data_5MIO # _model_server_result.job_id D7VY_ZXlp8jrbKYmWsFtGg _model_server_result.datetime_utc '2024-11-22 21:20:48' _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 5mio # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5MIO # _exptl.entry_id 5MIO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-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 5MIO _cell.length_a 51.81 _cell.length_b 229.76 _cell.length_c 293.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MIO _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E 1 1 B,F,G 2 1 C,H,I 3 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 6 _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 disulf ? disulf1 C SG CYS 74 C CYS 287 1_555 C SG CYS 74 C CYS 287 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc1 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 D O1B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 C OG1 THR 142 C THR 355 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc4 C OG SER 255 C SER 468 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc5 C OD1 ASP 279 C ASP 492 1_555 H MG MG . C MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc6 H MG MG . C MG 801 1_555 I O1B ANP . C ANP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 133 n n PB O2B GDP sing 134 n n PB O3B GDP sing 135 n n PB O3A GDP sing 136 n n O2B HOB2 GDP sing 137 n n O3B HOB3 GDP sing 138 n n O3A PA GDP sing 139 n n PA O1A GDP doub 140 n n PA O2A GDP sing 141 n n PA O5' GDP sing 142 n n O2A HOA2 GDP sing 143 n n O5' C5' GDP sing 144 n n C5' C4' GDP sing 145 n n C5' H5' GDP sing 146 n n C5' "H5''" GDP sing 147 n n C4' O4' GDP sing 148 n n C4' C3' GDP sing 149 n n C4' H4' GDP sing 150 n n O4' C1' GDP sing 151 n n C3' O3' GDP sing 152 n n C3' C2' GDP sing 153 n n C3' H3' GDP sing 154 n n O3' HO3' GDP sing 155 n n C2' O2' GDP sing 156 n n C2' C1' GDP sing 157 n n C2' H2' GDP sing 158 n n O2' HO2' GDP sing 159 n n C1' N9 GDP sing 160 n n C1' H1' GDP sing 161 n n N9 C8 GDP sing 162 n y N9 C4 GDP sing 163 n y C8 N7 GDP doub 164 n y C8 H8 GDP sing 165 n n N7 C5 GDP sing 166 n y C5 C6 GDP sing 167 n n C5 C4 GDP doub 168 n y C6 O6 GDP doub 169 n n C6 N1 GDP sing 170 n n N1 C2 GDP sing 171 n n N1 HN1 GDP sing 172 n n C2 N2 GDP sing 173 n n C2 N3 GDP doub 174 n n N2 HN21 GDP sing 175 n n N2 HN22 GDP sing 176 n n N3 C4 GDP sing 177 n n # _atom_sites.entry_id 5MIO _atom_sites.fract_transf_matrix[1][1] 0.019301 _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] 0.004352 _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] 0.003402 _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 D 4 GTP A 1 501 501 GTP GTP . E 5 MG A 1 502 502 MG MG . F 6 GDP B 1 501 501 GDP GDP . G 7 LOC B 1 502 503 LOC LOC . H 5 MG C 1 801 801 MG MG . I 8 ANP C 1 802 800 ANP ANP . # 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 PB GDP . . . F 6 -16.769 -22.648 12.356 1 119.27 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 6 -17.098 -22.651 10.852 1 120.62 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 6 -17.059 -23.979 13.069 1 114.61 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 6 -17.47 -21.418 12.977 1 122.35 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 6 -15.205 -22.393 12.481 1 118.13 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 6 -14.027 -23.425 12.198 1 113.77 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 6 -13.269 -22.987 10.999 1 114.96 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 6 -14.616 -24.811 12.031 1 111.96 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 6 -13.162 -23.448 13.521 1 115.82 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 6 -11.801 -22.973 13.496 1 117.34 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 6 -10.935 -23.971 14.218 1 113.21 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 6 -11.031 -25.244 13.552 1 108.59 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 6 -9.449 -23.628 14.249 1 111.43 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 6 -8.862 -24.069 15.467 1 112.15 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 6 -8.902 -24.357 13.02 1 105.82 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 6 -7.547 -24.732 13.219 1 103.81 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 6 -9.795 -25.594 12.962 1 104.38 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 6 -10.064 -26.067 11.601 1 104.21 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 6 -10.774 -25.407 10.638 1 106.38 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 6 -10.878 -26.078 9.507 1 105.66 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 6 -10.197 -27.258 9.743 1 104.53 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 6 -9.952 -28.417 8.907 1 106.92 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 6 -10.312 -28.59 7.749 1 109.65 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 6 -9.225 -29.395 9.554 1 107.29 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 6 -8.77 -29.315 10.84 1 105.89 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 6 -8.075 -30.359 11.304 1 104.4 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 6 -8.982 -28.259 11.629 1 106.59 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 6 -9.69 -27.27 11.029 1 105.21 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #