data_1YQN # _model_server_result.job_id GGTcdLXcahflmT4WuPKpnA _model_server_result.datetime_utc '2024-11-25 22:34:31' _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 1yqn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 1YQN # _exptl.entry_id 1YQN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 314.209 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYL 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 1YQN _cell.length_a 143.778 _cell.length_b 143.778 _cell.length_c 143.778 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YQN _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 -z+1/2,-x,y+1/2 0 0 -1 -1 0 0 0 1 0 71.889 0 71.889 3 'crystal symmetry operation' 10_545 -y,z-1/2,-x+1/2 0 -1 0 0 0 1 -1 0 0 0 -71.889 71.889 # _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 10 A ASP 8 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc2 A NE2 HIS 12 A HIS 10 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc3 A ND1 HIS 44 A HIS 42 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 A OE2 GLU 137 A GLU 135 1_555 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc5 D O2B CDP . A CDP 200 1_555 B ZN ZN . A ZN 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc6 D O2A CDP . A CDP 200 1_555 C MN MN . A MN 500 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc7 D O1B CDP . A CDP 200 1_555 C MN MN . A MN 500 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc8 D O2A CDP . A CDP 200 10_545 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc9 D O1B CDP . A CDP 200 10_545 C MN MN . A MN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc10 C MN MN . A MN 500 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc11 C MN MN . A MN 500 1_555 F O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc12 C MN MN . A MN 500 1_555 F O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _chem_comp.formula 'C10 H20 O7 P2' _chem_comp.formula_weight 314.209 _chem_comp.id GPP _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYL 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 C1 O1 GPP sing 170 n n C1 C2 GPP sing 171 n n C1 H11 GPP sing 172 n n C1 H12 GPP sing 173 n n O1 PA GPP sing 174 n n C2 C3 GPP doub 175 e n C2 H2 GPP sing 176 n n C3 C4 GPP sing 177 n n C3 C5 GPP sing 178 n n C4 H41 GPP sing 179 n n C4 H42 GPP sing 180 n n C4 H43 GPP sing 181 n n C5 C6 GPP sing 182 n n C5 H51 GPP sing 183 n n C5 H52 GPP sing 184 n n C6 C7 GPP sing 185 n n C6 H61 GPP sing 186 n n C6 H62 GPP sing 187 n n C7 C8 GPP doub 188 n n C7 H7 GPP sing 189 n n C8 C9 GPP sing 190 n n C8 C10 GPP sing 191 n n C9 H91 GPP sing 192 n n C9 H92 GPP sing 193 n n C9 H93 GPP sing 194 n n C10 H101 GPP sing 195 n n C10 H102 GPP sing 196 n n C10 H103 GPP sing 197 n n PA O1A GPP doub 198 n n PA O2A GPP sing 199 n n PA O3A GPP sing 200 n n O2A HOA2 GPP sing 201 n n O3A PB GPP sing 202 n n PB O1B GPP doub 203 n n PB O2B GPP sing 204 n n PB O3B GPP sing 205 n n O2B HOB2 GPP sing 206 n n O3B HOB3 GPP sing 207 n n # _atom_sites.entry_id 1YQN _atom_sites.fract_transf_matrix[1][1] 0.006955 _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] 0.006955 _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] 0.006955 _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 ZN A 1 400 400 ZN ZN . C 3 MN A 1 500 500 MN MN . D 4 CDP A 1 200 200 CDP CDP . E 5 GPP A 1 300 300 GPP GPP . F 6 HOH A 1 601 601 HOH HOH . F 6 HOH A 2 602 602 HOH HOH . F 6 HOH A 3 603 603 HOH HOH . F 6 HOH A 4 604 604 HOH HOH . F 6 HOH A 5 605 605 HOH HOH . F 6 HOH A 6 606 606 HOH HOH . F 6 HOH A 7 607 607 HOH HOH . F 6 HOH A 8 608 608 HOH HOH . F 6 HOH A 9 609 609 HOH HOH . F 6 HOH A 10 610 610 HOH HOH . F 6 HOH A 11 611 611 HOH HOH . F 6 HOH A 12 612 612 HOH HOH . F 6 HOH A 13 613 613 HOH HOH . F 6 HOH A 14 614 614 HOH HOH . F 6 HOH A 15 615 615 HOH HOH . F 6 HOH A 16 616 616 HOH HOH . F 6 HOH A 17 617 617 HOH HOH . F 6 HOH A 18 618 618 HOH HOH . F 6 HOH A 19 619 619 HOH HOH . F 6 HOH A 20 620 620 HOH HOH . F 6 HOH A 21 621 621 HOH HOH . F 6 HOH A 22 622 622 HOH HOH . F 6 HOH A 23 623 623 HOH HOH . F 6 HOH A 24 624 624 HOH HOH . F 6 HOH A 25 625 625 HOH HOH . F 6 HOH A 26 626 626 HOH HOH . F 6 HOH A 27 627 627 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 GPP . . . E 5 12.517 -12.488 57.685 0.33 62.9 ? C1 GPP 300 A 1 HETATM 2 O O1 GPP . . . E 5 12.23 -11.475 58.648 0.33 65.09 ? O1 GPP 300 A 1 HETATM 3 C C2 GPP . . . E 5 13.937 -12.955 57.872 0.33 60.92 ? C2 GPP 300 A 1 HETATM 4 C C3 GPP . . . E 5 14.724 -13.403 56.887 0.33 59.31 ? C3 GPP 300 A 1 HETATM 5 C C4 GPP . . . E 5 14.325 -13.296 55.441 0.33 58.26 ? C4 GPP 300 A 1 HETATM 6 C C5 GPP . . . E 5 16.033 -14.026 57.315 0.33 58.58 ? C5 GPP 300 A 1 HETATM 7 C C6 GPP . . . E 5 16.864 -14.459 56.119 0.33 57.96 ? C6 GPP 300 A 1 HETATM 8 C C7 GPP . . . E 5 17.102 -15.947 56.218 0.33 57.34 ? C7 GPP 300 A 1 HETATM 9 C C8 GPP . . . E 5 17.202 -16.747 55.143 0.33 56.64 ? C8 GPP 300 A 1 HETATM 10 C C9 GPP . . . E 5 17.086 -16.222 53.742 0.33 56.63 ? C9 GPP 300 A 1 HETATM 11 C C10 GPP . . . E 5 17.435 -18.21 55.347 0.33 56.38 ? C10 GPP 300 A 1 HETATM 12 P PA GPP . . . E 5 11.555 -11.792 60.078 0.33 66.05 ? PA GPP 300 A 1 HETATM 13 O O1A GPP . . . E 5 10.646 -12.988 59.955 0.33 66.29 ? O1A GPP 300 A 1 HETATM 14 O O2A GPP . . . E 5 12.655 -11.81 61.109 0.33 65.95 ? O2A GPP 300 A 1 HETATM 15 O O3A GPP . . . E 5 10.642 -10.47 60.271 0.33 69.26 ? O3A GPP 300 A 1 HETATM 16 P PB GPP . . . E 5 10.004 -9.953 61.674 0.33 72.53 ? PB GPP 300 A 1 HETATM 17 O O1B GPP . . . E 5 10.761 -10.719 62.745 0.33 73.16 ? O1B GPP 300 A 1 HETATM 18 O O2B GPP . . . E 5 10.289 -8.461 61.664 0.33 71.96 ? O2B GPP 300 A 1 HETATM 19 O O3B GPP . . . E 5 8.525 -10.29 61.596 0.33 72.22 ? O3B GPP 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 19 #