data_1PHK # _model_server_result.job_id hbdaspSTbg0URp0sohsdFg _model_server_result.datetime_utc '2024-11-28 22:06:57' _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 1phk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":381}' # _entry.id 1PHK # _exptl.entry_id 1PHK _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 1PHK _cell.length_a 47.6 _cell.length_b 67.4 _cell.length_c 110.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PHK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,D,E _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 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 A OD1 ASN 154 A ASN 154 1_555 C MN MN . A MN 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc2 A OD1 ASP 167 A ASP 167 1_555 B MN MN . A MN 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc3 A OD2 ASP 167 A ASP 167 1_555 B MN MN . A MN 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc4 A OD2 ASP 167 A ASP 167 1_555 C MN MN . A MN 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc5 D O2B ATP . A ATP 381 1_555 B MN MN . A MN 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc6 D O3G ATP . A ATP 381 1_555 B MN MN . A MN 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc7 D O2G ATP . A ATP 381 1_555 C MN MN . A MN 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc8 D O2A ATP . A ATP 381 1_555 C MN MN . A MN 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc9 D O3B ATP . A ATP 381 1_555 C MN MN . A MN 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc10 B MN MN . A MN 382 1_555 E O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc11 C MN MN . A MN 383 1_555 E O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? # _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 1PHK _atom_sites.fract_transf_matrix[1][1] 0.021008 _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] 0.014837 _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] 0.009025 _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 MN A 1 382 382 MN MN . C 2 MN A 1 383 383 MN MN . D 3 ATP A 1 381 381 ATP ATP . E 4 HOH A 1 401 401 HOH HOH . E 4 HOH A 2 402 402 HOH HOH . E 4 HOH A 3 403 403 HOH HOH . E 4 HOH A 4 404 404 HOH HOH . E 4 HOH A 5 405 405 HOH HOH . E 4 HOH A 6 406 406 HOH HOH . E 4 HOH A 7 407 407 HOH HOH . E 4 HOH A 8 408 408 HOH HOH . E 4 HOH A 9 409 409 HOH HOH . E 4 HOH A 10 410 410 HOH HOH . E 4 HOH A 11 411 411 HOH HOH . E 4 HOH A 12 412 412 HOH HOH . E 4 HOH A 13 413 413 HOH HOH . E 4 HOH A 14 414 414 HOH HOH . E 4 HOH A 15 415 415 HOH HOH . E 4 HOH A 16 416 416 HOH HOH . E 4 HOH A 17 417 417 HOH HOH . E 4 HOH A 18 418 418 HOH HOH . E 4 HOH A 19 419 419 HOH HOH . E 4 HOH A 20 420 420 HOH HOH . E 4 HOH A 21 421 421 HOH HOH . E 4 HOH A 22 422 422 HOH HOH . E 4 HOH A 23 423 423 HOH HOH . E 4 HOH A 24 424 424 HOH HOH . E 4 HOH A 25 425 425 HOH HOH . E 4 HOH A 26 426 426 HOH HOH . E 4 HOH A 27 427 427 HOH HOH . E 4 HOH A 28 428 428 HOH HOH . E 4 HOH A 29 429 429 HOH HOH . E 4 HOH A 30 431 431 HOH HOH . E 4 HOH A 31 432 432 HOH HOH . E 4 HOH A 32 433 433 HOH HOH . E 4 HOH A 33 434 434 HOH HOH . E 4 HOH A 34 435 435 HOH HOH . E 4 HOH A 35 436 436 HOH HOH . E 4 HOH A 36 437 437 HOH HOH . E 4 HOH A 37 438 438 HOH HOH . E 4 HOH A 38 439 439 HOH HOH . E 4 HOH A 39 440 440 HOH HOH . E 4 HOH A 40 441 441 HOH HOH . E 4 HOH A 41 443 443 HOH HOH . E 4 HOH A 42 444 444 HOH HOH . E 4 HOH A 43 446 446 HOH HOH . E 4 HOH A 44 447 447 HOH HOH . E 4 HOH A 45 450 450 HOH HOH . E 4 HOH A 46 451 451 HOH HOH . E 4 HOH A 47 452 452 HOH HOH . E 4 HOH A 48 454 454 HOH HOH . E 4 HOH A 49 455 455 HOH HOH . E 4 HOH A 50 456 456 HOH HOH . E 4 HOH A 51 457 457 HOH HOH . E 4 HOH A 52 459 459 HOH HOH . E 4 HOH A 53 460 460 HOH HOH . E 4 HOH A 54 461 461 HOH HOH . E 4 HOH A 55 463 463 HOH HOH . E 4 HOH A 56 465 465 HOH HOH . E 4 HOH A 57 466 466 HOH HOH . E 4 HOH A 58 468 468 HOH HOH . E 4 HOH A 59 469 469 HOH HOH . E 4 HOH A 60 470 470 HOH HOH . E 4 HOH A 61 471 471 HOH HOH . E 4 HOH A 62 473 473 HOH HOH . E 4 HOH A 63 474 474 HOH HOH . E 4 HOH A 64 475 475 HOH HOH . E 4 HOH A 65 476 476 HOH HOH . E 4 HOH A 66 478 478 HOH HOH . E 4 HOH A 67 479 479 HOH HOH . E 4 HOH A 68 480 480 HOH HOH . E 4 HOH A 69 481 481 HOH HOH . E 4 HOH A 70 484 484 HOH HOH . E 4 HOH A 71 486 486 HOH HOH . E 4 HOH A 72 487 487 HOH HOH . E 4 HOH A 73 488 488 HOH HOH . E 4 HOH A 74 489 489 HOH HOH . E 4 HOH A 75 490 490 HOH HOH . E 4 HOH A 76 491 491 HOH HOH . E 4 HOH A 77 493 493 HOH HOH . E 4 HOH A 78 494 494 HOH HOH . E 4 HOH A 79 495 495 HOH HOH . E 4 HOH A 80 496 496 HOH HOH . E 4 HOH A 81 497 497 HOH HOH . E 4 HOH A 82 498 498 HOH HOH . E 4 HOH A 83 500 500 HOH HOH . E 4 HOH A 84 501 501 HOH HOH . E 4 HOH A 85 502 502 HOH HOH . E 4 HOH A 86 503 503 HOH HOH . E 4 HOH A 87 504 504 HOH HOH . E 4 HOH A 88 505 505 HOH HOH . E 4 HOH A 89 506 506 HOH HOH . E 4 HOH A 90 507 507 HOH HOH . E 4 HOH A 91 508 508 HOH HOH . E 4 HOH A 92 511 511 HOH HOH . E 4 HOH A 93 514 514 HOH HOH . E 4 HOH A 94 515 515 HOH HOH . E 4 HOH A 95 517 517 HOH HOH . E 4 HOH A 96 518 518 HOH HOH . E 4 HOH A 97 520 520 HOH HOH . E 4 HOH A 98 522 522 HOH HOH . E 4 HOH A 99 523 523 HOH HOH . E 4 HOH A 100 524 524 HOH HOH . E 4 HOH A 101 525 525 HOH HOH . E 4 HOH A 102 526 526 HOH HOH . E 4 HOH A 103 527 527 HOH HOH . E 4 HOH A 104 528 528 HOH HOH . E 4 HOH A 105 529 529 HOH HOH . E 4 HOH A 106 530 530 HOH HOH . E 4 HOH A 107 531 531 HOH HOH . E 4 HOH A 108 532 532 HOH HOH . E 4 HOH A 109 533 533 HOH HOH . E 4 HOH A 110 534 534 HOH HOH . E 4 HOH A 111 535 535 HOH HOH . E 4 HOH A 112 536 536 HOH HOH . E 4 HOH A 113 537 537 HOH HOH . E 4 HOH A 114 538 538 HOH HOH . E 4 HOH A 115 539 539 HOH HOH . E 4 HOH A 116 540 540 HOH HOH . E 4 HOH A 117 541 541 HOH HOH . E 4 HOH A 118 542 542 HOH HOH . E 4 HOH A 119 543 543 HOH HOH . E 4 HOH A 120 544 544 HOH HOH . E 4 HOH A 121 546 546 HOH HOH . E 4 HOH A 122 547 547 HOH HOH . E 4 HOH A 123 548 548 HOH HOH . E 4 HOH A 124 550 550 HOH HOH . E 4 HOH A 125 551 551 HOH HOH . E 4 HOH A 126 552 552 HOH HOH . E 4 HOH A 127 553 553 HOH HOH . E 4 HOH A 128 554 554 HOH HOH . E 4 HOH A 129 555 555 HOH HOH . E 4 HOH A 130 556 556 HOH HOH . E 4 HOH A 131 557 557 HOH HOH . E 4 HOH A 132 558 558 HOH HOH . E 4 HOH A 133 559 559 HOH HOH . E 4 HOH A 134 560 560 HOH HOH . E 4 HOH A 135 561 561 HOH HOH . E 4 HOH A 136 562 562 HOH HOH . E 4 HOH A 137 563 563 HOH HOH . E 4 HOH A 138 564 564 HOH HOH . E 4 HOH A 139 565 565 HOH HOH . E 4 HOH A 140 566 566 HOH HOH . E 4 HOH A 141 567 567 HOH HOH . E 4 HOH A 142 568 568 HOH HOH . E 4 HOH A 143 569 569 HOH HOH . E 4 HOH A 144 570 570 HOH HOH . E 4 HOH A 145 571 571 HOH HOH . E 4 HOH A 146 572 572 HOH HOH . E 4 HOH A 147 573 573 HOH HOH . E 4 HOH A 148 574 574 HOH HOH . E 4 HOH A 149 575 575 HOH HOH . E 4 HOH A 150 576 576 HOH HOH . E 4 HOH A 151 577 577 HOH HOH . E 4 HOH A 152 578 578 HOH HOH . E 4 HOH A 153 579 579 HOH HOH . E 4 HOH A 154 580 580 HOH HOH . E 4 HOH A 155 581 581 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 14.764 21.629 14.947 1 59.09 ? PG ATP 381 A 1 HETATM 2 O O1G ATP . . . D 3 16.192 21.428 14.593 1 54.58 ? O1G ATP 381 A 1 HETATM 3 O O2G ATP . . . D 3 13.94 22.221 13.823 1 45.73 ? O2G ATP 381 A 1 HETATM 4 O O3G ATP . . . D 3 14.686 22.548 16.051 1 51.18 ? O3G ATP 381 A 1 HETATM 5 P PB ATP . . . D 3 14.17 19.288 16.798 1 41.43 ? PB ATP 381 A 1 HETATM 6 O O1B ATP . . . D 3 15.544 18.953 17.198 1 43.9 ? O1B ATP 381 A 1 HETATM 7 O O2B ATP . . . D 3 13.325 19.952 17.782 1 43.62 ? O2B ATP 381 A 1 HETATM 8 O O3B ATP . . . D 3 14.153 20.169 15.444 1 48.49 ? O3B ATP 381 A 1 HETATM 9 P PA ATP . . . D 3 11.88 17.779 15.939 1 34.72 ? PA ATP 381 A 1 HETATM 10 O O1A ATP . . . D 3 11.018 17.583 17.114 1 34.38 ? O1A ATP 381 A 1 HETATM 11 O O2A ATP . . . D 3 11.437 18.846 15.064 1 42.31 ? O2A ATP 381 A 1 HETATM 12 O O3A ATP . . . D 3 13.395 18.012 16.381 1 31.9 ? O3A ATP 381 A 1 HETATM 13 O O5' ATP . . . D 3 12.036 16.424 15.124 1 46 ? O5' ATP 381 A 1 HETATM 14 C C5' ATP . . . D 3 13.155 16.417 14.182 1 36.1 ? C5' ATP 381 A 1 HETATM 15 C C4' ATP . . . D 3 12.822 15.627 12.919 1 36.96 ? C4' ATP 381 A 1 HETATM 16 O O4' ATP . . . D 3 12.607 14.238 13.321 1 32.69 ? O4' ATP 381 A 1 HETATM 17 C C3' ATP . . . D 3 11.516 15.987 12.221 1 37.04 ? C3' ATP 381 A 1 HETATM 18 O O3' ATP . . . D 3 11.658 17.024 11.33 1 35.74 ? O3' ATP 381 A 1 HETATM 19 C C2' ATP . . . D 3 11.067 14.645 11.601 1 39.91 ? C2' ATP 381 A 1 HETATM 20 O O2' ATP . . . D 3 11.634 14.319 10.36 1 40.28 ? O2' ATP 381 A 1 HETATM 21 C C1' ATP . . . D 3 11.52 13.664 12.614 1 33.46 ? C1' ATP 381 A 1 HETATM 22 N N9 ATP . . . D 3 10.459 13.258 13.554 1 31.09 ? N9 ATP 381 A 1 HETATM 23 C C8 ATP . . . D 3 10.124 14.05 14.648 1 23.76 ? C8 ATP 381 A 1 HETATM 24 N N7 ATP . . . D 3 8.972 13.726 15.218 1 28.92 ? N7 ATP 381 A 1 HETATM 25 C C5 ATP . . . D 3 8.547 12.609 14.498 1 26.71 ? C5 ATP 381 A 1 HETATM 26 C C6 ATP . . . D 3 7.417 11.684 14.62 1 24.35 ? C6 ATP 381 A 1 HETATM 27 N N6 ATP . . . D 3 6.525 11.677 15.605 1 18.95 ? N6 ATP 381 A 1 HETATM 28 N N1 ATP . . . D 3 7.263 10.781 13.613 1 29.49 ? N1 ATP 381 A 1 HETATM 29 C C2 ATP . . . D 3 8.183 10.741 12.614 1 26.99 ? C2 ATP 381 A 1 HETATM 30 N N3 ATP . . . D 3 9.388 11.29 12.607 1 26.06 ? N3 ATP 381 A 1 HETATM 31 C C4 ATP . . . D 3 9.416 12.383 13.416 1 31.56 ? C4 ATP 381 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 1322 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 31 #