data_5ORJ # _model_server_result.job_id VHMwgGqvugWoEgNjH8Kt0Q _model_server_result.datetime_utc '2024-11-24 16:33:38' _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 5orj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":404}' # _entry.id 5ORJ # _exptl.entry_id 5ORJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 5ORJ _cell.length_a 64.79 _cell.length_b 68.597 _cell.length_c 333.66 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORJ _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,L,M,N,O _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 ? 3 E N N ? 3 J 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 A OD1 ASN 184 B ASN 161 1_555 C MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc2 A OD2 ASP 198 B ASP 175 1_555 C MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc3 C MG MG . B MG 401 1_555 E O2A ADP . B ADP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 C MG MG . B MG 401 1_555 E O2B ADP . B ADP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc5 D MG MG . B MG 402 1_555 E O1A ADP . B ADP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc6 B OD1 ASN 184 A ASN 161 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc7 B OD2 ASP 198 A ASP 175 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc8 G MG MG . A MG 401 1_555 J O2A ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc9 G MG MG . A MG 401 1_555 O O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.982 ? metalc ? metalc10 I MG MG . A MG 403 1_555 J O1B ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc11 I MG MG . A MG 403 1_555 J O1A ADP . A ADP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? # _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 35 n n PB O2B ADP sing 36 n n PB O3B ADP sing 37 n n PB O3A ADP sing 38 n n O2B HOB2 ADP sing 39 n n O3B HOB3 ADP sing 40 n n PA O1A ADP doub 41 n n PA O2A ADP sing 42 n n PA O3A ADP sing 43 n n PA O5' ADP sing 44 n n O2A HOA2 ADP sing 45 n n O5' C5' ADP sing 46 n n C5' C4' ADP sing 47 n n C5' "H5'1" ADP sing 48 n n C5' "H5'2" ADP sing 49 n n C4' O4' ADP sing 50 n n C4' C3' ADP sing 51 n n C4' H4' ADP sing 52 n n O4' C1' ADP sing 53 n n C3' O3' ADP sing 54 n n C3' C2' ADP sing 55 n n C3' H3' ADP sing 56 n n O3' HO3' ADP sing 57 n n C2' O2' ADP sing 58 n n C2' C1' ADP sing 59 n n C2' H2' ADP sing 60 n n O2' HO2' ADP sing 61 n n C1' N9 ADP sing 62 n n C1' H1' ADP sing 63 n n N9 C8 ADP sing 64 n y N9 C4 ADP sing 65 n y C8 N7 ADP doub 66 n y C8 H8 ADP sing 67 n n N7 C5 ADP sing 68 n y C5 C6 ADP sing 69 n y C5 C4 ADP doub 70 n y C6 N6 ADP sing 71 n n C6 N1 ADP doub 72 n y N6 HN61 ADP sing 73 n n N6 HN62 ADP sing 74 n n N1 C2 ADP sing 75 n y C2 N3 ADP doub 76 n y C2 H2 ADP sing 77 n n N3 C4 ADP sing 78 n y # _atom_sites.entry_id 5ORJ _atom_sites.fract_transf_matrix[1][1] 0.015434 _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] 0.014578 _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] 0.002997 _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 MG B 1 401 4 MG MG . D 2 MG B 1 402 5 MG MG . E 3 ADP B 1 403 2 ADP ADP . F 4 A4Q B 1 404 2 A4Q L07 . G 2 MG A 1 401 1 MG MG . H 2 MG A 1 402 2 MG MG . I 2 MG A 1 403 3 MG MG . J 3 ADP A 1 404 1 ADP ADP . K 4 A4Q A 1 405 1 A4Q L07 . L 4 A4Q A 1 406 3 A4Q L07 . M 5 IHP A 1 407 1 IHP I6P . N 6 HOH B 1 501 73 HOH HOH . N 6 HOH B 2 502 85 HOH HOH . N 6 HOH B 3 503 45 HOH HOH . N 6 HOH B 4 504 158 HOH HOH . N 6 HOH B 5 505 52 HOH HOH . N 6 HOH B 6 506 32 HOH HOH . N 6 HOH B 7 507 76 HOH HOH . N 6 HOH B 8 508 163 HOH HOH . N 6 HOH B 9 509 112 HOH HOH . N 6 HOH B 10 510 62 HOH HOH . N 6 HOH B 11 511 113 HOH HOH . N 6 HOH B 12 512 31 HOH HOH . N 6 HOH B 13 513 96 HOH HOH . N 6 HOH B 14 514 100 HOH HOH . N 6 HOH B 15 515 156 HOH HOH . N 6 HOH B 16 516 101 HOH HOH . N 6 HOH B 17 517 24 HOH HOH . N 6 HOH B 18 518 121 HOH HOH . N 6 HOH B 19 519 122 HOH HOH . N 6 HOH B 20 520 169 HOH HOH . N 6 HOH B 21 521 157 HOH HOH . N 6 HOH B 22 522 109 HOH HOH . N 6 HOH B 23 523 48 HOH HOH . N 6 HOH B 24 524 132 HOH HOH . N 6 HOH B 25 525 150 HOH HOH . N 6 HOH B 26 526 138 HOH HOH . N 6 HOH B 27 527 75 HOH HOH . N 6 HOH B 28 528 68 HOH HOH . N 6 HOH B 29 529 47 HOH HOH . N 6 HOH B 30 530 95 HOH HOH . N 6 HOH B 31 531 143 HOH HOH . N 6 HOH B 32 532 131 HOH HOH . N 6 HOH B 33 533 144 HOH HOH . O 6 HOH A 1 501 16 HOH HOH . O 6 HOH A 2 502 124 HOH HOH . O 6 HOH A 3 503 50 HOH HOH . O 6 HOH A 4 504 108 HOH HOH . O 6 HOH A 5 505 111 HOH HOH . O 6 HOH A 6 506 105 HOH HOH . O 6 HOH A 7 507 34 HOH HOH . O 6 HOH A 8 508 18 HOH HOH . O 6 HOH A 9 509 5 HOH HOH . O 6 HOH A 10 510 70 HOH HOH . O 6 HOH A 11 511 118 HOH HOH . O 6 HOH A 12 512 35 HOH HOH . O 6 HOH A 13 513 33 HOH HOH . O 6 HOH A 14 514 74 HOH HOH . O 6 HOH A 15 515 30 HOH HOH . O 6 HOH A 16 516 57 HOH HOH . O 6 HOH A 17 517 7 HOH HOH . O 6 HOH A 18 518 175 HOH HOH . O 6 HOH A 19 519 102 HOH HOH . O 6 HOH A 20 520 117 HOH HOH . O 6 HOH A 21 521 14 HOH HOH . O 6 HOH A 22 522 173 HOH HOH . O 6 HOH A 23 523 152 HOH HOH . O 6 HOH A 24 524 81 HOH HOH . O 6 HOH A 25 525 10 HOH HOH . O 6 HOH A 26 526 141 HOH HOH . O 6 HOH A 27 527 147 HOH HOH . O 6 HOH A 28 528 27 HOH HOH . O 6 HOH A 29 529 9 HOH HOH . O 6 HOH A 30 530 36 HOH HOH . O 6 HOH A 31 531 103 HOH HOH . O 6 HOH A 32 532 12 HOH HOH . O 6 HOH A 33 533 21 HOH HOH . O 6 HOH A 34 534 149 HOH HOH . O 6 HOH A 35 535 171 HOH HOH . O 6 HOH A 36 536 84 HOH HOH . O 6 HOH A 37 537 165 HOH HOH . O 6 HOH A 38 538 97 HOH HOH . O 6 HOH A 39 539 69 HOH HOH . O 6 HOH A 40 540 28 HOH HOH . O 6 HOH A 41 541 4 HOH HOH . O 6 HOH A 42 542 66 HOH HOH . O 6 HOH A 43 543 17 HOH HOH . O 6 HOH A 44 544 140 HOH HOH . O 6 HOH A 45 545 116 HOH HOH . O 6 HOH A 46 546 106 HOH HOH . O 6 HOH A 47 547 126 HOH HOH . O 6 HOH A 48 548 164 HOH HOH . O 6 HOH A 49 549 88 HOH HOH . O 6 HOH A 50 550 119 HOH HOH . O 6 HOH A 51 551 115 HOH HOH . O 6 HOH A 52 552 25 HOH HOH . O 6 HOH A 53 553 49 HOH HOH . O 6 HOH A 54 554 13 HOH HOH . O 6 HOH A 55 555 168 HOH HOH . O 6 HOH A 56 556 29 HOH HOH . O 6 HOH A 57 557 53 HOH HOH . O 6 HOH A 58 558 65 HOH HOH . O 6 HOH A 59 559 146 HOH HOH . O 6 HOH A 60 560 125 HOH HOH . O 6 HOH A 61 561 155 HOH HOH . O 6 HOH A 62 562 92 HOH HOH . O 6 HOH A 63 563 133 HOH HOH . O 6 HOH A 64 564 159 HOH HOH . O 6 HOH A 65 565 3 HOH HOH . O 6 HOH A 66 566 114 HOH HOH . O 6 HOH A 67 567 120 HOH HOH . O 6 HOH A 68 568 51 HOH HOH . O 6 HOH A 69 569 166 HOH HOH . O 6 HOH A 70 570 104 HOH HOH . O 6 HOH A 71 571 39 HOH HOH . O 6 HOH A 72 572 43 HOH HOH . O 6 HOH A 73 573 78 HOH HOH . O 6 HOH A 74 574 153 HOH HOH . O 6 HOH A 75 575 123 HOH HOH . O 6 HOH A 76 576 56 HOH HOH . O 6 HOH A 77 577 54 HOH HOH . O 6 HOH A 78 578 23 HOH HOH . O 6 HOH A 79 579 176 HOH HOH . O 6 HOH A 80 580 41 HOH HOH . O 6 HOH A 81 581 142 HOH HOH . O 6 HOH A 82 582 64 HOH HOH . O 6 HOH A 83 583 72 HOH HOH . O 6 HOH A 84 584 161 HOH HOH . O 6 HOH A 85 585 82 HOH HOH . O 6 HOH A 86 586 42 HOH HOH . O 6 HOH A 87 587 20 HOH HOH . O 6 HOH A 88 588 86 HOH HOH . O 6 HOH A 89 589 135 HOH HOH . O 6 HOH A 90 590 107 HOH HOH . O 6 HOH A 91 591 79 HOH HOH . O 6 HOH A 92 592 170 HOH HOH . O 6 HOH A 93 593 162 HOH HOH . O 6 HOH A 94 594 167 HOH HOH . O 6 HOH A 95 595 80 HOH HOH . O 6 HOH A 96 596 151 HOH HOH . O 6 HOH A 97 597 37 HOH HOH . O 6 HOH A 98 598 139 HOH HOH . O 6 HOH A 99 599 71 HOH HOH . O 6 HOH A 100 600 145 HOH HOH . O 6 HOH A 101 601 77 HOH HOH . O 6 HOH A 102 602 99 HOH HOH . O 6 HOH A 103 603 19 HOH HOH . O 6 HOH A 104 604 174 HOH HOH . O 6 HOH A 105 605 160 HOH HOH . O 6 HOH A 106 606 128 HOH HOH . O 6 HOH A 107 607 63 HOH HOH . O 6 HOH A 108 608 89 HOH HOH . O 6 HOH A 109 609 127 HOH HOH . O 6 HOH A 110 610 137 HOH HOH . O 6 HOH A 111 611 129 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 . . . J 3 16.639 131.749 357.69 1 56.67 ? PB ADP 404 A 1 HETATM 2 O O1B ADP . . . J 3 16.029 132.373 356.403 1 49.68 ? O1B ADP 404 A 1 HETATM 3 O O2B ADP . . . J 3 17.222 130.397 357.481 1 57.93 ? O2B ADP 404 A 1 HETATM 4 O O3B ADP . . . J 3 17.759 132.729 358.133 1 57.77 ? O3B ADP 404 A 1 HETATM 5 P PA ADP . . . J 3 14.147 132.641 359.036 1 48.69 ? PA ADP 404 A 1 HETATM 6 O O1A ADP . . . J 3 13.948 133.666 357.908 1 41.9 ? O1A ADP 404 A 1 HETATM 7 O O2A ADP . . . J 3 14.264 133.349 360.344 1 45.66 ? O2A ADP 404 A 1 HETATM 8 O O3A ADP . . . J 3 15.437 131.734 358.75 1 54.38 ? O3A ADP 404 A 1 HETATM 9 O O5' ADP . . . J 3 12.872 131.67 358.991 1 47.81 ? O5' ADP 404 A 1 HETATM 10 C C5' ADP . . . J 3 12.558 130.773 357.902 1 49.94 ? C5' ADP 404 A 1 HETATM 11 C C4' ADP . . . J 3 11.071 130.757 357.643 1 48.45 ? C4' ADP 404 A 1 HETATM 12 O O4' ADP . . . J 3 10.349 130.246 358.793 1 46.51 ? O4' ADP 404 A 1 HETATM 13 C C3' ADP . . . J 3 10.441 132.114 357.363 1 50.37 ? C3' ADP 404 A 1 HETATM 14 O O3' ADP . . . J 3 10.684 132.516 356.02 1 53.52 ? O3' ADP 404 A 1 HETATM 15 C C2' ADP . . . J 3 8.973 131.863 357.73 1 50.15 ? C2' ADP 404 A 1 HETATM 16 O O2' ADP . . . J 3 8.301 131.123 356.716 1 53.62 ? O2' ADP 404 A 1 HETATM 17 C C1' ADP . . . J 3 9.126 130.958 358.96 1 46.71 ? C1' ADP 404 A 1 HETATM 18 N N9 ADP . . . J 3 9.161 131.678 360.238 1 45.59 ? N9 ADP 404 A 1 HETATM 19 C C8 ADP . . . J 3 10.275 132.201 360.846 1 40.58 ? C8 ADP 404 A 1 HETATM 20 N N7 ADP . . . J 3 10.025 132.855 361.954 1 40.95 ? N7 ADP 404 A 1 HETATM 21 C C5 ADP . . . J 3 8.649 132.752 362.094 1 41.25 ? C5 ADP 404 A 1 HETATM 22 C C6 ADP . . . J 3 7.755 133.259 363.057 1 43.86 ? C6 ADP 404 A 1 HETATM 23 N N6 ADP . . . J 3 8.144 133.956 364.128 1 40.75 ? N6 ADP 404 A 1 HETATM 24 N N1 ADP . . . J 3 6.433 133.003 362.888 1 43.76 ? N1 ADP 404 A 1 HETATM 25 C C2 ADP . . . J 3 6.049 132.273 361.831 1 41.44 ? C2 ADP 404 A 1 HETATM 26 N N3 ADP . . . J 3 6.805 131.719 360.877 1 38.88 ? N3 ADP 404 A 1 HETATM 27 C C4 ADP . . . J 3 8.103 132.015 361.052 1 43.4 ? C4 ADP 404 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #