data_8UTR # _model_server_result.job_id VlPVry59JB0YnpnhRalukw _model_server_result.datetime_utc '2024-10-11 02:26:21' _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 8utr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 8UTR # _exptl.entry_id 8UTR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H _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 ? _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 7 _struct_asym.id G _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 B OE2 GLU 71 A GLU 71 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc2 B OD2 ASP 98 A ASP 98 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc3 E O3B GTP . A GTP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc4 E O1B GTP . A GTP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc5 E O2B GTP . A GTP 501 1_555 F MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 127 n n PB O2B GDP sing 128 n n PB O3B GDP sing 129 n n PB O3A GDP sing 130 n n O2B HOB2 GDP sing 131 n n O3B HOB3 GDP sing 132 n n O3A PA GDP sing 133 n n PA O1A GDP doub 134 n n PA O2A GDP sing 135 n n PA O5' GDP sing 136 n n O2A HOA2 GDP sing 137 n n O5' C5' GDP sing 138 n n C5' C4' GDP sing 139 n n C5' H5' GDP sing 140 n n C5' "H5''" GDP sing 141 n n C4' O4' GDP sing 142 n n C4' C3' GDP sing 143 n n C4' H4' GDP sing 144 n n O4' C1' GDP sing 145 n n C3' O3' GDP sing 146 n n C3' C2' GDP sing 147 n n C3' H3' GDP sing 148 n n O3' HO3' GDP sing 149 n n C2' O2' GDP sing 150 n n C2' C1' GDP sing 151 n n C2' H2' GDP sing 152 n n O2' HO2' GDP sing 153 n n C1' N9 GDP sing 154 n n C1' H1' GDP sing 155 n n N9 C8 GDP sing 156 n y N9 C4 GDP sing 157 n y C8 N7 GDP doub 158 n y C8 H8 GDP sing 159 n n N7 C5 GDP sing 160 n y C5 C6 GDP sing 161 n n C5 C4 GDP doub 162 n y C6 O6 GDP doub 163 n n C6 N1 GDP sing 164 n n N1 C2 GDP sing 165 n n N1 HN1 GDP sing 166 n n C2 N2 GDP sing 167 n n C2 N3 GDP doub 168 n n N2 HN21 GDP sing 169 n n N2 HN22 GDP sing 170 n n N3 C4 GDP sing 171 n n # _atom_sites.entry_id 8UTR _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 ADP K 1 801 801 ADP ADP . E 5 GTP A 1 501 501 GTP GTP . F 6 MG A 1 502 502 MG MG . G 7 GDP B 1 501 501 GDP GDP . H 8 TA1 B 1 502 502 TA1 TA1 . # 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 . . . G 7 169.729 172.706 210.61 1 89.77 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 7 170.682 172.257 209.53 1 90.87 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 7 170.141 172.085 211.922 1 79.78 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 7 168.327 172.277 210.26 1 88.25 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 7 169.784 174.307 210.728 1 74.73 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 7 168.489 175.16 210.312 1 80.67 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 7 167.924 174.647 209.013 1 75.97 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 7 167.452 175.098 211.405 1 89.34 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 7 169.027 176.663 210.133 1 83.2 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 7 168.204 177.762 210.511 1 78.33 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 7 167.995 178.665 209.306 1 71.54 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 7 167.123 178.003 208.392 1 69.72 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 7 167.351 179.992 209.674 1 78.4 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 7 168.216 181.071 209.306 1 83.85 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 7 166.045 180.051 208.905 1 80.96 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 7 165.896 181.293 208.209 1 87.71 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 7 166.11 178.893 207.923 1 83.55 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 7 164.812 178.181 207.834 1 82.61 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 7 164.317 177.33 208.752 1 84.95 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 7 163.112 176.849 208.355 1 81.79 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 7 162.829 177.392 207.16 1 70.88 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 7 161.722 177.307 206.186 1 78.96 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 7 160.729 176.585 206.407 1 88.09 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 7 161.806 178.028 205.064 1 80.54 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 7 162.863 178.818 204.803 1 80.9 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 7 162.884 179.52 203.644 1 87.72 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 7 163.916 178.941 205.648 1 72.71 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 7 163.954 178.266 206.819 1 70.17 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #