data_8RHH # _model_server_result.job_id ydYqhNAxXaSRQvdLuFYnSw _model_server_result.datetime_utc '2024-11-21 09:40:24' _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 8rhh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 8RHH # _exptl.entry_id 8RHH _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 8RHH _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RHH _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 _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 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 4 _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 OG1 THR 92 K THR 92 1_555 J MG MG . K MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 B OG SER 202 K SER 202 1_555 J MG MG . K MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc3 I O3G ANP . K ANP 1001 1_555 J MG MG . K MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc4 I O2B ANP . K ANP 1001 1_555 J MG MG . K MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc5 K MG MG . L MG 1001 1_555 L O2G ANP . L ANP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc6 K MG MG . L MG 1001 1_555 L O1B ANP . L ANP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc7 D OE1 GLU 71 A GLU 71 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc8 D OE2 GLU 71 A GLU 71 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc9 M O3G GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc10 M O1B GTP . A GTP 501 1_555 N MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? # _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 8RHH _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 G 4 GDP B 1 501 501 GDP GDP . H 5 TA1 B 1 502 502 TA1 TA1 . I 6 ANP K 1 1001 602 ANP ANP . J 7 MG K 1 1002 502 MG MG . K 7 MG L 1 1001 501 MG MG . L 6 ANP L 1 1002 500 ANP ANP . M 8 GTP A 1 501 501 GTP GTP . N 7 MG A 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 . . . G 4 139.163 179.806 133.254 1 25.03 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 4 139.035 179.469 131.789 1 25.03 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 4 138.401 181.063 133.615 1 25.03 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 4 138.731 178.632 134.099 1 25.03 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 4 140.707 180.046 133.574 1 25.03 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 4 141.555 181.182 132.829 1 25.03 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 4 140.898 181.559 131.522 1 25.03 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 4 141.681 182.361 133.762 1 25.03 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 4 142.983 180.487 132.546 1 25.03 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 4 144.208 181.041 133.025 1 25.03 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 4 145.186 181.358 131.898 1 25.03 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 4 144.647 182.406 131.086 1 25.03 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 4 146.488 181.901 132.452 1 25.03 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 4 147.575 181.491 131.614 1 25.03 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 4 146.302 183.406 132.399 1 25.03 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 4 147.545 184.104 132.287 1 25.03 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 4 145.445 183.596 131.163 1 25.03 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 4 144.543 184.772 131.234 1 25.03 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 4 143.578 184.944 132.153 1 25.03 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 4 142.902 186.099 131.941 1 25.03 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 4 143.431 186.682 130.851 1 25.03 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 4 143.179 187.924 130.085 1 25.03 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 4 142.278 188.711 130.436 1 25.03 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 4 143.935 188.18 129.015 1 25.03 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 4 144.91 187.343 128.623 1 25.03 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 4 145.633 187.672 127.526 1 25.03 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 4 145.198 186.186 129.28 1 25.03 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 4 144.507 185.804 130.382 1 25.03 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #