data_5ORT # _model_server_result.job_id hhZGDNjdayQae_hug5_Jhw _model_server_result.datetime_utc '2024-11-07 19:09:36' _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 5ort # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5ORT # _exptl.entry_id 5ORT _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 5ORT _cell.length_a 82.44 _cell.length_b 82.44 _cell.length_c 176.18 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ORT _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,G,H _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 covale ? covale1 A C THR 161 A THR 287 1_555 A N TPO 162 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C TPO 162 A TPO 288 1_555 A N LEU 163 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASN 135 A ASN 261 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc2 A OD2 ASP 148 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc3 A OD1 ASP 148 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc4 B O3B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc6 B O1B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc7 C MG MG . A MG 402 1_555 H O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc8 C MG MG . A MG 402 1_555 H O HOH . A HOH 537 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc9 D MG MG . A MG 403 1_555 H O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc10 D MG MG . A MG 403 1_555 H O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? # _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 27 n n PB O2B ADP sing 28 n n PB O3B ADP sing 29 n n PB O3A ADP sing 30 n n O2B HOB2 ADP sing 31 n n O3B HOB3 ADP sing 32 n n PA O1A ADP doub 33 n n PA O2A ADP sing 34 n n PA O3A ADP sing 35 n n PA O5' ADP sing 36 n n O2A HOA2 ADP sing 37 n n O5' C5' ADP sing 38 n n C5' C4' ADP sing 39 n n C5' "H5'1" ADP sing 40 n n C5' "H5'2" ADP sing 41 n n C4' O4' ADP sing 42 n n C4' C3' ADP sing 43 n n C4' H4' ADP sing 44 n n O4' C1' ADP sing 45 n n C3' O3' ADP sing 46 n n C3' C2' ADP sing 47 n n C3' H3' ADP sing 48 n n O3' HO3' ADP sing 49 n n C2' O2' ADP sing 50 n n C2' C1' ADP sing 51 n n C2' H2' ADP sing 52 n n O2' HO2' ADP sing 53 n n C1' N9 ADP sing 54 n n C1' H1' ADP sing 55 n n N9 C8 ADP sing 56 n y N9 C4 ADP sing 57 n y C8 N7 ADP doub 58 n y C8 H8 ADP sing 59 n n N7 C5 ADP sing 60 n y C5 C6 ADP sing 61 n y C5 C4 ADP doub 62 n y C6 N6 ADP sing 63 n n C6 N1 ADP doub 64 n y N6 HN61 ADP sing 65 n n N6 HN62 ADP sing 66 n n N1 C2 ADP sing 67 n y C2 N3 ADP doub 68 n y C2 H2 ADP sing 69 n n N3 C4 ADP sing 70 n y # _atom_sites.entry_id 5ORT _atom_sites.fract_transf_matrix[1][1] 0.01213 _atom_sites.fract_transf_matrix[1][2] 0.007003 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014007 _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] 0.005676 _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 CL A 1 404 1399 CL CL . F 4 CL A 1 405 1400 CL CL . G 5 A5Z A 1 406 1 A5Z FRG . H 6 HOH A 1 501 5 HOH HOH . H 6 HOH A 2 502 46 HOH HOH . H 6 HOH A 3 503 12 HOH HOH . H 6 HOH A 4 504 4 HOH HOH . H 6 HOH A 5 505 17 HOH HOH . H 6 HOH A 6 506 8 HOH HOH . H 6 HOH A 7 507 3 HOH HOH . H 6 HOH A 8 508 27 HOH HOH . H 6 HOH A 9 509 22 HOH HOH . H 6 HOH A 10 510 28 HOH HOH . H 6 HOH A 11 511 20 HOH HOH . H 6 HOH A 12 512 45 HOH HOH . H 6 HOH A 13 513 23 HOH HOH . H 6 HOH A 14 514 38 HOH HOH . H 6 HOH A 15 515 7 HOH HOH . H 6 HOH A 16 516 10 HOH HOH . H 6 HOH A 17 517 13 HOH HOH . H 6 HOH A 18 518 11 HOH HOH . H 6 HOH A 19 519 26 HOH HOH . H 6 HOH A 20 520 35 HOH HOH . H 6 HOH A 21 521 39 HOH HOH . H 6 HOH A 22 522 16 HOH HOH . H 6 HOH A 23 523 9 HOH HOH . H 6 HOH A 24 524 14 HOH HOH . H 6 HOH A 25 525 40 HOH HOH . H 6 HOH A 26 526 24 HOH HOH . H 6 HOH A 27 527 29 HOH HOH . H 6 HOH A 28 528 31 HOH HOH . H 6 HOH A 29 529 33 HOH HOH . H 6 HOH A 30 530 2 HOH HOH . H 6 HOH A 31 531 6 HOH HOH . H 6 HOH A 32 532 15 HOH HOH . H 6 HOH A 33 533 44 HOH HOH . H 6 HOH A 34 534 32 HOH HOH . H 6 HOH A 35 535 47 HOH HOH . H 6 HOH A 36 536 25 HOH HOH . H 6 HOH A 37 537 19 HOH HOH . H 6 HOH A 38 538 30 HOH HOH . H 6 HOH A 39 539 41 HOH HOH . H 6 HOH A 40 540 21 HOH HOH . H 6 HOH A 41 541 43 HOH HOH . H 6 HOH A 42 542 42 HOH HOH . H 6 HOH A 43 543 34 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 -12.654 24.216 -6.337 1 42.47 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -13.512 24.131 -7.579 1 38.7 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -12.175 22.856 -5.885 1 44.03 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -13.212 25.089 -5.241 1 43.45 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -11.326 26.603 -7.241 1 45.27 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -11.136 26.611 -8.738 1 44.23 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -12.514 27.374 -6.701 1 41.12 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -11.326 25.051 -6.751 1 44.38 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -9.988 27.207 -6.537 1 42.23 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -9.696 27.018 -5.148 1 40.5 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -8.933 28.201 -4.556 1 43.83 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -7.594 28.3 -5.083 1 43.7 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -9.57 29.559 -4.836 1 42.82 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -10.595 29.917 -3.91 1 41.77 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -8.362 30.485 -4.754 1 44.95 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -8.038 30.755 -3.388 1 49.36 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -7.223 29.661 -5.311 1 36.65 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -7.187 29.856 -6.781 1 41.97 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -7.943 29.161 -7.671 1 38.41 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -7.692 29.545 -8.936 1 36.49 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -6.754 30.517 -8.872 1 37.79 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -6.034 31.362 -9.865 1 35.41 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -6.298 31.236 -11.182 1 33.25 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -5.133 32.263 -9.409 1 40.49 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -4.879 32.377 -8.084 1 42.73 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -5.491 31.636 -7.126 1 41.27 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -6.43 30.72 -7.454 1 36.12 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #