data_5RNT # _model_server_result.job_id dXGBdJBseKVG19FHHejfKw _model_server_result.datetime_utc '2024-11-29 19:50:39' _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 5rnt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":105}' # _entry.id 5RNT # _exptl.entry_id 5RNT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-3',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 5RNT _cell.length_a 86.47 _cell.length_b 86.47 _cell.length_c 86.47 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RNT _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 disulf ? disulf1 A SG CYS 2 A CYS 2 1_555 A SG CYS 10 A CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 6 A CYS 6 1_555 A SG CYS 103 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id PGP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-3',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 P1 O4P PGP doub 218 n n P1 O5P PGP sing 219 n n P1 O6P PGP sing 220 n n P1 O3' PGP sing 221 n n O5P HOP5 PGP sing 222 n n O6P HOP6 PGP sing 223 n n P OP1 PGP doub 224 n n P OP2 PGP sing 225 n n P OP3 PGP sing 226 n n P O5' PGP sing 227 n n OP2 HOP2 PGP sing 228 n n OP3 HOP3 PGP sing 229 n n O5' C5' PGP sing 230 n n C5' C4' PGP sing 231 n n C5' H5' PGP sing 232 n n C5' "H5''" PGP sing 233 n n C4' O4' PGP sing 234 n n C4' C3' PGP sing 235 n n C4' H4' PGP sing 236 n n O4' C1' PGP sing 237 n n C3' O3' PGP sing 238 n n C3' C2' PGP sing 239 n n C3' H3' PGP sing 240 n n C2' O2' PGP sing 241 n n C2' C1' PGP sing 242 n n C2' H2' PGP sing 243 n n O2' HO2' PGP sing 244 n n C1' N9 PGP sing 245 n n C1' H1' PGP sing 246 n n N9 C8 PGP sing 247 n y N9 C4 PGP sing 248 n y C8 N7 PGP doub 249 n y C8 H8 PGP sing 250 n n N7 C5 PGP sing 251 n y C5 C6 PGP sing 252 n n C5 C4 PGP doub 253 n y C6 O6 PGP doub 254 n n C6 N1 PGP sing 255 n n N1 C2 PGP sing 256 n n N1 HN1 PGP sing 257 n n C2 N2 PGP sing 258 n n C2 N3 PGP doub 259 n n N2 HN21 PGP sing 260 n n N2 HN22 PGP sing 261 n n N3 C4 PGP sing 262 n n # _atom_sites.entry_id 5RNT _atom_sites.fract_transf_matrix[1][1] 0.011565 _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] 0.011565 _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] 0.011565 _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 B 2 PGP A 1 105 105 PGP PGP . C 3 HOH A 1 106 106 HOH HOH . C 3 HOH A 2 107 107 HOH HOH . C 3 HOH A 3 108 108 HOH HOH . C 3 HOH A 4 109 109 HOH HOH . C 3 HOH A 5 110 110 HOH HOH . C 3 HOH A 6 111 111 HOH HOH . C 3 HOH A 7 112 112 HOH HOH . C 3 HOH A 8 113 113 HOH HOH . C 3 HOH A 9 114 114 HOH HOH . C 3 HOH A 10 115 115 HOH HOH . C 3 HOH A 11 116 116 HOH HOH . C 3 HOH A 12 117 117 HOH HOH . C 3 HOH A 13 118 118 HOH HOH . C 3 HOH A 14 119 119 HOH HOH . C 3 HOH A 15 120 120 HOH HOH . C 3 HOH A 16 121 121 HOH HOH . C 3 HOH A 17 122 122 HOH HOH . C 3 HOH A 18 123 123 HOH HOH . C 3 HOH A 19 124 124 HOH HOH . C 3 HOH A 20 125 125 HOH HOH . C 3 HOH A 21 126 126 HOH HOH . C 3 HOH A 22 127 127 HOH HOH . C 3 HOH A 23 128 128 HOH HOH . C 3 HOH A 24 129 129 HOH HOH . C 3 HOH A 25 130 130 HOH HOH . C 3 HOH A 26 131 131 HOH HOH . C 3 HOH A 27 132 132 HOH HOH . C 3 HOH A 28 133 133 HOH HOH . C 3 HOH A 29 134 134 HOH HOH . C 3 HOH A 30 135 135 HOH HOH . C 3 HOH A 31 136 136 HOH HOH . C 3 HOH A 32 137 137 HOH HOH . C 3 HOH A 33 138 138 HOH HOH . C 3 HOH A 34 139 139 HOH HOH . C 3 HOH A 35 140 140 HOH HOH . C 3 HOH A 36 141 141 HOH HOH . C 3 HOH A 37 142 142 HOH HOH . C 3 HOH A 38 143 143 HOH HOH . C 3 HOH A 39 144 144 HOH HOH . C 3 HOH A 40 145 145 HOH HOH . C 3 HOH A 41 146 146 HOH HOH . C 3 HOH A 42 147 147 HOH HOH . C 3 HOH A 43 148 148 HOH HOH . C 3 HOH A 44 149 149 HOH HOH . C 3 HOH A 45 150 150 HOH HOH . C 3 HOH A 46 151 151 HOH HOH . C 3 HOH A 47 152 152 HOH HOH . C 3 HOH A 48 153 153 HOH HOH . C 3 HOH A 49 154 154 HOH HOH . C 3 HOH A 50 155 155 HOH HOH . C 3 HOH A 51 156 156 HOH HOH . C 3 HOH A 52 157 157 HOH HOH . C 3 HOH A 53 158 158 HOH HOH . C 3 HOH A 54 159 159 HOH HOH . C 3 HOH A 55 160 160 HOH HOH . C 3 HOH A 56 161 161 HOH HOH . C 3 HOH A 57 162 162 HOH HOH . C 3 HOH A 58 163 163 HOH HOH . C 3 HOH A 59 164 164 HOH HOH . C 3 HOH A 60 165 165 HOH HOH . C 3 HOH A 61 166 166 HOH HOH . C 3 HOH A 62 167 167 HOH HOH . C 3 HOH A 63 168 168 HOH HOH . C 3 HOH A 64 169 169 HOH HOH . C 3 HOH A 65 170 170 HOH HOH . C 3 HOH A 66 171 171 HOH HOH . C 3 HOH A 67 172 172 HOH HOH . C 3 HOH A 68 173 173 HOH HOH . C 3 HOH A 69 174 174 HOH HOH . C 3 HOH A 70 175 175 HOH HOH . C 3 HOH A 71 176 176 HOH HOH . C 3 HOH A 72 177 177 HOH HOH . C 3 HOH A 73 178 178 HOH HOH . C 3 HOH A 74 179 179 HOH HOH . C 3 HOH A 75 180 180 HOH HOH . C 3 HOH A 76 181 181 HOH HOH . C 3 HOH A 77 182 182 HOH HOH . C 3 HOH A 78 183 183 HOH HOH . C 3 HOH A 79 184 184 HOH HOH . C 3 HOH A 80 185 185 HOH HOH . C 3 HOH A 81 186 186 HOH HOH . C 3 HOH A 82 187 187 HOH HOH . C 3 HOH A 83 200 200 HOH HOH . # 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 P1 PGP . . . B 2 47.061 19.983 1.449 1 10.02 ? P1 PGP 105 A 1 HETATM 2 O O4P PGP . . . B 2 47.148 21.505 1.559 1 10.02 ? O4P PGP 105 A 1 HETATM 3 O O5P PGP . . . B 2 47.038 19.52 -0.065 1 10.02 ? O5P PGP 105 A 1 HETATM 4 O O6P PGP . . . B 2 48.526 19.457 1.923 1 10.02 ? O6P PGP 105 A 1 HETATM 5 P P PGP . . . B 2 48.026 18.076 4.791 1 10.02 ? P PGP 105 A 1 HETATM 6 O OP1 PGP . . . B 2 48.632 19.528 4.539 1 10.02 ? OP1 PGP 105 A 1 HETATM 7 O OP2 PGP . . . B 2 47.611 17.238 3.588 1 10.02 ? OP2 PGP 105 A 1 HETATM 8 O OP3 PGP . . . B 2 48.963 17.186 5.728 1 10.02 ? OP3 PGP 105 A 1 HETATM 9 O O5' PGP . . . B 2 46.886 18.317 5.895 1 10.02 ? O5' PGP 105 A 1 HETATM 10 C C5' PGP . . . B 2 45.51 18.007 5.444 1 10.02 ? C5' PGP 105 A 1 HETATM 11 C C4' PGP . . . B 2 45.042 19.241 4.675 1 10.02 ? C4' PGP 105 A 1 HETATM 12 O O4' PGP . . . B 2 45.145 20.243 5.596 1 10.02 ? O4' PGP 105 A 1 HETATM 13 C C3' PGP . . . B 2 45.942 19.761 3.591 1 10.02 ? C3' PGP 105 A 1 HETATM 14 O O3' PGP . . . B 2 45.979 19.136 2.334 1 10.02 ? O3' PGP 105 A 1 HETATM 15 C C2' PGP . . . B 2 45.366 21.202 3.477 1 10.02 ? C2' PGP 105 A 1 HETATM 16 O O2' PGP . . . B 2 44.218 21.155 2.615 1 10.02 ? O2' PGP 105 A 1 HETATM 17 C C1' PGP . . . B 2 45.272 21.534 4.958 1 10.02 ? C1' PGP 105 A 1 HETATM 18 N N9 PGP . . . B 2 46.486 22.26 5.293 1 10.02 ? N9 PGP 105 A 1 HETATM 19 C C8 PGP . . . B 2 47.645 21.774 5.748 1 10.02 ? C8 PGP 105 A 1 HETATM 20 N N7 PGP . . . B 2 48.558 22.732 5.936 1 10.02 ? N7 PGP 105 A 1 HETATM 21 C C5 PGP . . . B 2 47.963 23.865 5.58 1 10.02 ? C5 PGP 105 A 1 HETATM 22 C C6 PGP . . . B 2 48.376 25.246 5.529 1 10.02 ? C6 PGP 105 A 1 HETATM 23 O O6 PGP . . . B 2 49.457 25.768 5.84 1 10.02 ? O6 PGP 105 A 1 HETATM 24 N N1 PGP . . . B 2 47.373 26.058 5.09 1 10.02 ? N1 PGP 105 A 1 HETATM 25 C C2 PGP . . . B 2 46.076 25.62 4.713 1 10.02 ? C2 PGP 105 A 1 HETATM 26 N N2 PGP . . . B 2 45.238 26.627 4.295 1 10.02 ? N2 PGP 105 A 1 HETATM 27 N N3 PGP . . . B 2 45.678 24.377 4.735 1 10.02 ? N3 PGP 105 A 1 HETATM 28 C C4 PGP . . . B 2 46.664 23.574 5.18 1 10.02 ? C4 PGP 105 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #