data_5ORK # _model_server_result.job_id gXTUQhS_cHuoAWHeelptCw _model_server_result.datetime_utc '2024-11-28 10:32:38' _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 5ork # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5ORK # _exptl.entry_id 5ORK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5ORK _cell.length_a 64.98 _cell.length_b 68.738 _cell.length_c 332.075 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORK _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _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,F,G,H,I,J,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 B OD1 ASN 184 A ASN 161 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc2 B OD2 ASP 198 A ASP 175 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc3 D O1B ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc4 D O1A ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc5 D O2A ADP . A ADP 401 1_555 F MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc6 E MG MG . A MG 402 1_555 K O HOH . A HOH 563 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? # _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 29 n n PB O2B ADP sing 30 n n PB O3B ADP sing 31 n n PB O3A ADP sing 32 n n O2B HOB2 ADP sing 33 n n O3B HOB3 ADP sing 34 n n PA O1A ADP doub 35 n n PA O2A ADP sing 36 n n PA O3A ADP sing 37 n n PA O5' ADP sing 38 n n O2A HOA2 ADP sing 39 n n O5' C5' ADP sing 40 n n C5' C4' ADP sing 41 n n C5' "H5'1" ADP sing 42 n n C5' "H5'2" ADP sing 43 n n C4' O4' ADP sing 44 n n C4' C3' ADP sing 45 n n C4' H4' ADP sing 46 n n O4' C1' ADP sing 47 n n C3' O3' ADP sing 48 n n C3' C2' ADP sing 49 n n C3' H3' ADP sing 50 n n O3' HO3' ADP sing 51 n n C2' O2' ADP sing 52 n n C2' C1' ADP sing 53 n n C2' H2' ADP sing 54 n n O2' HO2' ADP sing 55 n n C1' N9 ADP sing 56 n n C1' H1' ADP sing 57 n n N9 C8 ADP sing 58 n y N9 C4 ADP sing 59 n y C8 N7 ADP doub 60 n y C8 H8 ADP sing 61 n n N7 C5 ADP sing 62 n y C5 C6 ADP sing 63 n y C5 C4 ADP doub 64 n y C6 N6 ADP sing 65 n n C6 N1 ADP doub 66 n y N6 HN61 ADP sing 67 n n N6 HN62 ADP sing 68 n n N1 C2 ADP sing 69 n y C2 N3 ADP doub 70 n y C2 H2 ADP sing 71 n n N3 C4 ADP sing 72 n y # _atom_sites.entry_id 5ORK _atom_sites.fract_transf_matrix[1][1] 0.015389 _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] 0.014548 _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] 0.003011 _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 2 ADP B 1 401 2 ADP ADP . D 2 ADP A 1 401 1 ADP ADP . E 3 MG A 1 402 1 MG MG . F 3 MG A 1 403 2 MG MG . G 4 A4T A 1 404 1 A4T 008 . H 5 CL A 1 405 1 CL CL . I 6 PO4 A 1 406 1 PO4 PO4 . J 7 HOH B 1 501 168 HOH HOH . J 7 HOH B 2 502 166 HOH HOH . J 7 HOH B 3 503 115 HOH HOH . J 7 HOH B 4 504 117 HOH HOH . J 7 HOH B 5 505 143 HOH HOH . J 7 HOH B 6 506 27 HOH HOH . J 7 HOH B 7 507 140 HOH HOH . J 7 HOH B 8 508 47 HOH HOH . J 7 HOH B 9 509 40 HOH HOH . J 7 HOH B 10 510 138 HOH HOH . J 7 HOH B 11 511 61 HOH HOH . J 7 HOH B 12 512 161 HOH HOH . J 7 HOH B 13 513 156 HOH HOH . J 7 HOH B 14 514 71 HOH HOH . J 7 HOH B 15 515 52 HOH HOH . J 7 HOH B 16 516 87 HOH HOH . J 7 HOH B 17 517 99 HOH HOH . J 7 HOH B 18 518 141 HOH HOH . J 7 HOH B 19 519 17 HOH HOH . J 7 HOH B 20 520 162 HOH HOH . J 7 HOH B 21 521 79 HOH HOH . J 7 HOH B 22 522 109 HOH HOH . J 7 HOH B 23 523 14 HOH HOH . J 7 HOH B 24 524 34 HOH HOH . J 7 HOH B 25 525 64 HOH HOH . J 7 HOH B 26 526 149 HOH HOH . J 7 HOH B 27 527 16 HOH HOH . J 7 HOH B 28 528 37 HOH HOH . J 7 HOH B 29 529 43 HOH HOH . J 7 HOH B 30 530 120 HOH HOH . J 7 HOH B 31 531 46 HOH HOH . J 7 HOH B 32 532 129 HOH HOH . J 7 HOH B 33 533 150 HOH HOH . J 7 HOH B 34 534 68 HOH HOH . J 7 HOH B 35 535 134 HOH HOH . J 7 HOH B 36 536 63 HOH HOH . J 7 HOH B 37 537 121 HOH HOH . J 7 HOH B 38 538 55 HOH HOH . J 7 HOH B 39 539 96 HOH HOH . J 7 HOH B 40 540 142 HOH HOH . J 7 HOH B 41 541 74 HOH HOH . J 7 HOH B 42 542 107 HOH HOH . J 7 HOH B 43 543 135 HOH HOH . J 7 HOH B 44 544 97 HOH HOH . J 7 HOH B 45 545 154 HOH HOH . J 7 HOH B 46 546 72 HOH HOH . J 7 HOH B 47 547 130 HOH HOH . J 7 HOH B 48 548 133 HOH HOH . J 7 HOH B 49 549 164 HOH HOH . K 7 HOH A 1 501 139 HOH HOH . K 7 HOH A 2 502 118 HOH HOH . K 7 HOH A 3 503 114 HOH HOH . K 7 HOH A 4 504 5 HOH HOH . K 7 HOH A 5 505 41 HOH HOH . K 7 HOH A 6 506 13 HOH HOH . K 7 HOH A 7 507 53 HOH HOH . K 7 HOH A 8 508 28 HOH HOH . K 7 HOH A 9 509 146 HOH HOH . K 7 HOH A 10 510 23 HOH HOH . K 7 HOH A 11 511 148 HOH HOH . K 7 HOH A 12 512 21 HOH HOH . K 7 HOH A 13 513 12 HOH HOH . K 7 HOH A 14 514 159 HOH HOH . K 7 HOH A 15 515 22 HOH HOH . K 7 HOH A 16 516 59 HOH HOH . K 7 HOH A 17 517 50 HOH HOH . K 7 HOH A 18 518 29 HOH HOH . K 7 HOH A 19 519 19 HOH HOH . K 7 HOH A 20 520 30 HOH HOH . K 7 HOH A 21 521 167 HOH HOH . K 7 HOH A 22 522 26 HOH HOH . K 7 HOH A 23 523 82 HOH HOH . K 7 HOH A 24 524 78 HOH HOH . K 7 HOH A 25 525 136 HOH HOH . K 7 HOH A 26 526 1 HOH HOH . K 7 HOH A 27 527 70 HOH HOH . K 7 HOH A 28 528 51 HOH HOH . K 7 HOH A 29 529 119 HOH HOH . K 7 HOH A 30 530 83 HOH HOH . K 7 HOH A 31 531 101 HOH HOH . K 7 HOH A 32 532 2 HOH HOH . K 7 HOH A 33 533 25 HOH HOH . K 7 HOH A 34 534 9 HOH HOH . K 7 HOH A 35 535 7 HOH HOH . K 7 HOH A 36 536 15 HOH HOH . K 7 HOH A 37 537 62 HOH HOH . K 7 HOH A 38 538 116 HOH HOH . K 7 HOH A 39 539 24 HOH HOH . K 7 HOH A 40 540 128 HOH HOH . K 7 HOH A 41 541 32 HOH HOH . K 7 HOH A 42 542 48 HOH HOH . K 7 HOH A 43 543 65 HOH HOH . K 7 HOH A 44 544 81 HOH HOH . K 7 HOH A 45 545 20 HOH HOH . K 7 HOH A 46 546 92 HOH HOH . K 7 HOH A 47 547 49 HOH HOH . K 7 HOH A 48 548 127 HOH HOH . K 7 HOH A 49 549 151 HOH HOH . K 7 HOH A 50 550 98 HOH HOH . K 7 HOH A 51 551 4 HOH HOH . K 7 HOH A 52 552 131 HOH HOH . K 7 HOH A 53 553 93 HOH HOH . K 7 HOH A 54 554 105 HOH HOH . K 7 HOH A 55 555 126 HOH HOH . K 7 HOH A 56 556 86 HOH HOH . K 7 HOH A 57 557 163 HOH HOH . K 7 HOH A 58 558 160 HOH HOH . K 7 HOH A 59 559 111 HOH HOH . K 7 HOH A 60 560 80 HOH HOH . K 7 HOH A 61 561 42 HOH HOH . K 7 HOH A 62 562 100 HOH HOH . K 7 HOH A 63 563 39 HOH HOH . K 7 HOH A 64 564 60 HOH HOH . K 7 HOH A 65 565 122 HOH HOH . K 7 HOH A 66 566 67 HOH HOH . K 7 HOH A 67 567 106 HOH HOH . K 7 HOH A 68 568 103 HOH HOH . K 7 HOH A 69 569 145 HOH HOH . K 7 HOH A 70 570 75 HOH HOH . K 7 HOH A 71 571 88 HOH HOH . K 7 HOH A 72 572 36 HOH HOH . K 7 HOH A 73 573 31 HOH HOH . K 7 HOH A 74 574 132 HOH HOH . K 7 HOH A 75 575 102 HOH HOH . K 7 HOH A 76 576 76 HOH HOH . K 7 HOH A 77 577 110 HOH HOH . K 7 HOH A 78 578 18 HOH HOH . K 7 HOH A 79 579 91 HOH HOH . K 7 HOH A 80 580 77 HOH HOH . K 7 HOH A 81 581 33 HOH HOH . K 7 HOH A 82 582 112 HOH HOH . K 7 HOH A 83 583 108 HOH HOH . K 7 HOH A 84 584 157 HOH HOH . K 7 HOH A 85 585 125 HOH HOH . K 7 HOH A 86 586 35 HOH HOH . K 7 HOH A 87 587 155 HOH HOH . K 7 HOH A 88 588 153 HOH HOH . K 7 HOH A 89 589 104 HOH HOH . K 7 HOH A 90 590 123 HOH HOH . K 7 HOH A 91 591 90 HOH HOH . K 7 HOH A 92 592 137 HOH HOH . K 7 HOH A 93 593 57 HOH HOH . K 7 HOH A 94 594 84 HOH HOH . K 7 HOH A 95 595 124 HOH HOH . K 7 HOH A 96 596 69 HOH HOH . K 7 HOH A 97 597 165 HOH HOH . K 7 HOH A 98 598 158 HOH HOH . K 7 HOH A 99 599 89 HOH HOH . K 7 HOH A 100 600 113 HOH HOH . K 7 HOH A 101 601 147 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 2 82.081 131.758 356.068 1 72.32 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . D 2 81.551 131.929 354.635 1 68.52 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . D 2 83.125 132.815 356.491 1 73.65 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . D 2 82.855 130.454 356.235 1 74.44 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . D 2 79.565 132.712 357.326 1 55.35 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . D 2 79.348 133.713 356.156 1 52.47 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . D 2 79.631 133.421 358.626 1 49.34 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . D 2 80.886 131.831 357.128 1 64.52 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . D 2 78.316 131.71 357.225 1 58.24 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . D 2 77.995 130.878 356.09 1 59.36 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . D 2 76.496 130.826 355.941 1 58.53 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . D 2 75.88 130.42 357.185 1 56.3 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . D 2 75.824 132.151 355.619 1 62 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . D 2 76.015 132.526 354.261 1 64.57 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . D 2 74.383 131.873 356.047 1 60.82 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . D 2 73.644 131.141 355.067 1 63.63 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . D 2 74.615 131.052 357.326 1 56.49 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . D 2 74.614 131.843 358.56 1 51.29 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . D 2 75.698 132.344 359.237 1 48.23 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . D 2 75.389 133.016 360.318 1 47.18 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . D 2 74.006 132.948 360.364 1 45.93 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . D 2 73.068 133.366 361.33 1 46.16 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . D 2 73.393 134.045 362.427 1 48.19 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . D 2 71.768 133.034 361.133 1 46.56 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . D 2 71.439 132.352 360.028 1 41.27 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . D 2 72.23 131.932 359.04 1 42.38 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . D 2 73.513 132.238 359.28 1 45.9 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #