data_1MO5 # _model_server_result.job_id F5pFUp8lyBEiH1qZZbbjgw _model_server_result.datetime_utc '2024-11-09 23:19:12' _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 1mo5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 1MO5 # _exptl.entry_id 1MO5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 1MO5 _cell.length_a 108.032 _cell.length_b 108.032 _cell.length_c 72.475 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MO5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 1MO5 _atom_sites.fract_transf_matrix[1][1] 0.009257 _atom_sites.fract_transf_matrix[1][2] 0.005344 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010689 _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] 0.013798 _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 B 2 AGS A 1 500 500 AGS SAP . C 3 HOH A 1 501 330 HOH WAT . C 3 HOH A 2 502 331 HOH WAT . C 3 HOH A 3 503 332 HOH WAT . C 3 HOH A 4 504 333 HOH WAT . C 3 HOH A 5 505 334 HOH WAT . C 3 HOH A 6 506 335 HOH WAT . C 3 HOH A 7 507 336 HOH WAT . C 3 HOH A 8 508 337 HOH WAT . C 3 HOH A 9 509 338 HOH WAT . C 3 HOH A 10 510 339 HOH WAT . C 3 HOH A 11 511 340 HOH WAT . C 3 HOH A 12 512 341 HOH WAT . C 3 HOH A 13 513 342 HOH WAT . C 3 HOH A 14 514 343 HOH WAT . C 3 HOH A 15 515 344 HOH WAT . C 3 HOH A 16 516 345 HOH WAT . C 3 HOH A 17 517 346 HOH WAT . C 3 HOH A 18 518 347 HOH WAT . C 3 HOH A 19 519 348 HOH WAT . C 3 HOH A 20 520 349 HOH WAT . C 3 HOH A 21 521 350 HOH WAT . C 3 HOH A 22 522 351 HOH WAT . C 3 HOH A 23 523 352 HOH WAT . C 3 HOH A 24 524 353 HOH WAT . C 3 HOH A 25 525 354 HOH WAT . C 3 HOH A 26 526 355 HOH WAT . C 3 HOH A 27 527 356 HOH WAT . C 3 HOH A 28 528 357 HOH WAT . C 3 HOH A 29 529 358 HOH WAT . C 3 HOH A 30 530 359 HOH WAT . C 3 HOH A 31 531 360 HOH WAT . C 3 HOH A 32 532 361 HOH WAT . C 3 HOH A 33 533 362 HOH WAT . C 3 HOH A 34 534 363 HOH WAT . C 3 HOH A 35 535 364 HOH WAT . C 3 HOH A 36 536 365 HOH WAT . C 3 HOH A 37 537 366 HOH WAT . C 3 HOH A 38 538 367 HOH WAT . C 3 HOH A 39 539 368 HOH WAT . C 3 HOH A 40 540 369 HOH WAT . C 3 HOH A 41 541 370 HOH WAT . C 3 HOH A 42 542 371 HOH WAT . C 3 HOH A 43 543 372 HOH WAT . C 3 HOH A 44 544 373 HOH WAT . C 3 HOH A 45 545 374 HOH WAT . C 3 HOH A 46 546 375 HOH WAT . C 3 HOH A 47 547 376 HOH WAT . C 3 HOH A 48 548 377 HOH WAT . C 3 HOH A 49 549 378 HOH WAT . C 3 HOH A 50 550 379 HOH WAT . C 3 HOH A 51 551 380 HOH WAT . C 3 HOH A 52 552 381 HOH WAT . C 3 HOH A 53 553 382 HOH WAT . C 3 HOH A 54 554 383 HOH WAT . C 3 HOH A 55 555 384 HOH WAT . C 3 HOH A 56 556 385 HOH WAT . C 3 HOH A 57 557 386 HOH WAT . C 3 HOH A 58 558 387 HOH WAT . C 3 HOH A 59 559 388 HOH WAT . C 3 HOH A 60 560 389 HOH WAT . C 3 HOH A 61 561 390 HOH WAT . # 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 PG AGS . . . B 2 30.847 84.87 7.748 1 70.23 ? PG AGS 500 A 1 HETATM 2 S S1G AGS . . . B 2 30.285 82.986 7.869 1 70.23 ? S1G AGS 500 A 1 HETATM 3 O O2G AGS . . . B 2 30.924 85.733 6.436 1 70.23 ? O2G AGS 500 A 1 HETATM 4 O O3G AGS . . . B 2 30.733 85.681 9.022 1 70.23 ? O3G AGS 500 A 1 HETATM 5 P PB AGS . . . B 2 28.355 86.45 7.513 1 71.52 ? PB AGS 500 A 1 HETATM 6 O O1B AGS . . . B 2 27.425 86.431 6.377 1 71.52 ? O1B AGS 500 A 1 HETATM 7 O O2B AGS . . . B 2 28.318 87.174 8.796 1 71.52 ? O2B AGS 500 A 1 HETATM 8 O O3B AGS . . . B 2 29.221 85.131 7.657 1 71.52 ? O3B AGS 500 A 1 HETATM 9 P PA AGS . . . B 2 27.043 84.7 9.586 1 71.52 ? PA AGS 500 A 1 HETATM 10 O O1A AGS . . . B 2 26.483 83.361 9.222 1 71.52 ? O1A AGS 500 A 1 HETATM 11 O O2A AGS . . . B 2 28.352 84.64 10.335 1 71.52 ? O2A AGS 500 A 1 HETATM 12 O O3A AGS . . . B 2 27.208 85.55 8.197 1 71.52 ? O3A AGS 500 A 1 HETATM 13 O O5' AGS . . . B 2 25.895 85.568 10.337 1 71.52 ? O5' AGS 500 A 1 HETATM 14 C C5' AGS . . . B 2 26.395 86.404 11.4 1 71.52 ? C5' AGS 500 A 1 HETATM 15 C C4' AGS . . . B 2 25.44 86.578 12.583 1 71.52 ? C4' AGS 500 A 1 HETATM 16 O O4' AGS . . . B 2 24.678 85.339 12.872 1 71.52 ? O4' AGS 500 A 1 HETATM 17 C C3' AGS . . . B 2 26.082 86.916 13.932 1 71.52 ? C3' AGS 500 A 1 HETATM 18 O O3' AGS . . . B 2 25.295 87.811 14.724 1 71.52 ? O3' AGS 500 A 1 HETATM 19 C C2' AGS . . . B 2 26.337 85.514 14.54 1 71.52 ? C2' AGS 500 A 1 HETATM 20 O O2' AGS . . . B 2 26.517 85.459 15.938 1 71.52 ? O2' AGS 500 A 1 HETATM 21 C C1' AGS . . . B 2 25.172 84.684 14.07 1 71.52 ? C1' AGS 500 A 1 HETATM 22 N N9 AGS . . . B 2 25.517 83.214 13.8 1 71.52 ? N9 AGS 500 A 1 HETATM 23 C C8 AGS . . . B 2 26.018 82.765 12.591 1 71.52 ? C8 AGS 500 A 1 HETATM 24 N N7 AGS . . . B 2 26.271 81.449 12.524 1 71.52 ? N7 AGS 500 A 1 HETATM 25 C C5 AGS . . . B 2 25.924 80.985 13.772 1 71.52 ? C5 AGS 500 A 1 HETATM 26 C C6 AGS . . . B 2 25.946 79.663 14.397 1 71.52 ? C6 AGS 500 A 1 HETATM 27 N N6 AGS . . . B 2 26.36 78.531 13.782 1 71.52 ? N6 AGS 500 A 1 HETATM 28 N N1 AGS . . . B 2 25.509 79.567 15.698 1 71.52 ? N1 AGS 500 A 1 HETATM 29 C C2 AGS . . . B 2 25.079 80.693 16.36 1 71.52 ? C2 AGS 500 A 1 HETATM 30 N N3 AGS . . . B 2 25.016 81.972 15.884 1 71.52 ? N3 AGS 500 A 1 HETATM 31 C C4 AGS . . . B 2 25.453 82.066 14.577 1 71.52 ? C4 AGS 500 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #