data_5ORN # _model_server_result.job_id HL2AiZxBKJyKRuKxf3sRCQ _model_server_result.datetime_utc '2024-11-06 22:32:56' _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 5orn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5ORN # _exptl.entry_id 5ORN _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 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 120 _cell.entry_id 5ORN _cell.length_a 82.38 _cell.length_b 82.38 _cell.length_c 175.99 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORN _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? covale ? covale1 A C THR 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc3 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc6 C MG MG . A MG 402 1_555 F O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc7 C MG MG . A MG 402 1_555 F O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc8 D MG MG . A MG 403 1_555 F O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc10 D MG MG . A MG 403 1_555 F O HOH . A HOH 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? # _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 ? # _atom_sites.entry_id 5ORN _atom_sites.fract_transf_matrix[1][1] 0.012139 _atom_sites.fract_transf_matrix[1][2] 0.007008 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014017 _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] 0.005682 _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 ADP A 1 401 1392 ADP ADP . C 3 MG A 1 402 1395 MG MG . D 3 MG A 1 403 1396 MG MG . E 4 A5E A 1 404 1 A5E FRG . F 5 HOH A 1 501 15 HOH HOH . F 5 HOH A 2 502 37 HOH HOH . F 5 HOH A 3 503 6 HOH HOH . F 5 HOH A 4 504 49 HOH HOH . F 5 HOH A 5 505 28 HOH HOH . F 5 HOH A 6 506 40 HOH HOH . F 5 HOH A 7 507 59 HOH HOH . F 5 HOH A 8 508 53 HOH HOH . F 5 HOH A 9 509 38 HOH HOH . F 5 HOH A 10 510 31 HOH HOH . F 5 HOH A 11 511 50 HOH HOH . F 5 HOH A 12 512 9 HOH HOH . F 5 HOH A 13 513 20 HOH HOH . F 5 HOH A 14 514 5 HOH HOH . F 5 HOH A 15 515 35 HOH HOH . F 5 HOH A 16 516 12 HOH HOH . F 5 HOH A 17 517 25 HOH HOH . F 5 HOH A 18 518 27 HOH HOH . F 5 HOH A 19 519 24 HOH HOH . F 5 HOH A 20 520 21 HOH HOH . F 5 HOH A 21 521 16 HOH HOH . F 5 HOH A 22 522 13 HOH HOH . F 5 HOH A 23 523 29 HOH HOH . F 5 HOH A 24 524 23 HOH HOH . F 5 HOH A 25 525 18 HOH HOH . F 5 HOH A 26 526 17 HOH HOH . F 5 HOH A 27 527 8 HOH HOH . F 5 HOH A 28 528 4 HOH HOH . F 5 HOH A 29 529 10 HOH HOH . F 5 HOH A 30 530 30 HOH HOH . F 5 HOH A 31 531 7 HOH HOH . F 5 HOH A 32 532 44 HOH HOH . F 5 HOH A 33 533 19 HOH HOH . F 5 HOH A 34 534 43 HOH HOH . F 5 HOH A 35 535 52 HOH HOH . F 5 HOH A 36 536 11 HOH HOH . F 5 HOH A 37 537 48 HOH HOH . F 5 HOH A 38 538 14 HOH HOH . F 5 HOH A 39 539 58 HOH HOH . F 5 HOH A 40 540 1 HOH HOH . F 5 HOH A 41 541 41 HOH HOH . F 5 HOH A 42 542 45 HOH HOH . F 5 HOH A 43 543 32 HOH HOH . F 5 HOH A 44 544 3 HOH HOH . F 5 HOH A 45 545 36 HOH HOH . F 5 HOH A 46 546 42 HOH HOH . F 5 HOH A 47 547 54 HOH HOH . F 5 HOH A 48 548 22 HOH HOH . F 5 HOH A 49 549 56 HOH HOH . F 5 HOH A 50 550 46 HOH HOH . F 5 HOH A 51 551 39 HOH HOH . F 5 HOH A 52 552 34 HOH HOH . F 5 HOH A 53 553 57 HOH HOH . F 5 HOH A 54 554 47 HOH HOH . F 5 HOH A 55 555 2 HOH HOH . F 5 HOH A 56 556 26 HOH HOH . F 5 HOH A 57 557 33 HOH HOH . F 5 HOH A 58 558 51 HOH HOH . F 5 HOH A 59 559 55 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 . . . B 2 -12.154 24.356 -6.096 1 49.07 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -12.802 23.892 -7.375 1 44.38 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -11.595 23.226 -5.281 1 43.46 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -12.968 25.342 -5.291 1 45.16 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -10.75 26.627 -7.186 1 40.04 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -10.515 26.576 -8.68 1 42.17 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -11.883 27.458 -6.632 1 41.22 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -10.811 25.143 -6.553 1 38.62 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.38 27.162 -6.526 1 47.86 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.134 26.95 -5.133 1 47.62 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.395 28.14 -4.534 1 35.58 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.085 28.27 -5.102 1 39.79 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.105 29.456 -4.812 1 38.46 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.075 29.77 -3.808 1 40.64 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -7.963 30.451 -4.84 1 43.3 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -7.645 30.817 -3.496 1 43.84 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -6.804 29.643 -5.385 1 40.25 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -6.777 29.797 -6.855 1 42.33 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.486 29.071 -7.747 1 39.64 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.232 29.474 -9.016 1 39.24 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.337 30.477 -8.946 1 41.57 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -5.631 31.355 -9.911 1 45.12 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -5.838 31.239 -11.246 1 46.02 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -4.775 32.279 -9.416 1 44.43 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.563 32.415 -8.09 1 40.63 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.166 31.652 -7.16 1 40.21 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.045 30.687 -7.519 1 37.21 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #