data_8UTP # _model_server_result.job_id wChR2a-Q8r7iRDv7bf2RaQ _model_server_result.datetime_utc '2024-11-14 19:22:06' _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 8utp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 8UTP # _exptl.entry_id 8UTP _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 A OG SER 104 K SER 104 1_555 H MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc2 A OG SER 215 K SER 215 1_555 H MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc3 H MG MG . K MG 501 1_555 I O1G ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc4 H MG MG . K MG 501 1_555 I O2B ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc5 C OE2 GLU 71 A GLU 71 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc6 K O1G GTP . A GTP 501 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc7 K O1B GTP . A GTP 501 1_555 L MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc8 E OE2 GLU 71 E GLU 71 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc9 O O1G GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc10 O O1B GTP . E GTP 501 1_555 P MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc11 G OE1 GLU 71 S GLU 71 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc12 S O1G GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc13 S O3B GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc14 S O1B GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc15 S O2B GTP . S GTP 501 1_555 T MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? # _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 8UTP _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 7 173.073 187.76 167.011 1 86.6 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . M 7 172.49 188.975 166.334 1 84.77 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . M 7 172.338 186.522 166.566 1 92.28 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . M 7 172.963 187.908 168.508 1 78.73 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . M 7 174.618 187.619 166.608 1 76.84 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . M 7 175.654 188.765 167.037 1 85.53 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . M 7 175.499 189.967 166.14 1 86.91 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . M 7 175.465 189.141 168.485 1 87.58 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . M 7 177.078 188.063 166.799 1 86.07 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . M 7 178.275 188.635 167.314 1 84.88 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . M 7 179.217 188.797 166.135 1 81.26 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . M 7 178.619 189.718 165.228 1 78.86 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . M 7 180.578 189.352 166.521 1 84.85 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . M 7 181.59 188.386 166.223 1 91.25 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . M 7 180.762 190.613 165.699 1 81.07 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . M 7 182.003 190.607 164.99 1 86.17 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . M 7 179.6 190.619 164.721 1 86.55 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . M 7 179.015 191.971 164.567 1 83.17 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . M 7 178.253 192.626 165.462 1 78.37 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . M 7 177.889 193.84 164.974 1 76.8 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . M 7 178.415 193.963 163.744 1 72.18 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . M 7 178.42 194.982 162.675 1 77.48 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . M 7 177.816 196.064 162.819 1 87.11 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . M 7 179.092 194.714 161.551 1 79.27 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . M 7 179.754 193.56 161.364 1 82.08 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . M 7 180.41 193.361 160.195 1 84.99 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . M 7 179.791 192.582 162.3 1 85.36 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . M 7 179.153 192.726 163.482 1 82.08 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 458 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #