data_8UTU # _model_server_result.job_id p4sI7uosYhAKPA6u1g488w _model_server_result.datetime_utc '2024-11-09 01:58:59' _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 8utu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 8UTU # _exptl.entry_id 8UTU _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 I _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 A OG SER 104 K SER 104 1_555 E MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc2 A OG SER 215 K SER 215 1_555 E MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc3 E MG MG . K MG 501 1_555 F O2B ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc4 E MG MG . K MG 501 1_555 F O3G ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc5 B OE2 GLU 71 A GLU 71 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc6 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc7 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc8 D OE1 GLU 71 E GLU 71 1_555 L MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc9 K O1G GTP . E GTP 501 1_555 L MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc10 K O2G GTP . E GTP 501 1_555 L MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc11 K O3B GTP . E GTP 501 1_555 L MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc12 K O1B GTP . E GTP 501 1_555 L MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? # _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 8UTU _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 E 4 MG K 1 501 501 MG MG . F 5 ANP K 1 502 502 ANP ANP . G 6 GTP A 1 501 501 GTP GTP . H 4 MG A 1 502 502 MG MG . I 7 GDP B 1 501 501 GDP GDP . J 8 TA1 B 1 502 502 TA1 TA1 . K 6 GTP E 1 501 501 GTP GTP . L 4 MG E 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 . . . I 7 168.349 184.987 166.745 1 68.66 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . I 7 167.067 185.606 166.248 1 69.99 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . I 7 168.405 183.537 166.333 1 79.79 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . I 7 168.413 185.095 168.248 1 63.35 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . I 7 169.603 185.753 166.097 1 68.35 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . I 7 169.999 187.233 166.574 1 68.68 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . I 7 169.115 188.255 165.904 1 74.85 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . I 7 169.93 187.355 168.076 1 79.41 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . I 7 171.51 187.376 166.05 1 66.22 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . I 7 172.42 188.282 166.662 1 70.1 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . I 7 173.247 188.91 165.553 1 67.8 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . I 7 172.354 189.586 164.67 1 74.11 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . I 7 174.245 189.933 166.068 1 69.82 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . I 7 175.581 189.512 165.776 1 73.65 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . I 7 173.919 191.232 165.359 1 71.79 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . I 7 175.073 191.784 164.719 1 75.11 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . I 7 172.86 190.875 164.326 1 74.32 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . I 7 171.757 191.867 164.301 1 69.19 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . I 7 170.838 192.062 165.265 1 72.01 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . I 7 169.974 193.046 164.906 1 71.38 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . I 7 170.334 193.484 163.688 1 63.87 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . I 7 169.849 194.501 162.73 1 71.97 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . I 7 168.858 195.212 162.989 1 84.83 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . I 7 170.5 194.645 161.573 1 68.97 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . I 7 171.575 193.899 161.263 1 68.06 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . I 7 172.187 194.097 160.072 1 75.7 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . I 7 172.073 192.947 162.092 1 60.39 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . I 7 171.506 192.701 163.293 1 61.6 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #