data_7AG5 # _model_server_result.job_id cbSjl_HgM3LfPiIpuAtWCg _model_server_result.datetime_utc '2024-10-20 20:40:02' _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 7ag5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":103}' # _entry.id 7AG5 # _exptl.entry_id 7AG5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 234.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Geranyl phosphate' _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 7AG5 _cell.length_a 40.428 _cell.length_b 40.428 _cell.length_c 31.033 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AG5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 covale ? covale1 A C ASP 1 A ASP 1 1_555 A N DNP 2 A DNP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 A N ASP 1 A ASP 1 1_555 E C 9GE . A 9GE 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale3 A C DNP 2 A DNP 2 1_555 A N CPI 3 A CPI 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale4 A NG DNP 2 A DNP 2 1_555 A C PRO 11 A PRO 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale5 A C CPI 3 A CPI 3 1_555 A N ASP 4 A ASP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale6 A C GLY 8 A GLY 8 1_555 A N 2RA 9 A 2RA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale7 A C 2RA 9 A 2RA 9 1_555 A N ILE 10 A ILE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? metalc ? metalc1 A OD1 ASP 1 A ASP 1 1_555 C CA CA . A CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc2 A O DNP 2 A DNP 2 1_555 B CA CA . A CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 A OD2 ASP 4 A ASP 4 1_555 C CA CA . A CA 102 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc4 A OD1 ASP 5 A ASP 5 1_555 B CA CA . A CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? metalc ? metalc5 A O GLY 6 A GLY 6 1_555 B CA CA . A CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc6 A OD1 ASP 7 A ASP 7 1_555 C CA CA . A CA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc7 A O GLY 8 A GLY 8 1_555 B CA CA . A CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 A O ILE 10 A ILE 10 1_555 B CA CA . A CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc9 B CA CA . A CA 101 1_555 D O3 RDZ . A RDZ 103 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.264 ? metalc ? metalc10 B CA CA . A CA 101 1_555 D O3 RDZ . A RDZ 103 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.289 ? metalc ? metalc11 C CA CA . A CA 102 1_555 D O2 RDZ . A RDZ 103 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.288 ? metalc ? metalc12 C CA CA . A CA 102 1_555 D O2 RDZ . A RDZ 103 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.218 ? metalc ? metalc13 C CA CA . A CA 102 1_555 E O 9GE . A 9GE 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc14 C CA CA . A CA 102 1_555 F O HOH . A HOH 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? # _chem_comp.formula 'C10 H19 O4 P' _chem_comp.formula_weight 234.229 _chem_comp.id RDZ _chem_comp.mon_nstd_flag . _chem_comp.name 'Geranyl phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(2E)-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate;[(2~{E})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate' # 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 C10 C2 RDZ sing 158 n n C1 C2 RDZ sing 159 n n C2 C3 RDZ doub 160 n n C3 C4 RDZ sing 161 n n C5 C4 RDZ sing 162 n n C5 C6 RDZ sing 163 n n C6 C9 RDZ sing 164 n n C6 C7 RDZ doub 165 e n C7 C8 RDZ sing 166 n n C8 O1 RDZ sing 167 n n O1 P1 RDZ sing 168 n n P1 O4 RDZ doub 169 n n P1 O3 RDZ sing 170 n n P1 O2 RDZ sing 171 n n C1 H2 RDZ sing 172 n n C1 H3 RDZ sing 173 n n C1 H1 RDZ sing 174 n n C3 H4 RDZ sing 175 n n C4 H5 RDZ sing 176 n n C4 H6 RDZ sing 177 n n C5 H7 RDZ sing 178 n n C5 H8 RDZ sing 179 n n C7 H9 RDZ sing 180 n n C8 H10 RDZ sing 181 n n C8 H11 RDZ sing 182 n n O2 H22 RDZ sing 183 n n O3 H23 RDZ sing 184 n n C9 H13 RDZ sing 185 n n C9 H14 RDZ sing 186 n n C9 H12 RDZ sing 187 n n C10 H16 RDZ sing 188 n n C10 H17 RDZ sing 189 n n C10 H15 RDZ sing 190 n n # _atom_sites.entry_id 7AG5 _atom_sites.fract_transf_matrix[1][1] 0.024735 _atom_sites.fract_transf_matrix[1][2] 0.014281 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028562 _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] 0.032224 _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 CA A 1 101 102 CA CA . C 2 CA A 1 102 103 CA CA . D 3 RDZ A 1 103 201 RDZ UNL . E 4 9GE A 1 104 0 9GE 9GE . F 5 HOH A 1 201 19 HOH HOH . F 5 HOH A 2 202 11 HOH HOH . F 5 HOH A 3 203 8 HOH HOH . F 5 HOH A 4 204 4 HOH HOH . F 5 HOH A 5 205 6 HOH HOH . F 5 HOH A 6 206 15 HOH HOH . F 5 HOH A 7 207 17 HOH HOH . F 5 HOH A 8 208 14 HOH HOH . F 5 HOH A 9 209 2 HOH HOH . F 5 HOH A 10 210 3 HOH HOH . F 5 HOH A 11 211 5 HOH HOH . F 5 HOH A 12 212 1 HOH HOH . F 5 HOH A 13 213 9 HOH HOH . F 5 HOH A 14 214 16 HOH HOH . F 5 HOH A 15 215 18 HOH HOH . F 5 HOH A 16 216 22 HOH HOH . F 5 HOH A 17 217 20 HOH HOH . F 5 HOH A 18 218 7 HOH HOH . F 5 HOH A 19 219 13 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 RDZ . A . D 3 -6.471 15.755 -0.365 0.72 61.64 ? C1 RDZ 103 A 1 HETATM 2 C C1 RDZ . B . D 3 -3.971 14.077 2.179 0.28 15.94 ? C1 RDZ 103 A 1 HETATM 3 C C2 RDZ . A . D 3 -6.568 17.212 -0.038 0.72 51.63 ? C2 RDZ 103 A 1 HETATM 4 C C2 RDZ . B . D 3 -5.324 14.128 1.534 0.28 17.22 ? C2 RDZ 103 A 1 HETATM 5 C C3 RDZ . A . D 3 -6.782 17.663 1.186 0.72 50.85 ? C3 RDZ 103 A 1 HETATM 6 C C3 RDZ . B . D 3 -6.45 14.029 2.223 0.28 16.5 ? C3 RDZ 103 A 1 HETATM 7 C C4 RDZ . A . D 3 -7.87 17.299 2.157 0.72 41.85 ? C4 RDZ 103 A 1 HETATM 8 C C4 RDZ . B . D 3 -7.852 13.915 1.702 0.28 15.72 ? C4 RDZ 103 A 1 HETATM 9 C C5 RDZ . A . D 3 -8.394 15.863 2.102 0.72 35.17 ? C5 RDZ 103 A 1 HETATM 10 C C5 RDZ . B . D 3 -8.82 14.986 2.141 0.28 13.49 ? C5 RDZ 103 A 1 HETATM 11 C C6 RDZ . A . D 3 -8.857 15.313 3.426 0.72 24.65 ? C6 RDZ 103 A 1 HETATM 12 C C6 RDZ . B . D 3 -9.235 14.873 3.579 0.28 9.41 ? C6 RDZ 103 A 1 HETATM 13 C C7 RDZ . A . D 3 -9.028 16.113 4.468 0.72 20.22 ? C7 RDZ 103 A 1 HETATM 14 C C7 RDZ . B . D 3 -9.148 15.917 4.395 0.28 9.51 ? C7 RDZ 103 A 1 HETATM 15 C C8 RDZ . A . D 3 -9.172 15.72 5.889 0.72 12.28 ? C8 RDZ 103 A 1 HETATM 16 C C8 RDZ . B . D 3 -9.295 15.885 5.885 0.28 9.36 ? C8 RDZ 103 A 1 HETATM 17 O O1 RDZ . A . D 3 -7.962 16.096 6.578 0.72 8.65 ? O1 RDZ 103 A 1 HETATM 18 O O1 RDZ . B . D 3 -8.111 16.424 6.504 0.28 10.97 ? O1 RDZ 103 A 1 HETATM 19 P P1 RDZ . A . D 3 -7.983 16.49 8.164 0.72 7.04 ? P1 RDZ 103 A 1 HETATM 20 P P1 RDZ . B . D 3 -7.987 16.518 8.116 0.28 10.76 ? P1 RDZ 103 A 1 HETATM 21 O O2 RDZ . A . D 3 -8.512 15.381 9.004 0.72 7.83 ? O2 RDZ 103 A 1 HETATM 22 O O2 RDZ . B . D 3 -8.605 15.279 8.691 0.28 9.36 ? O2 RDZ 103 A 1 HETATM 23 O O3 RDZ . A . D 3 -6.548 16.793 8.396 0.72 7.51 ? O3 RDZ 103 A 1 HETATM 24 O O3 RDZ . B . D 3 -6.518 16.658 8.389 0.28 11.23 ? O3 RDZ 103 A 1 HETATM 25 O O4 RDZ . A . D 3 -8.898 17.715 8.31 0.72 7.64 ? O4 RDZ 103 A 1 HETATM 26 O O4 RDZ . B . D 3 -8.775 17.757 8.529 0.28 11.71 ? O4 RDZ 103 A 1 HETATM 27 C C9 RDZ . A . D 3 -9.124 13.835 3.463 0.72 26.5 ? C9 RDZ 103 A 1 HETATM 28 C C9 RDZ . B . D 3 -9.74 13.518 3.996 0.28 9.2 ? C9 RDZ 103 A 1 HETATM 29 C C10 RDZ . A . D 3 -6.418 18.116 -1.216 0.72 52.83 ? C10 RDZ 103 A 1 HETATM 30 C C10 RDZ . B . D 3 -5.299 14.303 0.044 0.28 17.99 ? C10 RDZ 103 A 1 HETATM 31 H H2 RDZ . A . D 3 -6.055 15.643 -1.234 0.72 60 ? H2 RDZ 103 A 1 HETATM 32 H H2 RDZ . B . D 3 -3.634 14.979 2.302 0.28 16.01 ? H2 RDZ 103 A 1 HETATM 33 H H3 RDZ . A . D 3 -7.358 15.362 -0.383 0.72 58.36 ? H3 RDZ 103 A 1 HETATM 34 H H3 RDZ . B . D 3 -3.358 13.58 1.613 0.28 16.05 ? H3 RDZ 103 A 1 HETATM 35 H H1 RDZ . A . D 3 -5.934 15.305 0.307 0.72 59.14 ? H1 RDZ 103 A 1 HETATM 36 H H1 RDZ . B . D 3 -4.037 13.638 3.043 0.28 16.13 ? H1 RDZ 103 A 1 HETATM 37 H H4 RDZ . A . D 3 -6.144 18.276 1.512 0.72 50.34 ? H4 RDZ 103 A 1 HETATM 38 H H4 RDZ . B . D 3 -6.363 14.031 3.164 0.28 16.31 ? H4 RDZ 103 A 1 HETATM 39 H H5 RDZ . A . D 3 -8.629 17.898 2.013 0.72 41.03 ? H5 RDZ 103 A 1 HETATM 40 H H5 RDZ . B . D 3 -8.21 13.045 1.968 0.28 15.01 ? H5 RDZ 103 A 1 HETATM 41 H H6 RDZ . A . D 3 -7.533 17.47 3.059 0.72 39.77 ? H6 RDZ 103 A 1 HETATM 42 H H6 RDZ . B . D 3 -7.814 13.925 0.738 0.28 15.06 ? H6 RDZ 103 A 1 HETATM 43 H H7 RDZ . A . D 3 -7.687 15.283 1.762 0.72 34.23 ? H7 RDZ 103 A 1 HETATM 44 H H7 RDZ . B . D 3 -9.619 14.939 1.577 0.28 12.77 ? H7 RDZ 103 A 1 HETATM 45 H H8 RDZ . A . D 3 -9.139 15.827 1.47 0.72 33.55 ? H8 RDZ 103 A 1 HETATM 46 H H8 RDZ . B . D 3 -8.407 15.862 1.997 0.28 12.71 ? H8 RDZ 103 A 1 HETATM 47 H H9 RDZ . A . D 3 -9.074 17.037 4.294 0.72 15.67 ? H9 RDZ 103 A 1 HETATM 48 H H9 RDZ . B . D 3 -8.981 16.76 4.001 0.28 9.23 ? H9 RDZ 103 A 1 HETATM 49 H H10 RDZ . A . D 3 -9.321 14.752 5.961 0.72 12.11 ? H10 RDZ 103 A 1 HETATM 50 H H10 RDZ . B . D 3 -9.428 14.96 6.187 0.28 9.59 ? H10 RDZ 103 A 1 HETATM 51 H H11 RDZ . A . D 3 -9.946 16.178 6.285 0.72 12.06 ? H11 RDZ 103 A 1 HETATM 52 H H11 RDZ . B . D 3 -10.085 16.404 6.153 0.28 9.86 ? H11 RDZ 103 A 1 HETATM 53 H H13 RDZ . A . D 3 -8.759 13.418 2.666 0.72 26.27 ? H13 RDZ 103 A 1 HETATM 54 H H13 RDZ . B . D 3 -8.998 12.978 4.312 0.28 9.31 ? H13 RDZ 103 A 1 HETATM 55 H H14 RDZ . A . D 3 -10.081 13.677 3.499 0.72 26.3 ? H14 RDZ 103 A 1 HETATM 56 H H14 RDZ . B . D 3 -10.158 13.079 3.238 0.28 9.18 ? H14 RDZ 103 A 1 HETATM 57 H H12 RDZ . A . D 3 -8.703 13.447 4.247 0.72 24.93 ? H12 RDZ 103 A 1 HETATM 58 H H12 RDZ . B . D 3 -10.392 13.617 4.708 0.28 9.24 ? H12 RDZ 103 A 1 HETATM 59 H H16 RDZ . A . D 3 -5.709 17.79 -1.789 0.72 53.62 ? H16 RDZ 103 A 1 HETATM 60 H H16 RDZ . B . D 3 -4.42 14.608 -0.234 0.28 17.7 ? H16 RDZ 103 A 1 HETATM 61 H H17 RDZ . A . D 3 -6.198 19.011 -0.916 0.72 52.76 ? H17 RDZ 103 A 1 HETATM 62 H H17 RDZ . B . D 3 -5.964 14.96 -0.218 0.28 17.57 ? H17 RDZ 103 A 1 HETATM 63 H H15 RDZ . A . D 3 -7.244 18.132 -1.718 0.72 51.23 ? H15 RDZ 103 A 1 HETATM 64 H H15 RDZ . B . D 3 -5.496 13.456 -0.386 0.28 18.02 ? H15 RDZ 103 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 64 #