data_8UTO # _model_server_result.job_id JLWhxaJ-ZdHeWu0uqFEumw _model_server_result.datetime_utc '2024-11-14 19:45:32' _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 8uto # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 8UTO # _exptl.entry_id 8UTO _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,I,J,K,L,M,N,O,P,Q,R,S,T _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 M N N ? 7 Q 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 metalc ? metalc1 H MG MG . K MG 501 1_555 I O2B ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc2 H MG MG . K MG 501 1_555 I O1G ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc3 C OE2 GLU 71 A GLU 71 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc4 K O1G GTP . A GTP 501 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc5 K O1B GTP . A GTP 501 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc6 E OE1 GLU 71 E GLU 71 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc7 O O1G GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc8 O O1B GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc9 G OE1 GLU 71 S GLU 71 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc10 S O1G GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc11 S O3B GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc12 S O1B GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? # _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 8UTO _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 H 4 MG K 1 501 501 MG MG . I 5 ANP K 1 502 502 ANP ANP . J 5 ANP N 1 501 501 ANP ANP . K 6 GTP A 1 501 501 GTP GTP . L 4 MG A 1 502 502 MG MG . M 7 GDP B 1 501 501 GDP GDP . N 8 TA1 B 1 502 502 TA1 TA1 . O 6 GTP E 1 501 501 GTP GTP . P 4 MG E 1 502 502 MG MG . Q 7 GDP I 1 501 501 GDP GDP . R 8 TA1 I 1 502 502 TA1 TA1 . S 6 GTP S 1 501 501 GTP GTP . T 4 MG S 1 502 502 MG MG . # 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 . . . M 7 172.997 187.501 167.267 1 96.7 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . M 7 172.276 186.259 166.811 1 97.75 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . M 7 173.12 187.489 168.771 1 87.43 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . M 7 172.235 188.726 166.83 1 89.24 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . M 7 174.464 187.526 166.617 1 71.99 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . M 7 175.467 188.731 166.959 1 77.32 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . M 7 175.117 189.944 166.134 1 91.95 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . M 7 175.439 189.051 168.433 1 91.71 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . M 7 176.899 188.154 166.518 1 82.66 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . M 7 178.101 188.675 167.078 1 86.77 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . M 7 179.135 188.738 165.967 1 87.31 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . M 7 178.633 189.61 164.959 1 89.93 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . M 7 180.473 189.288 166.433 1 87.73 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . M 7 181.492 188.3 166.261 1 88.7 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . M 7 180.748 190.512 165.581 1 86.57 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . M 7 182.004 190.412 164.904 1 91.22 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . M 7 179.613 190.569 164.571 1 89.58 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . M 7 178.997 191.915 164.538 1 84.16 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . M 7 178.206 192.446 165.488 1 82.33 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . M 7 177.809 193.694 165.134 1 84.85 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . M 7 178.345 193.966 163.933 1 81.38 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . M 7 178.327 195.099 162.987 1 83.36 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . M 7 177.691 196.143 163.239 1 93.88 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . M 7 179.015 194.981 161.85 1 76.92 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . M 7 179.715 193.878 161.541 1 80.25 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . M 7 180.386 193.841 160.364 1 86.43 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . M 7 179.777 192.8 162.359 1 84.29 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . M 7 179.125 192.789 163.543 1 83.07 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 519 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 28 #