data_5CG6 # _model_server_result.job_id rsrrU00EnfSKJRMfLO4pXw _model_server_result.datetime_utc '2025-03-06 22:27:56' _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 5cg6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":406}' # _entry.id 5CG6 # loop_ _exptl.entry_id _exptl.method 5CG6 'X-RAY DIFFRACTION' 5CG6 'NEUTRON 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 90 _cell.entry_id 5CG6 _cell.length_a 111.627 _cell.length_b 111.627 _cell.length_c 72.553 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CG6 _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 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -36.2765 # _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 97 A ASP 103 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc2 A OD2 ASP 97 A ASP 103 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 A OD2 ASP 101 A ASP 107 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc4 A OD2 ASP 101 A ASP 107 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc5 A OD2 ASP 237 A ASP 243 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc6 B MG MG . A MG 401 1_555 E O17 RIS . A RIS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc7 B MG MG . A MG 401 1_555 G O DOD . A DOD 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc8 B MG MG . A MG 401 1_555 G O DOD . A DOD 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc9 B MG MG . A MG 401 1_555 G O DOD . A DOD 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc10 C MG MG . A MG 402 1_555 E O12 RIS . A RIS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc11 C MG MG . A MG 402 1_555 E O17 RIS . A RIS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc12 C MG MG . A MG 402 1_555 G O DOD . A DOD 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc13 C MG MG . A MG 402 1_555 G O DOD . A DOD 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc14 D MG MG . A MG 403 1_555 E O10 RIS . A RIS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc15 D MG MG . A MG 403 1_555 E O15 RIS . A RIS 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc16 D MG MG . A MG 403 1_555 G O DOD . A DOD 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc17 D MG MG . A MG 403 1_555 G O DOD . A DOD 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc18 D MG MG . A MG 403 1_555 G O DOD . A DOD 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? # _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 5CG6 _atom_sites.fract_transf_matrix[1][1] 0.008958 _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] 0.008958 _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] 0.013783 _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 RIS A 1 404 400 RIS DRG . F 4 IPE A 1 406 404 IPE IPP . G 5 DOD A 1 501 534 DOD DOD . G 5 DOD A 2 502 526 DOD DOD . G 5 DOD A 3 503 544 DOD DOD . G 5 DOD A 4 504 545 DOD DOD . G 5 DOD A 5 505 501 DOD DOD . G 5 DOD A 6 506 529 DOD DOD . G 5 DOD A 7 507 505 DOD DOD . G 5 DOD A 8 508 527 DOD DOD . G 5 DOD A 9 509 524 DOD DOD . G 5 DOD A 10 510 518 DOD DOD . G 5 DOD A 11 511 547 DOD DOD . G 5 DOD A 12 512 559 DOD DOD . G 5 DOD A 13 513 536 DOD DOD . G 5 DOD A 14 514 506 DOD DOD . G 5 DOD A 15 515 558 DOD DOD . G 5 DOD A 16 516 521 DOD DOD . G 5 DOD A 17 517 508 DOD DOD . G 5 DOD A 18 518 592 DOD DOD . G 5 DOD A 19 519 537 DOD DOD . G 5 DOD A 20 520 550 DOD DOD . G 5 DOD A 21 521 507 DOD DOD . G 5 DOD A 22 522 530 DOD DOD . G 5 DOD A 23 523 525 DOD DOD . G 5 DOD A 24 524 551 DOD DOD . G 5 DOD A 25 525 554 DOD DOD . G 5 DOD A 26 526 502 DOD DOD . G 5 DOD A 27 527 515 DOD DOD . G 5 DOD A 28 528 516 DOD DOD . G 5 DOD A 29 529 607 DOD DOD . G 5 DOD A 30 530 519 DOD DOD . G 5 DOD A 31 531 546 DOD DOD . G 5 DOD A 32 532 532 DOD DOD . G 5 DOD A 33 533 552 DOD DOD . G 5 DOD A 34 534 528 DOD DOD . G 5 DOD A 35 535 523 DOD DOD . G 5 DOD A 36 536 522 DOD DOD . G 5 DOD A 37 537 533 DOD DOD . G 5 DOD A 38 538 549 DOD DOD . G 5 DOD A 39 539 503 DOD DOD . G 5 DOD A 40 540 531 DOD DOD . G 5 DOD A 41 541 504 DOD DOD . G 5 DOD A 42 542 514 DOD DOD . G 5 DOD A 43 543 553 DOD DOD . G 5 DOD A 44 544 520 DOD DOD . G 5 DOD A 45 545 538 DOD DOD . G 5 DOD A 46 546 517 DOD DOD . G 5 DOD A 47 547 535 DOD DOD . # 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 11.192 -35.171 -11.37 1 20.9 ? C1 IPE 406 A 1 HETATM 2 O O1 IPE . . . F 4 9.895 -34.604 -11.587 1 21.47 ? O1 IPE 406 A 1 HETATM 3 C C2 IPE . . . F 4 12.089 -34.128 -10.838 1 23.08 ? C2 IPE 406 A 1 HETATM 4 C C3 IPE . . . F 4 11.554 -33.702 -9.448 1 18.35 ? C3 IPE 406 A 1 HETATM 5 C C4 IPE . . . F 4 11.347 -32.255 -9.166 1 21.36 ? C4 IPE 406 A 1 HETATM 6 C C5 IPE . . . F 4 11.375 -34.728 -8.329 1 22.5 ? C5 IPE 406 A 1 HETATM 7 P PA IPE . . . F 4 8.817 -35.567 -12.264 1 20.83 ? PA IPE 406 A 1 HETATM 8 O O1A IPE . . . F 4 7.457 -34.777 -12.283 1 21.52 ? O1A IPE 406 A 1 HETATM 9 O O2A IPE . . . F 4 8.861 -36.915 -11.612 1 20.92 ? O2A IPE 406 A 1 HETATM 10 O O3A IPE . . . F 4 9.432 -35.804 -13.755 1 18.85 ? O3A IPE 406 A 1 HETATM 11 P PB IPE . . . F 4 8.69 -35.844 -15.151 1 20.72 ? PB IPE 406 A 1 HETATM 12 O O1B IPE . . . F 4 8.661 -34.403 -15.763 1 21.25 ? O1B IPE 406 A 1 HETATM 13 O O2B IPE . . . F 4 9.586 -36.819 -15.966 1 18.72 ? O2B IPE 406 A 1 HETATM 14 O O3B IPE . . . F 4 7.293 -36.437 -15.059 1 22.88 ? O3B IPE 406 A 1 HETATM 15 H H11 IPE . . . F 4 11.586 -35.532 -12.321 1 18.49 ? H11 IPE 406 A 1 HETATM 16 H H12 IPE . . . F 4 11.144 -36 -10.651 1 20.6 ? H12 IPE 406 A 1 HETATM 17 H H21 IPE . . . F 4 13.042 -34.481 -10.599 1 20.24 ? H21 IPE 406 A 1 HETATM 18 H H22 IPE . . . F 4 12.089 -33.218 -11.364 1 20.88 ? H22 IPE 406 A 1 HETATM 19 H H41 IPE . . . F 4 11.003 -31.972 -8.162 1 19.94 ? H41 IPE 406 A 1 HETATM 20 H H42 IPE . . . F 4 11.527 -31.556 -9.993 1 20.98 ? H42 IPE 406 A 1 HETATM 21 H H51 IPE . . . F 4 12.308 -34.808 -7.781 1 20.49 ? H51 IPE 406 A 1 HETATM 22 H H52 IPE . . . F 4 11.12 -35.699 -8.762 1 18.4 ? H52 IPE 406 A 1 HETATM 23 H H53 IPE . . . F 4 10.6 -34.403 -7.632 1 23.86 ? H53 IPE 406 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #