data_1RDW # _model_server_result.job_id 2TG9smg2aNRgJQts32CF2Q _model_server_result.datetime_utc '2025-09-04 02:56:59' _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 1rdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":390}' # _entry.id 1RDW # _exptl.entry_id 1RDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 1RDW _cell.length_a 100.917 _cell.length_b 100.917 _cell.length_c 103.871 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 metalc ? metalc1 D O3G ATP . X ATP 390 1_555 B MG MG . X MG 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc2 D O2B ATP . X ATP 390 1_555 B MG MG . X MG 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 B MG MG . X MG 392 1_555 F O HOH . X HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc4 B MG MG . X MG 392 1_555 F O HOH . X HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc5 B MG MG . X MG 392 1_555 F O HOH . X HOH 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc6 B MG MG . X MG 392 1_555 F O HOH . X HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc7 B MG MG . X MG 392 1_555 F O HOH . X HOH 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 1RDW _atom_sites.fract_transf_matrix[1][1] 0.009909 _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] 0.009909 _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] 0.009627 _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 MG X 1 392 392 MG MG . C 2 MG X 1 393 393 MG MG . D 3 ATP X 1 390 390 ATP ATP . E 4 LAR X 1 391 391 LAR LAR . F 5 HOH X 1 401 401 HOH HOH . F 5 HOH X 2 402 402 HOH HOH . F 5 HOH X 3 403 403 HOH HOH . F 5 HOH X 4 404 404 HOH HOH . F 5 HOH X 5 405 405 HOH HOH . F 5 HOH X 6 406 406 HOH HOH . F 5 HOH X 7 407 407 HOH HOH . F 5 HOH X 8 408 408 HOH HOH . F 5 HOH X 9 409 409 HOH HOH . F 5 HOH X 10 410 410 HOH HOH . F 5 HOH X 11 411 411 HOH HOH . F 5 HOH X 12 412 412 HOH HOH . F 5 HOH X 13 413 413 HOH HOH . F 5 HOH X 14 414 414 HOH HOH . F 5 HOH X 15 415 415 HOH HOH . F 5 HOH X 16 416 416 HOH HOH . F 5 HOH X 17 417 417 HOH HOH . F 5 HOH X 18 418 418 HOH HOH . F 5 HOH X 19 419 419 HOH HOH . F 5 HOH X 20 420 420 HOH HOH . F 5 HOH X 21 421 421 HOH HOH . F 5 HOH X 22 422 422 HOH HOH . F 5 HOH X 23 423 423 HOH HOH . F 5 HOH X 24 424 424 HOH HOH . F 5 HOH X 25 425 425 HOH HOH . F 5 HOH X 26 426 426 HOH HOH . F 5 HOH X 27 427 427 HOH HOH . F 5 HOH X 28 428 428 HOH HOH . F 5 HOH X 29 429 429 HOH HOH . F 5 HOH X 30 430 430 HOH HOH . F 5 HOH X 31 431 431 HOH HOH . F 5 HOH X 32 432 432 HOH HOH . F 5 HOH X 33 433 433 HOH HOH . F 5 HOH X 34 434 434 HOH HOH . F 5 HOH X 35 435 435 HOH HOH . F 5 HOH X 36 436 436 HOH HOH . F 5 HOH X 37 437 437 HOH HOH . F 5 HOH X 38 438 438 HOH HOH . F 5 HOH X 39 439 439 HOH HOH . F 5 HOH X 40 440 440 HOH HOH . F 5 HOH X 41 441 441 HOH HOH . F 5 HOH X 42 442 442 HOH HOH . F 5 HOH X 43 443 443 HOH HOH . F 5 HOH X 44 444 444 HOH HOH . F 5 HOH X 45 445 445 HOH HOH . F 5 HOH X 46 446 446 HOH HOH . F 5 HOH X 47 447 447 HOH HOH . F 5 HOH X 48 448 448 HOH HOH . F 5 HOH X 49 449 449 HOH HOH . F 5 HOH X 50 450 450 HOH HOH . F 5 HOH X 51 451 451 HOH HOH . F 5 HOH X 52 452 452 HOH HOH . F 5 HOH X 53 453 453 HOH HOH . F 5 HOH X 54 454 454 HOH HOH . F 5 HOH X 55 455 455 HOH HOH . F 5 HOH X 56 456 456 HOH HOH . F 5 HOH X 57 457 457 HOH HOH . F 5 HOH X 58 458 458 HOH HOH . F 5 HOH X 59 459 459 HOH HOH . F 5 HOH X 60 460 460 HOH HOH . F 5 HOH X 61 461 461 HOH HOH . F 5 HOH X 62 462 462 HOH HOH . F 5 HOH X 63 463 463 HOH HOH . F 5 HOH X 64 464 464 HOH HOH . F 5 HOH X 65 465 465 HOH HOH . F 5 HOH X 66 466 466 HOH HOH . F 5 HOH X 67 467 467 HOH HOH . F 5 HOH X 68 468 468 HOH HOH . F 5 HOH X 69 469 469 HOH HOH . F 5 HOH X 70 470 470 HOH HOH . F 5 HOH X 71 471 471 HOH HOH . F 5 HOH X 72 472 472 HOH HOH . F 5 HOH X 73 473 473 HOH HOH . F 5 HOH X 74 474 474 HOH HOH . F 5 HOH X 75 475 475 HOH HOH . F 5 HOH X 76 476 476 HOH HOH . F 5 HOH X 77 477 477 HOH HOH . F 5 HOH X 78 478 478 HOH HOH . F 5 HOH X 79 479 479 HOH HOH . F 5 HOH X 80 480 480 HOH HOH . F 5 HOH X 81 481 481 HOH HOH . F 5 HOH X 82 482 482 HOH HOH . F 5 HOH X 83 483 483 HOH HOH . F 5 HOH X 84 484 484 HOH HOH . F 5 HOH X 85 485 485 HOH HOH . F 5 HOH X 86 486 486 HOH HOH . F 5 HOH X 87 487 487 HOH HOH . F 5 HOH X 88 488 488 HOH HOH . F 5 HOH X 89 489 489 HOH HOH . F 5 HOH X 90 490 490 HOH HOH . F 5 HOH X 91 491 491 HOH HOH . F 5 HOH X 92 492 492 HOH HOH . F 5 HOH X 93 493 493 HOH HOH . F 5 HOH X 94 494 494 HOH HOH . F 5 HOH X 95 495 495 HOH HOH . F 5 HOH X 96 496 496 HOH HOH . F 5 HOH X 97 497 497 HOH HOH . F 5 HOH X 98 498 498 HOH HOH . F 5 HOH X 99 499 499 HOH HOH . F 5 HOH X 100 500 500 HOH HOH . F 5 HOH X 101 501 501 HOH HOH . F 5 HOH X 102 502 502 HOH HOH . F 5 HOH X 103 503 503 HOH HOH . F 5 HOH X 104 504 504 HOH HOH . F 5 HOH X 105 505 505 HOH HOH . F 5 HOH X 106 506 506 HOH HOH . F 5 HOH X 107 507 507 HOH HOH . F 5 HOH X 108 508 508 HOH HOH . F 5 HOH X 109 509 509 HOH HOH . F 5 HOH X 110 510 510 HOH HOH . F 5 HOH X 111 511 511 HOH HOH . F 5 HOH X 112 512 512 HOH HOH . F 5 HOH X 113 513 513 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 PG ATP . . . D 3 85.018 75.905 26.682 1 24.26 ? PG ATP 390 X 1 HETATM 2 O O1G ATP . . . D 3 85.954 76.821 25.998 1 23.13 ? O1G ATP 390 X 1 HETATM 3 O O2G ATP . . . D 3 84.508 76.648 27.951 1 24.92 ? O2G ATP 390 X 1 HETATM 4 O O3G ATP . . . D 3 83.949 75.446 25.693 1 24.7 ? O3G ATP 390 X 1 HETATM 5 P PB ATP . . . D 3 86.107 73.248 26.581 1 27.64 ? PB ATP 390 X 1 HETATM 6 O O1B ATP . . . D 3 87.527 72.913 26.888 1 32.33 ? O1B ATP 390 X 1 HETATM 7 O O2B ATP . . . D 3 85.666 73.189 25.158 1 30.2 ? O2B ATP 390 X 1 HETATM 8 O O3B ATP . . . D 3 86.004 74.721 27.153 1 29.9 ? O3B ATP 390 X 1 HETATM 9 P PA ATP . . . D 3 84.655 70.968 27.419 1 27.7 ? PA ATP 390 X 1 HETATM 10 O O1A ATP . . . D 3 83.288 70.926 26.842 1 28.53 ? O1A ATP 390 X 1 HETATM 11 O O2A ATP . . . D 3 85.758 70.065 26.747 1 26.27 ? O2A ATP 390 X 1 HETATM 12 O O3A ATP . . . D 3 85.16 72.479 27.545 1 27.49 ? O3A ATP 390 X 1 HETATM 13 O O5' ATP . . . D 3 84.455 70.568 28.952 1 29.67 ? O5' ATP 390 X 1 HETATM 14 C C5' ATP . . . D 3 85.445 70.401 29.923 1 24.98 ? C5' ATP 390 X 1 HETATM 15 C C4' ATP . . . D 3 84.764 70.688 31.226 1 30.7 ? C4' ATP 390 X 1 HETATM 16 O O4' ATP . . . D 3 83.681 69.8 31.436 1 27.71 ? O4' ATP 390 X 1 HETATM 17 C C3' ATP . . . D 3 85.718 70.561 32.441 1 31.44 ? C3' ATP 390 X 1 HETATM 18 O O3' ATP . . . D 3 85.373 71.583 33.362 1 29.36 ? O3' ATP 390 X 1 HETATM 19 C C2' ATP . . . D 3 85.313 69.23 33.005 1 28.72 ? C2' ATP 390 X 1 HETATM 20 O O2' ATP . . . D 3 85.532 69.121 34.354 1 28.77 ? O2' ATP 390 X 1 HETATM 21 C C1' ATP . . . D 3 83.782 69.28 32.741 1 31.68 ? C1' ATP 390 X 1 HETATM 22 N N9 ATP . . . D 3 83.241 67.943 32.789 1 32.37 ? N9 ATP 390 X 1 HETATM 23 C C8 ATP . . . D 3 83.718 66.857 32.046 1 29.06 ? C8 ATP 390 X 1 HETATM 24 N N7 ATP . . . D 3 82.961 65.796 32.401 1 24.95 ? N7 ATP 390 X 1 HETATM 25 C C5 ATP . . . D 3 82.092 66.181 33.355 1 27.55 ? C5 ATP 390 X 1 HETATM 26 C C6 ATP . . . D 3 81.094 65.499 33.999 1 26.91 ? C6 ATP 390 X 1 HETATM 27 N N6 ATP . . . D 3 80.921 64.186 33.758 1 22.51 ? N6 ATP 390 X 1 HETATM 28 N N1 ATP . . . D 3 80.322 66.145 34.907 1 28.11 ? N1 ATP 390 X 1 HETATM 29 C C2 ATP . . . D 3 80.506 67.472 35.163 1 32.15 ? C2 ATP 390 X 1 HETATM 30 N N3 ATP . . . D 3 81.48 68.149 34.476 1 33.36 ? N3 ATP 390 X 1 HETATM 31 C C4 ATP . . . D 3 82.269 67.514 33.62 1 29.94 ? C4 ATP 390 X 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #