data_4E1E # _model_server_result.job_id SDHyKtOw8nvM8M9vGdLr0g _model_server_result.datetime_utc '2024-11-28 02:31:14' _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 4e1e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 4E1E # _exptl.entry_id 4E1E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 4 _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 120 _cell.entry_id 4E1E _cell.length_a 58.575 _cell.length_b 58.575 _cell.length_c 393.933 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4E1E _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 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 _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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -29.2875 -50.727438 -65.6555 # _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 OD2 ASP 97 A ASP 98 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc2 A OD1 ASP 97 A ASP 98 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 A OD2 ASP 101 A ASP 102 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 A OD2 ASP 101 A ASP 102 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 A OD2 ASP 249 A ASP 250 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O5 0MW . A 0MW 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc7 B MG MG . A MG 401 1_555 E O2 0MW . A 0MW 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc8 B MG MG . A MG 401 1_555 H O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc9 B MG MG . A MG 401 1_555 H O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc10 C MG MG . A MG 402 1_555 E O1 0MW . A 0MW 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O4 0MW . A 0MW 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc12 C MG MG . A MG 402 1_555 H O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc13 D MG MG . A MG 403 1_555 E O4 0MW . A 0MW 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc14 D MG MG . A MG 403 1_555 H O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc15 D MG MG . A MG 403 1_555 H O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc16 D MG MG . A MG 403 1_555 H O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc17 G NA NA . A NA 406 1_555 H O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? # _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 210 n n C1 C2 IPE sing 211 n n C1 H11 IPE sing 212 n n C1 H12 IPE sing 213 n n O1 PA IPE sing 214 n n C2 C3 IPE sing 215 n n C2 H21 IPE sing 216 n n C2 H22 IPE sing 217 n n C3 C4 IPE doub 218 n n C3 C5 IPE sing 219 n n C4 H41 IPE sing 220 n n C4 H42 IPE sing 221 n n C5 H51 IPE sing 222 n n C5 H52 IPE sing 223 n n C5 H53 IPE sing 224 n n PA O1A IPE doub 225 n n PA O2A IPE sing 226 n n PA O3A IPE sing 227 n n O2A H2A IPE sing 228 n n O3A PB IPE sing 229 n n PB O1B IPE sing 230 n n PB O2B IPE doub 231 n n PB O3B IPE sing 232 n n O1B H1B IPE sing 233 n n O3B H3B IPE sing 234 n n # _atom_sites.entry_id 4E1E _atom_sites.fract_transf_matrix[1][1] 0.017072 _atom_sites.fract_transf_matrix[1][2] 0.009857 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019713 _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] 0.002539 _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 1 401 401 MG MG . C 2 MG A 1 402 402 MG MG . D 2 MG A 1 403 403 MG MG . E 3 0MW A 1 404 500 0MW B18 . F 4 IPE A 1 405 501 IPE IPR . G 5 NA A 1 406 1 NA NA . H 6 HOH A 1 501 3 HOH HOH . H 6 HOH A 2 502 5 HOH HOH . H 6 HOH A 3 503 6 HOH HOH . H 6 HOH A 4 504 8 HOH HOH . H 6 HOH A 5 505 10 HOH HOH . H 6 HOH A 6 506 11 HOH HOH . H 6 HOH A 7 507 12 HOH HOH . H 6 HOH A 8 508 13 HOH HOH . H 6 HOH A 9 509 14 HOH HOH . H 6 HOH A 10 510 15 HOH HOH . H 6 HOH A 11 511 17 HOH HOH . H 6 HOH A 12 512 18 HOH HOH . H 6 HOH A 13 513 21 HOH HOH . H 6 HOH A 14 514 22 HOH HOH . H 6 HOH A 15 515 23 HOH HOH . H 6 HOH A 16 516 27 HOH HOH . H 6 HOH A 17 517 28 HOH HOH . H 6 HOH A 18 518 29 HOH HOH . H 6 HOH A 19 519 30 HOH HOH . H 6 HOH A 20 520 32 HOH HOH . H 6 HOH A 21 521 33 HOH HOH . H 6 HOH A 22 522 39 HOH HOH . H 6 HOH A 23 523 40 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 . . . F 4 -8.688 -13.375 -19.252 1 52.87 ? C1 IPE 405 A 1 HETATM 2 O O1 IPE . . . F 4 -7.514 -12.647 -19.661 1 52.05 ? O1 IPE 405 A 1 HETATM 3 C C2 IPE . . . F 4 -8.917 -14.683 -20.03 1 51.51 ? C2 IPE 405 A 1 HETATM 4 C C3 IPE . . . F 4 -9.014 -15.89 -19.1 1 51.83 ? C3 IPE 405 A 1 HETATM 5 C C4 IPE . . . F 4 -8.65 -17.085 -19.531 1 51.06 ? C4 IPE 405 A 1 HETATM 6 C C5 IPE . . . F 4 -9.529 -15.775 -17.693 1 50.57 ? C5 IPE 405 A 1 HETATM 7 P PA IPE . . . F 4 -6.273 -13.366 -20.389 1 50.45 ? PA IPE 405 A 1 HETATM 8 O O1A IPE . . . F 4 -6.557 -14.839 -20.358 1 50.77 ? O1A IPE 405 A 1 HETATM 9 O O2A IPE . . . F 4 -4.97 -12.883 -19.807 1 51.9 ? O2A IPE 405 A 1 HETATM 10 O O3A IPE . . . F 4 -6.421 -12.89 -21.926 1 51.06 ? O3A IPE 405 A 1 HETATM 11 P PB IPE . . . F 4 -5.435 -11.962 -22.806 1 50.03 ? PB IPE 405 A 1 HETATM 12 O O1B IPE . . . F 4 -6.168 -10.645 -22.862 1 51.47 ? O1B IPE 405 A 1 HETATM 13 O O2B IPE . . . F 4 -5.445 -12.674 -24.13 1 50.16 ? O2B IPE 405 A 1 HETATM 14 O O3B IPE . . . F 4 -4.091 -11.911 -22.11 1 50.69 ? O3B IPE 405 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #