data_7PB1 # _model_server_result.job_id qC0Ns-WMnd-y3MfZLeRm-A _model_server_result.datetime_utc '2024-12-01 08:29:41' _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 7pb1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":403}' # _entry.id 7PB1 # _exptl.entry_id 7PB1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.158 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid' _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 7PB1 _cell.length_a 183.47 _cell.length_b 183.47 _cell.length_c 112.29 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 212.55 150.124 # _struct_asym.details ? _struct_asym.entity_id 5 _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 OD1 ASP 41 A ASP 34 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc2 C MG MG . A MG 401 1_555 D O3B GRG . A GRG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc3 C MG MG . A MG 401 1_555 D O2A GRG . A GRG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc4 C MG MG . A MG 401 1_555 E O7 ISY . A ISY 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc5 C MG MG . A MG 401 1_555 F O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? # _chem_comp.formula 'C5 H12 O6 P2 S' _chem_comp.formula_weight 262.158 _chem_comp.id ISY _chem_comp.mon_nstd_flag . _chem_comp.name '3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Isopentyl S-Thiolodiphosphate' # 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 O2 ISY sing 237 n n P1 O4 ISY sing 238 n n P1 O5 ISY doub 239 n n P1 O6 ISY sing 240 n n O2 P3 ISY sing 241 n n P3 O7 ISY doub 242 n n P3 O8 ISY sing 243 n n P3 S9 ISY sing 244 n n S9 C10 ISY sing 245 n n C10 C11 ISY sing 246 n n C11 C12 ISY sing 247 n n C12 C13 ISY sing 248 n n C12 C14 ISY doub 249 n n O4 HO4 ISY sing 250 n n O6 HO6 ISY sing 251 n n O8 HO8 ISY sing 252 n n C10 H10 ISY sing 253 n n C10 H10A ISY sing 254 n n C11 H11 ISY sing 255 n n C11 H11A ISY sing 256 n n C13 H13 ISY sing 257 n n C13 H13A ISY sing 258 n n C13 H13B ISY sing 259 n n C14 H14 ISY sing 260 n n C14 H14A ISY sing 261 n n # _atom_sites.entry_id 7PB1 _atom_sites.fract_transf_matrix[1][1] 0.00545 _atom_sites.fract_transf_matrix[1][2] 0.003147 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006294 _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] 0.008906 _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 C 3 MG A 1 401 1 MG MG . D 4 GRG A 1 402 401 GRG GRG . E 5 ISY A 1 403 501 ISY ISY . F 6 HOH A 1 501 1 HOH HOH . G 6 HOH B 1 301 2 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 ISY . . . E 5 34.036 111.048 28.535 1 68.45 ? P1 ISY 403 A 1 HETATM 2 O O2 ISY . . . E 5 32.752 111.923 29.021 1 76.77 ? O2 ISY 403 A 1 HETATM 3 P P3 ISY . . . E 5 32.573 113.478 28.526 1 77.74 ? P3 ISY 403 A 1 HETATM 4 O O4 ISY . . . E 5 34.804 110.535 29.738 1 73.38 -1 O4 ISY 403 A 1 HETATM 5 O O5 ISY . . . E 5 33.546 109.906 27.679 1 81.66 ? O5 ISY 403 A 1 HETATM 6 O O6 ISY . . . E 5 34.888 111.966 27.689 1 73.96 -1 O6 ISY 403 A 1 HETATM 7 O O7 ISY . . . E 5 31.92 113.532 27.167 1 62.75 ? O7 ISY 403 A 1 HETATM 8 O O8 ISY . . . E 5 33.906 114.185 28.505 1 78.36 -1 O8 ISY 403 A 1 HETATM 9 S S9 ISY . . . E 5 31.356 114.402 29.978 1 73.08 ? S9 ISY 403 A 1 HETATM 10 C C10 ISY . . . E 5 32.388 115.783 30.532 1 82.07 ? C10 ISY 403 A 1 HETATM 11 C C11 ISY . . . E 5 31.623 116.587 31.568 1 83.78 ? C11 ISY 403 A 1 HETATM 12 C C12 ISY . . . E 5 30.551 117.395 30.855 1 85.16 ? C12 ISY 403 A 1 HETATM 13 C C13 ISY . . . E 5 29.129 116.849 30.731 1 88.32 ? C13 ISY 403 A 1 HETATM 14 C C14 ISY . . . E 5 30.869 118.566 30.359 1 87.22 ? C14 ISY 403 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #