454 255 HOH HOH . E 3 HOH A 121 455 256 HOH HOH . E 3 HOH A 122 456 257 HOH HOH . E 3 HOH A 123 457 258 HOH HOH . E 3 HOH A 124 458 259 HOH HOH . E 3 HOH A 125 459 260 HOH HOH . E 3 HOH A 126 460 261 HOH HOH . F 3 HOH B 1 334 2 HOH HOH . F 3 HOH B 2 335 3 HOH HOH . F 3 HOH B 3 336 9 HOH HOH . F 3 HOH B 4 337 13 HOH HOH . F 3 HOH B 5 338 14 HOH HOH . F 3 HOH B 6 339 17 HOH HOH . F 3 HOH B 7 340 18 HOH HOH . F 3 HOH B 8 341 20 HOH HOH . F 3 HOH B 9 342 21 HOH HOH . F 3 HOH B 10 343 24 HOH HOH . F 3 HOH B 11 344 25 HOH HOH . F 3 HOH B 12 345 28 HOH HOH . F 3 HOH B 13 346 31 HOH HOH . F 3 HOH B 14 347 32 HOH HOH . F 3 HOH B 15 348 33 HOH HOH . F 3 HOH B 16 349 34 HOH HOH . F 3 HOH B 17 350 37 HOH HOH . F 3 HOH B 18 351 40 HOH HOH . F 3 HOH B 19 352 44 HOH HOH . F 3 HOH B 20 353 45 HOH HOH . F 3 HOH B 21 354 46 HOH HOH . F 3 HOH B 22 355 48 HOH HOH . F 3 HOH B 23 356 50 HOH HOH . F 3 HOH B 24 357 52 HOH HOH . F 3 HOH B 25 358 53 HOH HOH . F 3 HOH B 26 359 55 HOH HOH . F 3 HOH B 27 360 56 HOH HOH . F 3 HOH B 28 361 58 HOH HOH . F 3 HOH B 29 362 60 HOH HOH . F 3 HOH B 30 363 66 HOH HOH . F 3 HOH B 31 364 67 HOH HOH . F 3 HOH B 32 365 75 HOH HOH . F 3 HOH B 33 366 77 HOH HOH . F 3 HOH B 34 367 80 HOH HOH . F 3 HOH B 35 368 83 HOH HOH . F 3 HOH B 36 369 84 HOH HOH . F 3 HOH B 37 370 86 HOH HOH . F 3 HOH B 38 371 88 HOH HOH . F 3 HOH B 39 372 90 HOH HOH . F 3 HOH B 40 373 91 HOH HOH . F 3 HOH B 41 374 92 HOH HOH . F 3 HOH B 42 375 99 HOH HOH . F 3 HOH B 43 376 101 HOH HOH . F 3 HOH B 44 377 103 HOH HOH . F 3 HOH B 45 378 104 HOH HOH . F 3 HOH B 46 379 105 HOH HOH . F 3 HOH B 47 380 106 HOH HOH . F 3 HOH B 48 381 110 HOH HOH . F 3 HOH B 49 382 111 HOH HOH . F 3 HOH B 50 383 113 HOH HOH . F 3 HOH B 51 384 114 HOH HOH . F 3 HOH B 52 385 115 HOH HOH . F 3 HOH B 53 386 119 HOH HOH . F 3 HOH B 54 387 121 HOH HOH . F 3 HOH B 55 388 123 HOH HOH . F 3 HOH B 56 389 125 HOH HOH . F 3 HOH B 57 390 127 HOH HOH . F 3 HOH B 58 391 128 HOH HOH . F 3 HOH B 59 392 129 HOH HOH . F 3 HOH B 60 393 130 HOH HOH . F 3 HOH B 61 394 132 HOH HOH . F 3 HOH B 62 395 134 HOH HOH . F 3 HOH B 63 396 135 HOH HOH . F 3 HOH B 64 397 136 HOH HOH . F 3 HOH B 65 398 137 HOH HOH . F 3 HOH B 66 399 140 HOH HOH . F 3 HOH B 67 400 141 HOH HOH . F 3 HOH B 68 402 142 HOH HOH . F 3 HOH B 69 403 143 HOH HOH . F 3 HOH B 70 404 144 HOH HOH . F 3 HOH B 71 405 145 HOH HOH . F 3 HOH B 72 406 149 HOH HOH . F 3 HOH B 73 407 151 HOH HOH . F 3 HOH B 74 408 154 HOH HOH . F 3 HOH B 75 409 155 HOH HOH . F 3 HOH B 76 410 156 HOH HOH . F 3 HOH B 77 411 157 HOH HOH . F 3 HOH B 78 412 158 HOH HOH . F 3 HOH B 79 413 162 HOH HOH . F 3 HOH B 80 414 164 HOH HOH . F 3 HOH B 81 415 165 HOH HOH . F 3 HOH B 82 416 166 HOH HOH . F 3 HOH B 83 417 167 HOH HOH . F 3 HOH B 84 418 168 HOH HOH . F 3 HOH B 85 419 169 HOH HOH . F 3 HOH B 86 420 172 HOH HOH . F 3 HOH B 87 421 173 HOH HOH . F 3 HOH B 88 422 176 HOH HOH . F 3 HOH B 89 423 177 HOH HOH . F 3 HOH B 90 424 179 HOH HOH . F 3 HOH B 91 425 180 HOH HOH . F 3 HOH B 92 426 187 HOH HOH . F 3 HOH B 93 427 189 HOH HOH . F 3 HOH B 94 428 190 HOH HOH . F 3 HOH B 95 429 191 HOH HOH . F 3 HOH B 96 430 192 HOH HOH . F 3 HOH B 97 431 193 HOH HOH . F 3 HOH B 98 432 195 HOH HOH . F 3 HOH B 99 433 201 HOH HOH . F 3 HOH B 100 434 204 HOH HOH . F 3 HOH B 101 435 208 HOH HOH . F 3 HOH B 102 436 209 HOH HOH . F 3 HOH B 103 437 212 HOH HOH . F 3 HOH B 104 438 213 HOH HOH . F 3 HOH B 105 439 215 HOH HOH . F 3 HOH B 106 440 216 HOH HOH . F 3 HOH B 107 441 218 HOH HOH . F 3 HOH B 108 442 219 HOH HOH . F 3 HOH B 109 443 220 HOH HOH . F 3 HOH B 110 444 221 HOH HOH . F 3 HOH B 111 445 222 HOH HOH . F 3 HOH B 112 446 223 HOH HOH . F 3 HOH B 113 447 225 HOH HOH . F 3 HOH B 114 448 226 HOH HOH . F 3 HOH B 115 449 228 HOH HOH . F 3 HOH B 116 450 229 HOH HOH . F 3 HOH B 117 451 230 HOH HOH . F 3 HOH B 118 452 232 HOH HOH . F 3 HOH B 119 453 234 HOH HOH . F 3 HOH B 120 454 235 HOH HOH . F 3 HOH B 121 455 238 HOH HOH . F 3 HOH B 122 456 239 HOH HOH . F 3 HOH B 123 457 240 HOH HOH . F 3 HOH B 124 458 241 HOH HOH . F 3 HOH B 125 459 243 HOH HOH . F 3 HOH B 126 460 246 HOH HOH . F 3 HOH B 127 461 247 HOH HOH . F 3 HOH B 128 462 249 HOH HOH . F 3 HOH B 129 463 262 HOH HOH . F 3 HOH B 130 464 263 HOH HOH . F 3 HOH B 131 465 264 HOH HOH . F 3 HOH B 132 466 265 HOH HOH . F 3 HOH B 133 467 266 HOH HOH . F 3 HOH B 134 468 267 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 P P AMP . . . D 2 -36.385 34.601 -2.997 1 53.39 ? P AMP 401 B 1 HETATM 2 O O1P AMP . . . D 2 -37.342 34.997 -1.811 1 43.37 ? O1P AMP 401 B 1 HETATM 3 O O2P AMP . . . D 2 -35.077 33.837 -2.651 1 53.06 ? O2P AMP 401 B 1 HETATM 4 O O3P AMP . . . D 2 -36.258 35.531 -4.21 1 56.26 ? O3P AMP 401 B 1 HETATM 5 O O5' AMP . . . D 2 -37.344 33.406 -3.435 1 63.98 ? O5' AMP 401 B 1 HETATM 6 C C5' AMP . . . D 2 -38.018 33.463 -4.649 1 62.6 ? C5' AMP 401 B 1 HETATM 7 C C4' AMP . . . D 2 -38.205 31.993 -4.947 1 62.86 ? C4' AMP 401 B 1 HETATM 8 O O4' AMP . . . D 2 -39.508 31.9 -5.464 1 54.08 ? O4' AMP 401 B 1 HETATM 9 C C3' AMP . . . D 2 -37.245 31.515 -6.013 1 62.74 ? C3' AMP 401 B 1 HETATM 10 O O3' AMP . . . D 2 -36.146 30.732 -5.556 1 62.1 ? O3' AMP 401 B 1 HETATM 11 C C2' AMP . . . D 2 -38.138 30.594 -6.774 1 64.9 ? C2' AMP 401 B 1 HETATM 12 O O2' AMP . . . D 2 -38.349 29.429 -5.938 1 62.45 ? O2' AMP 401 B 1 HETATM 13 C C1' AMP . . . D 2 -39.428 31.333 -6.762 1 58.45 ? C1' AMP 401 B 1 HETATM 14 N N9 AMP . . . D 2 -39.425 32.361 -7.831 1 63.16 ? N9 AMP 401 B 1 HETATM 15 C C8 AMP . . . D 2 -39.144 33.684 -7.731 1 60.11 ? C8 AMP 401 B 1 HETATM 16 N N7 AMP . . . D 2 -39.312 34.275 -8.958 1 67.12 ? N7 AMP 401 B 1 HETATM 17 C C5 AMP . . . D 2 -39.703 33.302 -9.822 1 63.62 ? C5 AMP 401 B 1 HETATM 18 C C6 AMP . . . D 2 -40.03 33.215 -11.259 1 69.39 ? C6 AMP 401 B 1 HETATM 19 N N6 AMP . . . D 2 -39.979 34.343 -12.003 1 74.84 ? N6 AMP 401 B 1 HETATM 20 N N1 AMP . . . D 2 -40.373 32.003 -11.79 1 61.79 ? N1 AMP 401 B 1 HETATM 21 C C2 AMP . . . D 2 -40.413 30.87 -11.043 1 63.17 ? C2 AMP 401 B 1 HETATM 22 N N3 AMP . . . D 2 -40.112 30.851 -9.71 1 59.74 ? N3 AMP 401 B 1 HETATM 23 C C4 AMP . . . D 2 -39.78 32.034 -9.082 1 59.84 ? C4 AMP 401 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 23 #