data_5ILY # _model_server_result.job_id eCq4-RbmAqO03YXZX-LAHQ _model_server_result.datetime_utc '2024-11-05 05:38:20' _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 5ily # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 5ILY # _exptl.entry_id 5ILY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 173.943 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 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 5ILY _cell.length_a 126.74 _cell.length_b 126.74 _cell.length_c 124.76 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ILY _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 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 _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 4 _struct_asym.id F _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 ASP 303 A ASP 301 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc2 A OD2 ASP 303 A ASP 301 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc3 A OD1 ASP 303 A ASP 301 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc4 A OD1 ASP 446 A ASP 444 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc5 A OG1 THR 450 A THR 448 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 A OE2 GLU 454 A GLU 452 1_555 B MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc7 B MG MG . A MG 601 1_555 F O3 DPO . A DPO 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc8 B MG MG . A MG 601 1_555 F O7 DPO . A DPO 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc9 B MG MG . A MG 601 1_555 G O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc10 C MG MG . A MG 602 1_555 F O1 DPO . A DPO 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc11 C MG MG . A MG 602 1_555 F O5 DPO . A DPO 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc12 C MG MG . A MG 602 1_555 G O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc13 D MG MG . A MG 603 1_555 F O5 DPO . A DPO 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc14 D MG MG . A MG 603 1_555 G O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? # _chem_comp.formula 'O7 P2 -4' _chem_comp.formula_weight 173.943 _chem_comp.id DPO _chem_comp.mon_nstd_flag . _chem_comp.name 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 P1 O1 DPO doub 115 n n P1 O2 DPO sing 116 n n P1 O3 DPO sing 117 n n P1 O4 DPO sing 118 n n O4 P2 DPO sing 119 n n P2 O5 DPO doub 120 n n P2 O6 DPO sing 121 n n P2 O7 DPO sing 122 n n # _atom_sites.entry_id 5ILY _atom_sites.fract_transf_matrix[1][1] 0.00789 _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] 0.00789 _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] 0.008015 _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 A 1 601 1 MG MG . C 2 MG A 1 602 2 MG MG . D 2 MG A 1 603 3 MG MG . E 3 BTB A 1 604 549 BTB BTB . F 4 DPO A 1 605 600 DPO DPO . G 5 HOH A 1 701 54 HOH HOH . G 5 HOH A 2 702 33 HOH HOH . G 5 HOH A 3 703 6 HOH HOH . G 5 HOH A 4 704 13 HOH HOH . G 5 HOH A 5 705 31 HOH HOH . G 5 HOH A 6 706 51 HOH HOH . G 5 HOH A 7 707 1 HOH HOH . G 5 HOH A 8 708 12 HOH HOH . G 5 HOH A 9 709 58 HOH HOH . G 5 HOH A 10 710 11 HOH HOH . G 5 HOH A 11 711 22 HOH HOH . G 5 HOH A 12 712 38 HOH HOH . G 5 HOH A 13 713 23 HOH HOH . G 5 HOH A 14 714 53 HOH HOH . G 5 HOH A 15 715 8 HOH HOH . G 5 HOH A 16 716 5 HOH HOH . G 5 HOH A 17 717 14 HOH HOH . G 5 HOH A 18 718 20 HOH HOH . G 5 HOH A 19 719 27 HOH HOH . G 5 HOH A 20 720 57 HOH HOH . G 5 HOH A 21 721 35 HOH HOH . G 5 HOH A 22 722 46 HOH HOH . G 5 HOH A 23 723 16 HOH HOH . G 5 HOH A 24 724 40 HOH HOH . G 5 HOH A 25 725 2 HOH HOH . G 5 HOH A 26 726 9 HOH HOH . G 5 HOH A 27 727 37 HOH HOH . G 5 HOH A 28 728 10 HOH HOH . G 5 HOH A 29 729 61 HOH HOH . G 5 HOH A 30 730 28 HOH HOH . G 5 HOH A 31 731 59 HOH HOH . G 5 HOH A 32 732 64 HOH HOH . G 5 HOH A 33 733 55 HOH HOH . G 5 HOH A 34 734 43 HOH HOH . G 5 HOH A 35 735 21 HOH HOH . G 5 HOH A 36 736 7 HOH HOH . G 5 HOH A 37 737 56 HOH HOH . G 5 HOH A 38 738 17 HOH HOH . G 5 HOH A 39 739 45 HOH HOH . G 5 HOH A 40 740 62 HOH HOH . G 5 HOH A 41 741 41 HOH HOH . G 5 HOH A 42 742 42 HOH HOH . G 5 HOH A 43 743 18 HOH HOH . G 5 HOH A 44 744 34 HOH HOH . G 5 HOH A 45 745 24 HOH HOH . G 5 HOH A 46 746 36 HOH HOH . G 5 HOH A 47 747 32 HOH HOH . G 5 HOH A 48 748 15 HOH HOH . G 5 HOH A 49 749 4 HOH HOH . G 5 HOH A 50 750 52 HOH HOH . G 5 HOH A 51 751 48 HOH HOH . G 5 HOH A 52 752 29 HOH HOH . G 5 HOH A 53 753 25 HOH HOH . G 5 HOH A 54 754 3 HOH HOH . G 5 HOH A 55 755 60 HOH HOH . G 5 HOH A 56 756 19 HOH HOH . G 5 HOH A 57 757 50 HOH HOH . G 5 HOH A 58 758 44 HOH HOH . G 5 HOH A 59 759 30 HOH HOH . G 5 HOH A 60 760 49 HOH HOH . G 5 HOH A 61 761 39 HOH HOH . G 5 HOH A 62 762 63 HOH HOH . G 5 HOH A 63 763 26 HOH HOH . G 5 HOH A 64 764 47 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 P1 DPO . . . F 4 23.375 81.153 10.305 0.8 82.81 ? P1 DPO 605 A 1 HETATM 2 O O1 DPO . . . F 4 21.965 81.712 10.201 0.8 85.18 ? O1 DPO 605 A 1 HETATM 3 O O2 DPO . . . F 4 23.459 79.762 10.869 0.8 91.65 ? O2 DPO 605 A 1 HETATM 4 O O3 DPO . . . F 4 24.235 81.367 9.079 0.8 78.39 ? O3 DPO 605 A 1 HETATM 5 O O4 DPO . . . F 4 24.089 81.991 11.481 0.8 157.29 ? O4 DPO 605 A 1 HETATM 6 P P2 DPO . . . F 4 24.308 83.583 11.388 0.8 70.17 ? P2 DPO 605 A 1 HETATM 7 O O5 DPO . . . F 4 22.914 84.126 11.139 0.8 82.57 ? O5 DPO 605 A 1 HETATM 8 O O6 DPO . . . F 4 24.876 83.903 12.754 0.8 62.2 ? O6 DPO 605 A 1 HETATM 9 O O7 DPO . . . F 4 25.207 83.73 10.183 0.8 58.85 ? O7 DPO 605 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 9 #