data_9NTO # _model_server_result.job_id VCb04fAHvCYN8FAGhFJhoA _model_server_result.datetime_utc '2025-07-12 17:05:13' _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 9nto # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 9NTO # _exptl.entry_id 9NTO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _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 9NTO _cell.length_a 92.664 _cell.length_b 58.219 _cell.length_c 89.228 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9NTO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 58.219 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A N GLY 1 A GLY 2 1_555 D C7A 2KA . A 2KA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 B SG CYS 169 B CYS 169 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc2 B SG CYS 177 B CYS 177 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 B SG CYS 180 B CYS 180 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 B SG CYS 183 B CYS 183 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _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 68 n n P O2P AMP sing 69 n n P O3P AMP sing 70 n n P O5' AMP sing 71 n n O2P HOP2 AMP sing 72 n n O3P HOP3 AMP sing 73 n n O5' C5' AMP sing 74 n n C5' C4' AMP sing 75 n n C5' "H5'1" AMP sing 76 n n C5' "H5'2" AMP sing 77 n n C4' O4' AMP sing 78 n n C4' C3' AMP sing 79 n n C4' H4' AMP sing 80 n n O4' C1' AMP sing 81 n n C3' O3' AMP sing 82 n n C3' C2' AMP sing 83 n n C3' H3' AMP sing 84 n n O3' HO3' AMP sing 85 n n C2' O2' AMP sing 86 n n C2' C1' AMP sing 87 n n C2' H2' AMP sing 88 n n O2' HO2' AMP sing 89 n n C1' N9 AMP sing 90 n n C1' H1' AMP sing 91 n n N9 C8 AMP sing 92 n y N9 C4 AMP sing 93 n y C8 N7 AMP doub 94 n y C8 H8 AMP sing 95 n n N7 C5 AMP sing 96 n y C5 C6 AMP sing 97 n y C5 C4 AMP doub 98 n y C6 N6 AMP sing 99 n n C6 N1 AMP doub 100 n y N6 HN61 AMP sing 101 n n N6 HN62 AMP sing 102 n n N1 C2 AMP sing 103 n y C2 N3 AMP doub 104 n y C2 H2 AMP sing 105 n n N3 C4 AMP sing 106 n y # _atom_sites.entry_id 9NTO _atom_sites.fract_transf_matrix[1][1] 0.010792 _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] 0.017177 _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] 0.011207 _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 AMP A 1 401 1 AMP AMP . D 4 2KA A 1 402 2 2KA LIG . E 5 ZN B 1 201 1 ZN ZN . F 6 ADN B 1 202 1 ADN ADN . G 7 HOH A 1 501 185 HOH HOH . G 7 HOH A 2 502 10 HOH HOH . G 7 HOH A 3 503 78 HOH HOH . G 7 HOH A 4 504 114 HOH HOH . G 7 HOH A 5 505 121 HOH HOH . G 7 HOH A 6 506 99 HOH HOH . G 7 HOH A 7 507 75 HOH HOH . G 7 HOH A 8 508 105 HOH HOH . G 7 HOH A 9 509 79 HOH HOH . G 7 HOH A 10 510 196 HOH HOH . G 7 HOH A 11 511 76 HOH HOH . G 7 HOH A 12 512 35 HOH HOH . G 7 HOH A 13 513 44 HOH HOH . G 7 HOH A 14 514 49 HOH HOH . G 7 HOH A 15 515 20 HOH HOH . G 7 HOH A 16 516 41 HOH HOH . G 7 HOH A 17 517 153 HOH HOH . G 7 HOH A 18 518 93 HOH HOH . G 7 HOH A 19 519 107 HOH HOH . G 7 HOH A 20 520 139 HOH HOH . G 7 HOH A 21 521 29 HOH HOH . G 7 HOH A 22 522 66 HOH HOH . G 7 HOH A 23 523 123 HOH HOH . G 7 HOH A 24 524 204 HOH HOH . G 7 HOH A 25 525 84 HOH HOH . G 7 HOH A 26 526 48 HOH HOH . G 7 HOH A 27 527 82 HOH HOH . G 7 HOH A 28 528 186 HOH HOH . G 7 HOH A 29 529 120 HOH HOH . G 7 HOH A 30 530 4 HOH HOH . G 7 HOH A 31 531 50 HOH HOH . G 7 HOH A 32 532 81 HOH HOH . G 7 HOH A 33 533 191 HOH HOH . G 7 HOH A 34 534 206 HOH HOH . G 7 HOH A 35 535 34 HOH HOH . G 7 HOH A 36 536 37 HOH HOH . G 7 HOH A 37 537 63 HOH HOH . G 7 HOH A 38 538 202 HOH HOH . G 7 HOH A 39 539 104 HOH HOH . G 7 HOH A 40 540 122 HOH HOH . G 7 HOH A 41 541 88 HOH HOH . G 7 HOH A 42 542 40 HOH HOH . G 7 HOH A 43 543 54 HOH HOH . G 7 HOH A 44 544 65 HOH HOH . G 7 HOH A 45 545 158 HOH HOH . G 7 HOH A 46 546 45 HOH HOH . G 7 HOH A 47 547 103 HOH HOH . G 7 HOH A 48 548 194 HOH HOH . G 7 HOH A 49 549 207 HOH HOH . G 7 HOH A 50 550 100 HOH HOH . G 7 HOH A 51 551 132 HOH HOH . G 7 HOH A 52 552 143 HOH HOH . G 7 HOH A 53 553 180 HOH HOH . G 7 HOH A 54 554 115 HOH HOH . G 7 HOH A 55 555 70 HOH HOH . G 7 HOH A 56 556 166 HOH HOH . G 7 HOH A 57 557 21 HOH HOH . G 7 HOH A 58 558 68 HOH HOH . G 7 HOH A 59 559 73 HOH HOH . G 7 HOH A 60 560 95 HOH HOH . G 7 HOH A 61 561 96 HOH HOH . G 7 HOH A 62 562 145 HOH HOH . G 7 HOH A 63 563 160 HOH HOH . G 7 HOH A 64 564 77 HOH HOH . G 7 HOH A 65 565 178 HOH HOH . G 7 HOH A 66 566 108 HOH HOH . G 7 HOH A 67 567 169 HOH HOH . G 7 HOH A 68 568 189 HOH HOH . G 7 HOH A 69 569 94 HOH HOH . G 7 HOH A 70 570 106 HOH HOH . G 7 HOH A 71 571 46 HOH HOH . G 7 HOH A 72 572 146 HOH HOH . G 7 HOH A 73 573 134 HOH HOH . G 7 HOH A 74 574 80 HOH HOH . G 7 HOH A 75 575 162 HOH HOH . G 7 HOH A 76 576 199 HOH HOH . G 7 HOH A 77 577 111 HOH HOH . G 7 HOH A 78 578 198 HOH HOH . G 7 HOH A 79 579 203 HOH HOH . G 7 HOH A 80 580 179 HOH HOH . G 7 HOH A 81 581 69 HOH HOH . G 7 HOH A 82 582 167 HOH HOH . G 7 HOH A 83 583 200 HOH HOH . G 7 HOH A 84 584 67 HOH HOH . G 7 HOH A 85 585 117 HOH HOH . G 7 HOH A 86 586 184 HOH HOH . G 7 HOH A 87 587 140 HOH HOH . G 7 HOH A 88 588 142 HOH HOH . G 7 HOH A 89 589 211 HOH HOH . G 7 HOH A 90 590 62 HOH HOH . G 7 HOH A 91 591 174 HOH HOH . G 7 HOH A 92 592 171 HOH HOH . G 7 HOH A 93 593 205 HOH HOH . G 7 HOH A 94 594 135 HOH HOH . G 7 HOH A 95 595 138 HOH HOH . G 7 HOH A 96 596 61 HOH HOH . G 7 HOH A 97 597 98 HOH HOH . G 7 HOH A 98 598 85 HOH HOH . G 7 HOH A 99 599 119 HOH HOH . G 7 HOH A 100 600 208 HOH HOH . H 7 HOH B 1 301 197 HOH HOH . H 7 HOH B 2 302 159 HOH HOH . H 7 HOH B 3 303 5 HOH HOH . H 7 HOH B 4 304 12 HOH HOH . H 7 HOH B 5 305 7 HOH HOH . H 7 HOH B 6 306 19 HOH HOH . H 7 HOH B 7 307 28 HOH HOH . H 7 HOH B 8 308 31 HOH HOH . H 7 HOH B 9 309 60 HOH HOH . H 7 HOH B 10 310 22 HOH HOH . H 7 HOH B 11 311 116 HOH HOH . H 7 HOH B 12 312 113 HOH HOH . H 7 HOH B 13 313 157 HOH HOH . H 7 HOH B 14 314 8 HOH HOH . H 7 HOH B 15 315 51 HOH HOH . H 7 HOH B 16 316 57 HOH HOH . H 7 HOH B 17 317 39 HOH HOH . H 7 HOH B 18 318 83 HOH HOH . H 7 HOH B 19 319 91 HOH HOH . H 7 HOH B 20 320 2 HOH HOH . H 7 HOH B 21 321 27 HOH HOH . H 7 HOH B 22 322 14 HOH HOH . H 7 HOH B 23 323 144 HOH HOH . H 7 HOH B 24 324 173 HOH HOH . H 7 HOH B 25 325 17 HOH HOH . H 7 HOH B 26 326 89 HOH HOH . H 7 HOH B 27 327 127 HOH HOH . H 7 HOH B 28 328 24 HOH HOH . H 7 HOH B 29 329 55 HOH HOH . H 7 HOH B 30 330 36 HOH HOH . H 7 HOH B 31 331 6 HOH HOH . H 7 HOH B 32 332 11 HOH HOH . H 7 HOH B 33 333 13 HOH HOH . H 7 HOH B 34 334 128 HOH HOH . H 7 HOH B 35 335 23 HOH HOH . H 7 HOH B 36 336 1 HOH HOH . H 7 HOH B 37 337 32 HOH HOH . H 7 HOH B 38 338 26 HOH HOH . H 7 HOH B 39 339 86 HOH HOH . H 7 HOH B 40 340 101 HOH HOH . H 7 HOH B 41 341 154 HOH HOH . H 7 HOH B 42 342 92 HOH HOH . H 7 HOH B 43 343 47 HOH HOH . H 7 HOH B 44 344 210 HOH HOH . H 7 HOH B 45 345 136 HOH HOH . H 7 HOH B 46 346 176 HOH HOH . H 7 HOH B 47 347 56 HOH HOH . H 7 HOH B 48 348 25 HOH HOH . H 7 HOH B 49 349 58 HOH HOH . H 7 HOH B 50 350 97 HOH HOH . H 7 HOH B 51 351 16 HOH HOH . H 7 HOH B 52 352 71 HOH HOH . H 7 HOH B 53 353 87 HOH HOH . H 7 HOH B 54 354 30 HOH HOH . H 7 HOH B 55 355 110 HOH HOH . H 7 HOH B 56 356 141 HOH HOH . H 7 HOH B 57 357 9 HOH HOH . H 7 HOH B 58 358 187 HOH HOH . H 7 HOH B 59 359 72 HOH HOH . H 7 HOH B 60 360 3 HOH HOH . H 7 HOH B 61 361 53 HOH HOH . H 7 HOH B 62 362 172 HOH HOH . H 7 HOH B 63 363 112 HOH HOH . H 7 HOH B 64 364 193 HOH HOH . H 7 HOH B 65 365 109 HOH HOH . H 7 HOH B 66 366 148 HOH HOH . H 7 HOH B 67 367 15 HOH HOH . H 7 HOH B 68 368 177 HOH HOH . H 7 HOH B 69 369 33 HOH HOH . H 7 HOH B 70 370 150 HOH HOH . H 7 HOH B 71 371 149 HOH HOH . H 7 HOH B 72 372 74 HOH HOH . H 7 HOH B 73 373 181 HOH HOH . H 7 HOH B 74 374 90 HOH HOH . H 7 HOH B 75 375 183 HOH HOH . H 7 HOH B 76 376 156 HOH HOH . H 7 HOH B 77 377 43 HOH HOH . H 7 HOH B 78 378 137 HOH HOH . H 7 HOH B 79 379 38 HOH HOH . H 7 HOH B 80 380 131 HOH HOH . H 7 HOH B 81 381 18 HOH HOH . H 7 HOH B 82 382 164 HOH HOH . H 7 HOH B 83 383 192 HOH HOH . H 7 HOH B 84 384 42 HOH HOH . H 7 HOH B 85 385 188 HOH HOH . H 7 HOH B 86 386 125 HOH HOH . H 7 HOH B 87 387 64 HOH HOH . H 7 HOH B 88 388 118 HOH HOH . H 7 HOH B 89 389 129 HOH HOH . H 7 HOH B 90 390 147 HOH HOH . H 7 HOH B 91 391 102 HOH HOH . H 7 HOH B 92 392 52 HOH HOH . H 7 HOH B 93 393 190 HOH HOH . H 7 HOH B 94 394 168 HOH HOH . H 7 HOH B 95 395 130 HOH HOH . H 7 HOH B 96 396 201 HOH HOH . H 7 HOH B 97 397 133 HOH HOH . H 7 HOH B 98 398 163 HOH HOH . H 7 HOH B 99 399 195 HOH HOH . H 7 HOH B 100 400 170 HOH HOH . H 7 HOH B 101 401 124 HOH HOH . H 7 HOH B 102 402 165 HOH HOH . H 7 HOH B 103 403 152 HOH HOH . H 7 HOH B 104 404 151 HOH HOH . H 7 HOH B 105 405 161 HOH HOH . H 7 HOH B 106 406 155 HOH HOH . H 7 HOH B 107 407 182 HOH HOH . H 7 HOH B 108 408 126 HOH HOH . H 7 HOH B 109 409 209 HOH HOH . H 7 HOH B 110 410 59 HOH HOH . H 7 HOH B 111 411 175 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 P P AMP . . . C 3 -18.08 23.042 -34.268 1 49.31 ? P AMP 401 A 1 HETATM 2 O O1P AMP . . . C 3 -18.102 23.355 -32.791 1 57.25 ? O1P AMP 401 A 1 HETATM 3 O O2P AMP . . . C 3 -18.241 21.578 -34.587 1 60.07 ? O2P AMP 401 A 1 HETATM 4 O O3P AMP . . . C 3 -16.996 23.768 -35.028 1 48.75 ? O3P AMP 401 A 1 HETATM 5 O O5' AMP . . . C 3 -19.439 23.661 -34.817 1 43.44 ? O5' AMP 401 A 1 HETATM 6 C C5' AMP . . . C 3 -20.569 23.813 -33.966 1 45.51 ? C5' AMP 401 A 1 HETATM 7 C C4' AMP . . . C 3 -21.752 24.384 -34.708 1 50.43 ? C4' AMP 401 A 1 HETATM 8 O O4' AMP . . . C 3 -21.468 25.763 -35.052 1 44.27 ? O4' AMP 401 A 1 HETATM 9 C C3' AMP . . . C 3 -22.116 23.681 -36.011 1 48.03 ? C3' AMP 401 A 1 HETATM 10 O O3' AMP . . . C 3 -23.527 23.75 -36.208 1 55.47 ? O3' AMP 401 A 1 HETATM 11 C C2' AMP . . . C 3 -21.411 24.53 -37.066 1 48.09 ? C2' AMP 401 A 1 HETATM 12 O O2' AMP . . . C 3 -22.005 24.482 -38.347 1 46.54 ? O2' AMP 401 A 1 HETATM 13 C C1' AMP . . . C 3 -21.485 25.932 -36.457 1 45.07 ? C1' AMP 401 A 1 HETATM 14 N N9 AMP . . . C 3 -20.345 26.784 -36.801 1 44.33 ? N9 AMP 401 A 1 HETATM 15 C C8 AMP . . . C 3 -19.067 26.368 -36.872 1 40.83 ? C8 AMP 401 A 1 HETATM 16 N N7 AMP . . . C 3 -18.236 27.386 -37.205 1 41.58 ? N7 AMP 401 A 1 HETATM 17 C C5 AMP . . . C 3 -18.991 28.488 -37.353 1 39.34 ? C5 AMP 401 A 1 HETATM 18 C C6 AMP . . . C 3 -18.744 29.905 -37.701 1 37.88 ? C6 AMP 401 A 1 HETATM 19 N N6 AMP . . . C 3 -17.493 30.355 -37.964 1 35.88 ? N6 AMP 401 A 1 HETATM 20 N N1 AMP . . . C 3 -19.811 30.732 -37.748 1 38.43 ? N1 AMP 401 A 1 HETATM 21 C C2 AMP . . . C 3 -21.057 30.297 -37.487 1 41.89 ? C2 AMP 401 A 1 HETATM 22 N N3 AMP . . . C 3 -21.355 29.025 -37.168 1 43.98 ? N3 AMP 401 A 1 HETATM 23 C C4 AMP . . . C 3 -20.382 28.087 -37.088 1 43.49 ? C4 AMP 401 A 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #