data_2Q80 # _model_server_result.job_id IjDz-2L6KwAcrJjzOX6K1Q _model_server_result.datetime_utc '2024-11-29 09:15:14' _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 2q80 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":500}' # _entry.id 2Q80 # _exptl.entry_id 2Q80 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.443 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GERANYLGERANYL DIPHOSPHATE' _entity.pdbx_number_of_molecules 6 _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 2Q80 _cell.length_a 141.248 _cell.length_b 141.248 _cell.length_c 211.705 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q80 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 L N N ? 3 O N N ? 3 R N N ? 3 U N N ? 3 X N 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 covale ? covale1 B OD2 ASP 65 B ASP 64 1_555 L O2B GRG . B GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc1 A OD1 ASP 65 A ASP 64 1_555 G MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 A OD2 ASP 65 A ASP 64 1_555 H MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc3 A OD1 ASP 69 A ASP 68 1_555 G MG MG . A MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 A OD1 ASP 69 A ASP 68 1_555 H MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc5 G MG MG . A MG 400 1_555 I O1A GRG . A GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc6 H MG MG . A MG 401 1_555 I O2B GRG . A GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc7 H MG MG . A MG 401 1_555 I O1A GRG . A GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc8 B OD1 ASP 65 B ASP 64 1_555 J MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc9 B OD2 ASP 65 B ASP 64 1_555 K MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc10 B OD1 ASP 69 B ASP 68 1_555 J MG MG . B MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc11 B OD1 ASP 69 B ASP 68 1_555 K MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc12 J MG MG . B MG 400 1_555 L O1A GRG . B GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc13 K MG MG . B MG 401 1_555 L O2B GRG . B GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc14 K MG MG . B MG 401 1_555 L O1A GRG . B GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc15 C OD1 ASP 65 C ASP 64 1_555 M MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc16 C OD2 ASP 65 C ASP 64 1_555 N MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc17 C OD1 ASP 69 C ASP 68 1_555 M MG MG . C MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc18 C OD1 ASP 69 C ASP 68 1_555 N MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc19 M MG MG . C MG 400 1_555 O O1A GRG . C GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc20 N MG MG . C MG 401 1_555 O O2B GRG . C GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc21 N MG MG . C MG 401 1_555 O O1A GRG . C GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc22 D OD1 ASP 65 D ASP 64 1_555 P MG MG . D MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc23 D OD2 ASP 65 D ASP 64 1_555 Q MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc24 D OD1 ASP 69 D ASP 68 1_555 P MG MG . D MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc25 D OD1 ASP 69 D ASP 68 1_555 Q MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc26 D OD2 ASP 130 D ASP 129 1_555 P MG MG . D MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc27 P MG MG . D MG 400 1_555 R O1A GRG . D GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc28 Q MG MG . D MG 401 1_555 R O2B GRG . D GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc29 Q MG MG . D MG 401 1_555 R O1A GRG . D GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc30 E OD1 ASP 65 E ASP 64 1_555 S MG MG . E MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc31 E OD2 ASP 65 E ASP 64 1_555 T MG MG . E MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc32 E OD1 ASP 69 E ASP 68 1_555 S MG MG . E MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc33 E OD1 ASP 69 E ASP 68 1_555 T MG MG . E MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc34 S MG MG . E MG 400 1_555 U O1A GRG . E GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc35 T MG MG . E MG 401 1_555 U O2B GRG . E GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc36 T MG MG . E MG 401 1_555 U O1A GRG . E GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc37 F OD1 ASP 65 F ASP 64 1_555 V MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc38 F OD2 ASP 65 F ASP 64 1_555 W MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc39 F OD1 ASP 65 F ASP 64 1_555 W MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc40 F OD1 ASP 69 F ASP 68 1_555 V MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc41 F OD2 ASP 69 F ASP 68 1_555 V MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc42 F OD1 ASP 69 F ASP 68 1_555 W MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc43 V MG MG . F MG 400 1_555 X O1A GRG . F GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc44 W MG MG . F MG 401 1_555 X O2B GRG . F GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc45 W MG MG . F MG 401 1_555 X O1A GRG . F GRG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? # _chem_comp.formula 'C20 H36 O7 P2' _chem_comp.formula_weight 450.443 _chem_comp.id GRG _chem_comp.mon_nstd_flag . _chem_comp.name 'GERANYLGERANYL 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 C20 C18 GRG sing 129 n n C20 H201 GRG sing 130 n n C20 H202 GRG sing 131 n n C20 H203 GRG sing 132 n n C19 C18 GRG sing 133 n n C19 H191 GRG sing 134 n n C19 H192 GRG sing 135 n n C19 H193 GRG sing 136 n n C18 C17 GRG doub 137 n n C17 C16 GRG sing 138 n n C17 H17 GRG sing 139 n n C16 C15 GRG sing 140 n n C16 H161 GRG sing 141 n n C16 H162 GRG sing 142 n n C14 C13 GRG sing 143 n n C14 H141 GRG sing 144 n n C14 H142 GRG sing 145 n n C14 H143 GRG sing 146 n n C13 C15 GRG sing 147 n n C13 C12 GRG doub 148 e n C15 H151 GRG sing 149 n n C15 H152 GRG sing 150 n n C12 C11 GRG sing 151 n n C12 H12 GRG sing 152 n n C11 C9 GRG sing 153 n n C11 H111 GRG sing 154 n n C11 H112 GRG sing 155 n n C9 C8 GRG sing 156 n n C9 HC91 GRG sing 157 n n C9 HC92 GRG sing 158 n n C8 C10 GRG sing 159 n n C8 C7 GRG doub 160 e n C10 H101 GRG sing 161 n n C10 H102 GRG sing 162 n n C10 H103 GRG sing 163 n n C7 C6 GRG sing 164 n n C7 HC7 GRG sing 165 n n C6 C5 GRG sing 166 n n C6 HC61 GRG sing 167 n n C6 HC62 GRG sing 168 n n C5 C3 GRG sing 169 n n C5 HC51 GRG sing 170 n n C5 HC52 GRG sing 171 n n C3 C4 GRG sing 172 n n C3 C2 GRG doub 173 e n C4 HC41 GRG sing 174 n n C4 HC42 GRG sing 175 n n C4 HC43 GRG sing 176 n n C2 C1 GRG sing 177 n n C2 HC2 GRG sing 178 n n C1 O1 GRG sing 179 n n C1 HC11 GRG sing 180 n n C1 HC12 GRG sing 181 n n O1 PA GRG sing 182 n n PA O1A GRG sing 183 n n PA O3A GRG sing 184 n n PA O2A GRG doub 185 n n O1A H1AO GRG sing 186 n n O3A PB GRG sing 187 n n PB O1B GRG sing 188 n n PB O2B GRG sing 189 n n PB O3B GRG doub 190 n n O1B H1BO GRG sing 191 n n O2B H2BO GRG sing 192 n n # _atom_sites.entry_id 2Q80 _atom_sites.fract_transf_matrix[1][1] 0.00708 _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] 0.00708 _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] 0.004724 _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 G 2 MG A 1 400 400 MG MG . H 2 MG A 1 401 401 MG MG . I 3 GRG A 1 500 500 GRG GRG . J 2 MG B 1 400 400 MG MG . K 2 MG B 1 401 401 MG MG . L 3 GRG B 1 500 500 GRG GRG . M 2 MG C 1 400 400 MG MG . N 2 MG C 1 401 401 MG MG . O 3 GRG C 1 500 500 GRG GRG . P 2 MG D 1 400 400 MG MG . Q 2 MG D 1 401 401 MG MG . R 3 GRG D 1 500 500 GRG GRG . S 2 MG E 1 400 400 MG MG . T 2 MG E 1 401 401 MG MG . U 3 GRG E 1 500 500 GRG GRG . V 2 MG F 1 400 400 MG MG . W 2 MG F 1 401 401 MG MG . X 3 GRG F 1 500 500 GRG GRG . Y 4 HOH A 1 501 1 HOH HOH . Y 4 HOH A 2 502 3 HOH HOH . Y 4 HOH A 3 503 4 HOH HOH . Z 4 HOH B 1 501 2 HOH HOH . Z 4 HOH B 2 502 5 HOH HOH . Z 4 HOH B 3 503 6 HOH HOH . Z 4 HOH B 4 504 7 HOH HOH . Z 4 HOH B 5 505 8 HOH HOH . Z 4 HOH B 6 506 9 HOH HOH . Z 4 HOH B 7 507 10 HOH HOH . Z 4 HOH B 8 508 11 HOH HOH . AA 4 HOH C 1 501 12 HOH HOH . AA 4 HOH C 2 502 15 HOH HOH . AA 4 HOH C 3 503 16 HOH HOH . BA 4 HOH D 1 501 13 HOH HOH . BA 4 HOH D 2 502 14 HOH HOH . BA 4 HOH D 3 503 17 HOH HOH . BA 4 HOH D 4 504 18 HOH HOH . BA 4 HOH D 5 505 19 HOH HOH . BA 4 HOH D 6 506 20 HOH HOH . CA 4 HOH E 1 501 22 HOH HOH . CA 4 HOH E 2 502 23 HOH HOH . DA 4 HOH F 1 501 21 HOH HOH . DA 4 HOH F 2 502 24 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 C9 GRG . . . X 3 -64.116 -34.24 -68.895 1 62.43 ? C9 GRG 500 F 1 HETATM 2 C C8 GRG . . . X 3 -64.028 -34.986 -67.546 1 61.86 ? C8 GRG 500 F 1 HETATM 3 C C10 GRG . . . X 3 -64.781 -36.311 -67.275 1 60.48 ? C10 GRG 500 F 1 HETATM 4 C C7 GRG . . . X 3 -63.222 -34.418 -66.569 1 61.65 ? C7 GRG 500 F 1 HETATM 5 C C6 GRG . . . X 3 -62.96 -34.9 -65.288 1 61.38 ? C6 GRG 500 F 1 HETATM 6 C C5 GRG . . . X 3 -61.595 -34.365 -64.803 1 60.18 ? C5 GRG 500 F 1 HETATM 7 C C3 GRG . . . X 3 -61.11 -35.027 -63.494 1 59.94 ? C3 GRG 500 F 1 HETATM 8 C C4 GRG . . . X 3 -60.252 -34.166 -62.553 1 60.39 ? C4 GRG 500 F 1 HETATM 9 C C2 GRG . . . X 3 -61.42 -36.355 -63.155 1 58.05 ? C2 GRG 500 F 1 HETATM 10 C C1 GRG . . . X 3 -61.056 -37.055 -61.998 1 57.54 ? C1 GRG 500 F 1 HETATM 11 O O1 GRG . . . X 3 -61.852 -38.264 -61.838 1 54.85 ? O1 GRG 500 F 1 HETATM 12 P PA GRG . . . X 3 -62.188 -39.075 -60.437 1 53.46 ? PA GRG 500 F 1 HETATM 13 O O1A GRG . . . X 3 -60.91 -38.795 -59.387 1 50.19 ? O1A GRG 500 F 1 HETATM 14 O O3A GRG . . . X 3 -62.095 -40.623 -60.859 1 53 ? O3A GRG 500 F 1 HETATM 15 O O2A GRG . . . X 3 -63.55 -38.72 -59.955 1 51.28 ? O2A GRG 500 F 1 HETATM 16 P PB GRG . . . X 3 -60.924 -41.027 -61.942 1 54.95 ? PB GRG 500 F 1 HETATM 17 O O1B GRG . . . X 3 -60.743 -39.97 -62.979 1 52.5 ? O1B GRG 500 F 1 HETATM 18 O O2B GRG . . . X 3 -59.551 -41.192 -61.091 1 53.2 ? O2B GRG 500 F 1 HETATM 19 O O3B GRG . . . X 3 -61.424 -42.528 -62.474 1 53.22 ? O3B GRG 500 F 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #