data_1ZW5 # _model_server_result.job_id b_X3HTGJ-SuTcUyIFUf9PA _model_server_result.datetime_utc '2024-11-05 10:45:03' _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 1zw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":900}' # _entry.id 1ZW5 # _exptl.entry_id 1ZW5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-METHYLBUT-3-ENYL TRIHYDROGEN 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 1ZW5 _cell.length_a 112.255 _cell.length_b 112.255 _cell.length_c 63.245 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZW5 _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,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _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 OD2 ASP 105 A ASP 117 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A OD1 ASP 105 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc3 A OD2 ASP 105 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.139 ? metalc ? metalc4 A OD2 ASP 109 A ASP 121 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc5 A OD2 ASP 109 A ASP 121 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc6 A OD2 ASP 245 A ASP 257 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc7 F O17 ZOL . A ZOL 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 F O11 ZOL . A ZOL 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc9 F O15 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.608 ? metalc ? metalc10 F O12 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc11 F O16 ZOL . A ZOL 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc12 F O17 ZOL . A ZOL 901 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc13 B MG MG . A MG 907 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc14 B MG MG . A MG 907 1_555 G O HOH . A HOH 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc15 B MG MG . A MG 907 1_555 G O HOH . A HOH 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc16 C MG MG . A MG 908 1_555 G O HOH . A HOH 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc17 C MG MG . A MG 908 1_555 G O HOH . A HOH 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc18 C MG MG . A MG 908 1_555 G O HOH . A HOH 960 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc19 D MG MG . A MG 909 1_555 G O HOH . A HOH 912 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc20 D MG MG . A MG 909 1_555 G O HOH . A HOH 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc21 D MG MG . A MG 909 1_555 G O HOH . A HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? # _chem_comp.formula 'C5 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id IPE _chem_comp.mon_nstd_flag . _chem_comp.name '3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ISOPENTENYL PYROPHOSPHATE' # 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 C1 O1 IPE sing 173 n n C1 C2 IPE sing 174 n n C1 H11 IPE sing 175 n n C1 H12 IPE sing 176 n n O1 PA IPE sing 177 n n C2 C3 IPE sing 178 n n C2 H21 IPE sing 179 n n C2 H22 IPE sing 180 n n C3 C4 IPE doub 181 n n C3 C5 IPE sing 182 n n C4 H41 IPE sing 183 n n C4 H42 IPE sing 184 n n C5 H51 IPE sing 185 n n C5 H52 IPE sing 186 n n C5 H53 IPE sing 187 n n PA O1A IPE doub 188 n n PA O2A IPE sing 189 n n PA O3A IPE sing 190 n n O2A H2A IPE sing 191 n n O3A PB IPE sing 192 n n PB O1B IPE sing 193 n n PB O2B IPE doub 194 n n PB O3B IPE sing 195 n n O1B H1B IPE sing 196 n n O3B H3B IPE sing 197 n n # _atom_sites.entry_id 1ZW5 _atom_sites.fract_transf_matrix[1][1] 0.008908 _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] 0.008908 _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] 0.015812 _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 1 907 907 MG MG . C 2 MG A 1 908 908 MG MG . D 2 MG A 1 909 909 MG MG . E 3 IPE A 1 900 900 IPE IPR . F 4 ZOL A 1 901 901 ZOL ZOL . G 5 HOH A 1 910 1 HOH HOH . G 5 HOH A 2 911 2 HOH HOH . G 5 HOH A 3 912 3 HOH HOH . G 5 HOH A 4 913 4 HOH HOH . G 5 HOH A 5 914 5 HOH HOH . G 5 HOH A 6 915 6 HOH HOH . G 5 HOH A 7 916 7 HOH HOH . G 5 HOH A 8 917 8 HOH HOH . G 5 HOH A 9 918 9 HOH HOH . G 5 HOH A 10 919 10 HOH HOH . G 5 HOH A 11 920 11 HOH HOH . G 5 HOH A 12 921 12 HOH HOH . G 5 HOH A 13 922 13 HOH HOH . G 5 HOH A 14 923 14 HOH HOH . G 5 HOH A 15 924 15 HOH HOH . G 5 HOH A 16 925 16 HOH HOH . G 5 HOH A 17 926 17 HOH HOH . G 5 HOH A 18 927 18 HOH HOH . G 5 HOH A 19 928 19 HOH HOH . G 5 HOH A 20 929 20 HOH HOH . G 5 HOH A 21 930 21 HOH HOH . G 5 HOH A 22 931 22 HOH HOH . G 5 HOH A 23 932 23 HOH HOH . G 5 HOH A 24 933 24 HOH HOH . G 5 HOH A 25 934 25 HOH HOH . G 5 HOH A 26 935 26 HOH HOH . G 5 HOH A 27 936 27 HOH HOH . G 5 HOH A 28 937 28 HOH HOH . G 5 HOH A 29 938 29 HOH HOH . G 5 HOH A 30 939 30 HOH HOH . G 5 HOH A 31 940 31 HOH HOH . G 5 HOH A 32 941 32 HOH HOH . G 5 HOH A 33 942 33 HOH HOH . G 5 HOH A 34 943 34 HOH HOH . G 5 HOH A 35 944 35 HOH HOH . G 5 HOH A 36 945 36 HOH HOH . G 5 HOH A 37 946 37 HOH HOH . G 5 HOH A 38 947 38 HOH HOH . G 5 HOH A 39 948 39 HOH HOH . G 5 HOH A 40 949 40 HOH HOH . G 5 HOH A 41 950 41 HOH HOH . G 5 HOH A 42 951 42 HOH HOH . G 5 HOH A 43 952 43 HOH HOH . G 5 HOH A 44 953 44 HOH HOH . G 5 HOH A 45 954 45 HOH HOH . G 5 HOH A 46 955 46 HOH HOH . G 5 HOH A 47 956 47 HOH HOH . G 5 HOH A 48 957 48 HOH HOH . G 5 HOH A 49 958 49 HOH HOH . G 5 HOH A 50 959 50 HOH HOH . G 5 HOH A 51 960 51 HOH HOH . G 5 HOH A 52 961 52 HOH HOH . G 5 HOH A 53 962 53 HOH HOH . G 5 HOH A 54 963 54 HOH HOH . G 5 HOH A 55 964 55 HOH HOH . G 5 HOH A 56 965 56 HOH HOH . G 5 HOH A 57 966 57 HOH HOH . G 5 HOH A 58 967 58 HOH HOH . G 5 HOH A 59 968 59 HOH HOH . G 5 HOH A 60 969 60 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 C C1 IPE . . . E 3 10.585 34.432 -5.654 1 42.62 ? C1 IPE 900 A 1 HETATM 2 O O1 IPE . . . E 3 9.236 33.979 -5.47 1 39.18 ? O1 IPE 900 A 1 HETATM 3 C C2 IPE . . . E 3 11.411 33.588 -6.618 1 31.33 ? C2 IPE 900 A 1 HETATM 4 C C3 IPE . . . E 3 10.743 33.341 -7.932 1 32.91 ? C3 IPE 900 A 1 HETATM 5 C C4 IPE . . . E 3 10.397 32.123 -8.276 1 45.74 ? C4 IPE 900 A 1 HETATM 6 C C5 IPE . . . E 3 10.491 34.461 -8.895 1 44.02 ? C5 IPE 900 A 1 HETATM 7 P PA IPE . . . E 3 8.173 34.97 -4.811 1 39.3 ? PA IPE 900 A 1 HETATM 8 O O1A IPE . . . E 3 8.341 36.2 -5.675 1 40.14 ? O1A IPE 900 A 1 HETATM 9 O O2A IPE . . . E 3 6.853 34.264 -4.695 1 42.53 ? O2A IPE 900 A 1 HETATM 10 O O3A IPE . . . E 3 8.753 35.333 -3.349 1 34.86 ? O3A IPE 900 A 1 HETATM 11 P PB IPE . . . E 3 8.092 35.268 -1.873 1 38.58 ? PB IPE 900 A 1 HETATM 12 O O1B IPE . . . E 3 8.97 36.201 -1.058 1 34.43 ? O1B IPE 900 A 1 HETATM 13 O O2B IPE . . . E 3 6.685 35.826 -1.915 1 54.45 ? O2B IPE 900 A 1 HETATM 14 O O3B IPE . . . E 3 8.173 33.8 -1.567 1 34.72 ? O3B IPE 900 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #