data_1P5Z # _model_server_result.job_id ivIU6pcxVySplPmogFld0A _model_server_result.datetime_utc '2024-10-16 10:23:22' _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 1p5z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 1P5Z # _exptl.entry_id 1P5Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1P5Z _cell.length_a 80.72 _cell.length_b 80.72 _cell.length_c 94.28 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P5Z _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 PISA,PQS _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 _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 80.72 80.72 47.14 # _struct_asym.details ? _struct_asym.entity_id 4 _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 OG SER 38 B SER 35 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 A OE1 GLU 130 B GLU 127 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 D O2B ADP . B ADP 301 1_555 B MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 B MG MG . B MG 401 1_555 E O HOH . B HOH 575 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc5 B MG MG . B MG 401 1_555 E O HOH . B HOH 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 B MG MG . B MG 401 1_555 E O HOH . B HOH 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1P5Z _atom_sites.fract_transf_matrix[1][1] 0.012389 _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] 0.012389 _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] 0.010607 _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 B 1 401 401 MG MG . C 3 AR3 B 1 304 304 AR3 ARA . D 4 ADP B 1 301 301 ADP ADP . E 5 HOH B 1 402 1 HOH HOH . E 5 HOH B 2 403 2 HOH HOH . E 5 HOH B 3 404 3 HOH HOH . E 5 HOH B 4 405 4 HOH HOH . E 5 HOH B 5 406 5 HOH HOH . E 5 HOH B 6 407 6 HOH HOH . E 5 HOH B 7 408 7 HOH HOH . E 5 HOH B 8 409 8 HOH HOH . E 5 HOH B 9 410 9 HOH HOH . E 5 HOH B 10 411 10 HOH HOH . E 5 HOH B 11 412 11 HOH HOH . E 5 HOH B 12 413 12 HOH HOH . E 5 HOH B 13 414 13 HOH HOH . E 5 HOH B 14 415 14 HOH HOH . E 5 HOH B 15 416 15 HOH HOH . E 5 HOH B 16 417 16 HOH HOH . E 5 HOH B 17 418 17 HOH HOH . E 5 HOH B 18 419 18 HOH HOH . E 5 HOH B 19 420 19 HOH HOH . E 5 HOH B 20 421 20 HOH HOH . E 5 HOH B 21 422 21 HOH HOH . E 5 HOH B 22 423 22 HOH HOH . E 5 HOH B 23 424 23 HOH HOH . E 5 HOH B 24 425 24 HOH HOH . E 5 HOH B 25 426 25 HOH HOH . E 5 HOH B 26 427 26 HOH HOH . E 5 HOH B 27 428 27 HOH HOH . E 5 HOH B 28 429 28 HOH HOH . E 5 HOH B 29 430 29 HOH HOH . E 5 HOH B 30 431 30 HOH HOH . E 5 HOH B 31 432 31 HOH HOH . E 5 HOH B 32 433 32 HOH HOH . E 5 HOH B 33 434 33 HOH HOH . E 5 HOH B 34 435 34 HOH HOH . E 5 HOH B 35 436 35 HOH HOH . E 5 HOH B 36 437 36 HOH HOH . E 5 HOH B 37 438 37 HOH HOH . E 5 HOH B 38 439 38 HOH HOH . E 5 HOH B 39 440 39 HOH HOH . E 5 HOH B 40 441 40 HOH HOH . E 5 HOH B 41 442 41 HOH HOH . E 5 HOH B 42 443 42 HOH HOH . E 5 HOH B 43 444 43 HOH HOH . E 5 HOH B 44 445 44 HOH HOH . E 5 HOH B 45 446 45 HOH HOH . E 5 HOH B 46 447 46 HOH HOH . E 5 HOH B 47 448 47 HOH HOH . E 5 HOH B 48 449 48 HOH HOH . E 5 HOH B 49 450 49 HOH HOH . E 5 HOH B 50 451 50 HOH HOH . E 5 HOH B 51 452 51 HOH HOH . E 5 HOH B 52 453 52 HOH HOH . E 5 HOH B 53 454 53 HOH HOH . E 5 HOH B 54 455 54 HOH HOH . E 5 HOH B 55 456 55 HOH HOH . E 5 HOH B 56 457 56 HOH HOH . E 5 HOH B 57 458 57 HOH HOH . E 5 HOH B 58 459 58 HOH HOH . E 5 HOH B 59 460 59 HOH HOH . E 5 HOH B 60 461 60 HOH HOH . E 5 HOH B 61 462 61 HOH HOH . E 5 HOH B 62 463 62 HOH HOH . E 5 HOH B 63 464 63 HOH HOH . E 5 HOH B 64 465 64 HOH HOH . E 5 HOH B 65 466 65 HOH HOH . E 5 HOH B 66 467 66 HOH HOH . E 5 HOH B 67 468 67 HOH HOH . E 5 HOH B 68 469 68 HOH HOH . E 5 HOH B 69 470 69 HOH HOH . E 5 HOH B 70 471 70 HOH HOH . E 5 HOH B 71 472 71 HOH HOH . E 5 HOH B 72 473 72 HOH HOH . E 5 HOH B 73 474 73 HOH HOH . E 5 HOH B 74 475 74 HOH HOH . E 5 HOH B 75 476 75 HOH HOH . E 5 HOH B 76 477 76 HOH HOH . E 5 HOH B 77 478 77 HOH HOH . E 5 HOH B 78 479 78 HOH HOH . E 5 HOH B 79 480 79 HOH HOH . E 5 HOH B 80 481 81 HOH HOH . E 5 HOH B 81 482 82 HOH HOH . E 5 HOH B 82 483 83 HOH HOH . E 5 HOH B 83 484 84 HOH HOH . E 5 HOH B 84 485 86 HOH HOH . E 5 HOH B 85 486 87 HOH HOH . E 5 HOH B 86 487 88 HOH HOH . E 5 HOH B 87 488 89 HOH HOH . E 5 HOH B 88 489 90 HOH HOH . E 5 HOH B 89 490 91 HOH HOH . E 5 HOH B 90 491 92 HOH HOH . E 5 HOH B 91 492 93 HOH HOH . E 5 HOH B 92 493 94 HOH HOH . E 5 HOH B 93 494 95 HOH HOH . E 5 HOH B 94 495 96 HOH HOH . E 5 HOH B 95 496 97 HOH HOH . E 5 HOH B 96 497 98 HOH HOH . E 5 HOH B 97 498 99 HOH HOH . E 5 HOH B 98 499 100 HOH HOH . E 5 HOH B 99 500 101 HOH HOH . E 5 HOH B 100 501 102 HOH HOH . E 5 HOH B 101 502 103 HOH HOH . E 5 HOH B 102 503 104 HOH HOH . E 5 HOH B 103 504 106 HOH HOH . E 5 HOH B 104 505 107 HOH HOH . E 5 HOH B 105 506 108 HOH HOH . E 5 HOH B 106 507 109 HOH HOH . E 5 HOH B 107 508 110 HOH HOH . E 5 HOH B 108 509 111 HOH HOH . E 5 HOH B 109 510 112 HOH HOH . E 5 HOH B 110 511 113 HOH HOH . E 5 HOH B 111 512 114 HOH HOH . E 5 HOH B 112 513 115 HOH HOH . E 5 HOH B 113 514 116 HOH HOH . E 5 HOH B 114 515 118 HOH HOH . E 5 HOH B 115 516 119 HOH HOH . E 5 HOH B 116 517 120 HOH HOH . E 5 HOH B 117 518 122 HOH HOH . E 5 HOH B 118 519 127 HOH HOH . E 5 HOH B 119 520 130 HOH HOH . E 5 HOH B 120 521 131 HOH HOH . E 5 HOH B 121 522 134 HOH HOH . E 5 HOH B 122 523 135 HOH HOH . E 5 HOH B 123 524 136 HOH HOH . E 5 HOH B 124 525 137 HOH HOH . E 5 HOH B 125 526 139 HOH HOH . E 5 HOH B 126 527 141 HOH HOH . E 5 HOH B 127 528 142 HOH HOH . E 5 HOH B 128 529 144 HOH HOH . E 5 HOH B 129 530 145 HOH HOH . E 5 HOH B 130 531 150 HOH HOH . E 5 HOH B 131 532 151 HOH HOH . E 5 HOH B 132 533 152 HOH HOH . E 5 HOH B 133 534 155 HOH HOH . E 5 HOH B 134 535 156 HOH HOH . E 5 HOH B 135 536 157 HOH HOH . E 5 HOH B 136 537 158 HOH HOH . E 5 HOH B 137 538 159 HOH HOH . E 5 HOH B 138 539 160 HOH HOH . E 5 HOH B 139 540 161 HOH HOH . E 5 HOH B 140 541 162 HOH HOH . E 5 HOH B 141 542 163 HOH HOH . E 5 HOH B 142 543 164 HOH HOH . E 5 HOH B 143 544 166 HOH HOH . E 5 HOH B 144 545 169 HOH HOH . E 5 HOH B 145 546 171 HOH HOH . E 5 HOH B 146 547 172 HOH HOH . E 5 HOH B 147 548 173 HOH HOH . E 5 HOH B 148 549 174 HOH HOH . E 5 HOH B 149 550 175 HOH HOH . E 5 HOH B 150 551 176 HOH HOH . E 5 HOH B 151 552 177 HOH HOH . E 5 HOH B 152 553 178 HOH HOH . E 5 HOH B 153 554 181 HOH HOH . E 5 HOH B 154 555 183 HOH HOH . E 5 HOH B 155 556 184 HOH HOH . E 5 HOH B 156 557 188 HOH HOH . E 5 HOH B 157 558 191 HOH HOH . E 5 HOH B 158 559 193 HOH HOH . E 5 HOH B 159 560 195 HOH HOH . E 5 HOH B 160 561 196 HOH HOH . E 5 HOH B 161 562 197 HOH HOH . E 5 HOH B 162 563 198 HOH HOH . E 5 HOH B 163 564 200 HOH HOH . E 5 HOH B 164 565 202 HOH HOH . E 5 HOH B 165 566 203 HOH HOH . E 5 HOH B 166 567 204 HOH HOH . E 5 HOH B 167 568 205 HOH HOH . E 5 HOH B 168 569 206 HOH HOH . E 5 HOH B 169 570 207 HOH HOH . E 5 HOH B 170 571 208 HOH HOH . E 5 HOH B 171 572 209 HOH HOH . E 5 HOH B 172 573 210 HOH HOH . E 5 HOH B 173 574 211 HOH HOH . E 5 HOH B 174 575 402 HOH HOH . E 5 HOH B 175 576 403 HOH HOH . E 5 HOH B 176 577 404 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 PB ADP . . . D 4 73.123 42.836 18.963 1 20.47 ? PB ADP 301 B 1 HETATM 2 O O1B ADP . . . D 4 73.307 41.367 19.338 1 21.34 ? O1B ADP 301 B 1 HETATM 3 O O2B ADP . . . D 4 72.17 43.594 19.873 1 22.48 ? O2B ADP 301 B 1 HETATM 4 O O3B ADP . . . D 4 72.784 43.1 17.527 1 20.37 ? O3B ADP 301 B 1 HETATM 5 P PA ADP . . . D 4 75.244 44.486 20.244 1 21.42 ? PA ADP 301 B 1 HETATM 6 O O1A ADP . . . D 4 74.626 45.823 20.125 1 20.67 ? O1A ADP 301 B 1 HETATM 7 O O2A ADP . . . D 4 75.133 43.705 21.533 1 23.12 ? O2A ADP 301 B 1 HETATM 8 O O3A ADP . . . D 4 74.593 43.549 19.099 1 20.67 ? O3A ADP 301 B 1 HETATM 9 O O5' ADP . . . D 4 76.748 44.637 19.8 1 20.05 ? O5' ADP 301 B 1 HETATM 10 C C5' ADP . . . D 4 77.681 43.545 19.829 1 18.8 ? C5' ADP 301 B 1 HETATM 11 C C4' ADP . . . D 4 79.104 43.998 20.086 1 19.34 ? C4' ADP 301 B 1 HETATM 12 O O4' ADP . . . D 4 79.589 44.733 18.94 1 20.75 ? O4' ADP 301 B 1 HETATM 13 C C3' ADP . . . D 4 79.236 44.944 21.296 1 21.64 ? C3' ADP 301 B 1 HETATM 14 O O3' ADP . . . D 4 80.468 44.675 21.959 1 23.93 ? O3' ADP 301 B 1 HETATM 15 C C2' ADP . . . D 4 79.173 46.334 20.689 1 23.29 ? C2' ADP 301 B 1 HETATM 16 O O2' ADP . . . D 4 79.921 47.311 21.395 1 25.58 ? O2' ADP 301 B 1 HETATM 17 C C1' ADP . . . D 4 79.841 46.101 19.353 1 22.2 ? C1' ADP 301 B 1 HETATM 18 N N9 ADP . . . D 4 79.364 46.916 18.24 1 23.24 ? N9 ADP 301 B 1 HETATM 19 C C8 ADP . . . D 4 78.11 46.855 17.691 1 23.96 ? C8 ADP 301 B 1 HETATM 20 N N7 ADP . . . D 4 78.014 47.683 16.598 1 23.33 ? N7 ADP 301 B 1 HETATM 21 C C5 ADP . . . D 4 79.234 48.235 16.457 1 21.33 ? C5 ADP 301 B 1 HETATM 22 C C6 ADP . . . D 4 79.788 49.156 15.461 1 23.1 ? C6 ADP 301 B 1 HETATM 23 N N6 ADP . . . D 4 79.068 49.565 14.48 1 23.19 ? N6 ADP 301 B 1 HETATM 24 N N1 ADP . . . D 4 81.062 49.45 15.658 1 24.58 ? N1 ADP 301 B 1 HETATM 25 C C2 ADP . . . D 4 81.931 48.99 16.68 1 25.63 ? C2 ADP 301 B 1 HETATM 26 N N3 ADP . . . D 4 81.33 48.084 17.612 1 24.05 ? N3 ADP 301 B 1 HETATM 27 C C4 ADP . . . D 4 80.023 47.729 17.446 1 22.67 ? C4 ADP 301 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #