data_3URP # _model_server_result.job_id YNhE8jJmj-yY6Ksxi67Xfw _model_server_result.datetime_utc '2024-11-29 17:51:26' _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 3urp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":105}' # _entry.id 3URP # _exptl.entry_id 3URP _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 3URP _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 3URP _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 6 A CYS 6 1_555 A SG CYS 103 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _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 3URP _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 PO4 A 1 106 106 PO4 PO4 . D 4 UNX A 1 107 107 UNX UNX . E 5 HOH A 1 201 201 HOH HOH . E 5 HOH A 2 202 202 HOH HOH . E 5 HOH A 3 203 203 HOH HOH . E 5 HOH A 4 204 204 HOH HOH . E 5 HOH A 5 205 205 HOH HOH . E 5 HOH A 6 213 213 HOH HOH . E 5 HOH A 7 220 220 HOH HOH . E 5 HOH A 8 256 256 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 46.562 19.801 0.755 1 62.15 ? P1 PGP 105 A 1 HETATM 2 O O4P PGP . . . B 2 45.742 19.472 -0.487 1 63.9 ? O4P PGP 105 A 1 HETATM 3 O O5P PGP . . . B 2 47.762 18.835 0.966 1 63.3 ? O5P PGP 105 A 1 HETATM 4 O O6P PGP . . . B 2 47.107 21.245 0.761 1 61.27 ? O6P PGP 105 A 1 HETATM 5 P P PGP . . . B 2 48.866 18.309 5.163 1 45.95 ? P PGP 105 A 1 HETATM 6 O OP1 PGP . . . B 2 48.784 16.831 5.059 1 46.38 ? OP1 PGP 105 A 1 HETATM 7 O OP2 PGP . . . B 2 49.799 18.79 6.298 1 45.03 ? OP2 PGP 105 A 1 HETATM 8 O OP3 PGP . . . B 2 49.303 18.963 3.839 1 46.7 ? OP3 PGP 105 A 1 HETATM 9 O O5' PGP . . . B 2 47.424 18.92 5.49 1 44.38 ? O5' PGP 105 A 1 HETATM 10 C C5' PGP . . . B 2 46.14 18.482 5.009 1 42.87 ? C5' PGP 105 A 1 HETATM 11 C C4' PGP . . . B 2 45.367 19.673 4.503 1 41.67 ? C4' PGP 105 A 1 HETATM 12 O O4' PGP . . . B 2 45.323 20.701 5.515 1 37.18 ? O4' PGP 105 A 1 HETATM 13 C C3' PGP . . . B 2 45.975 20.407 3.324 1 46.38 ? C3' PGP 105 A 1 HETATM 14 O O3' PGP . . . B 2 45.694 19.701 2.097 1 55.27 ? O3' PGP 105 A 1 HETATM 15 C C2' PGP . . . B 2 45.231 21.736 3.379 1 41.73 ? C2' PGP 105 A 1 HETATM 16 O O2' PGP . . . B 2 43.914 21.656 2.844 1 43.68 ? O2' PGP 105 A 1 HETATM 17 C C1' PGP . . . B 2 45.194 21.969 4.894 1 33.94 ? C1' PGP 105 A 1 HETATM 18 N N9 PGP . . . B 2 46.298 22.824 5.333 1 24.91 ? N9 PGP 105 A 1 HETATM 19 C C8 PGP . . . B 2 47.552 22.443 5.729 1 23.27 ? C8 PGP 105 A 1 HETATM 20 N N7 PGP . . . B 2 48.392 23.443 5.84 1 22.1 ? N7 PGP 105 A 1 HETATM 21 C C5 PGP . . . B 2 47.638 24.555 5.508 1 20.67 ? C5 PGP 105 A 1 HETATM 22 C C6 PGP . . . B 2 48 25.947 5.377 1 19.88 ? C6 PGP 105 A 1 HETATM 23 O O6 PGP . . . B 2 49.084 26.469 5.64 1 19.02 ? O6 PGP 105 A 1 HETATM 24 N N1 PGP . . . B 2 46.943 26.718 4.93 1 20.09 ? N1 PGP 105 A 1 HETATM 25 C C2 PGP . . . B 2 45.681 26.251 4.663 1 20.45 ? C2 PGP 105 A 1 HETATM 26 N N2 PGP . . . B 2 44.818 27.111 4.123 1 20.89 ? N2 PGP 105 A 1 HETATM 27 N N3 PGP . . . B 2 45.318 24.977 4.824 1 20.54 ? N3 PGP 105 A 1 HETATM 28 C C4 PGP . . . B 2 46.339 24.188 5.215 1 21.23 ? C4 PGP 105 A 1 HETATM 29 H HOP5 PGP . . . B 2 48.394 18.881 1.731 0 63.3 ? HOP5 PGP 105 A 1 HETATM 30 H HOP2 PGP . . . B 2 49.699 19.683 6.722 0 45.05 ? HOP2 PGP 105 A 1 HETATM 31 H H5' PGP . . . B 2 45.597 17.992 5.816 0 42.85 ? H5' PGP 105 A 1 HETATM 32 H "H5''" PGP . . . B 2 46.326 17.75 4.225 0 42.85 ? "H5''" PGP 105 A 1 HETATM 33 H H4' PGP . . . B 2 44.338 19.383 4.296 0 41.65 ? H4' PGP 105 A 1 HETATM 34 H H3' PGP . . . B 2 47.047 20.578 3.409 0 46.36 ? H3' PGP 105 A 1 HETATM 35 H H2' PGP . . . B 2 45.78 22.532 2.878 0 41.72 ? H2' PGP 105 A 1 HETATM 36 H HO2' PGP . . . B 2 44.059 21.395 1.897 0 43.67 ? HO2' PGP 105 A 1 HETATM 37 H H1' PGP . . . B 2 44.256 22.401 5.24 0 33.93 ? H1' PGP 105 A 1 HETATM 38 H H8 PGP . . . B 2 47.831 21.413 5.943 0 23.23 ? H8 PGP 105 A 1 HETATM 39 H HN1 PGP . . . B 2 47.163 27.697 4.788 0 20.1 ? HN1 PGP 105 A 1 HETATM 40 H HN21 PGP . . . B 2 45.093 28.064 3.911 0 20.88 ? HN21 PGP 105 A 1 HETATM 41 H HN22 PGP . . . B 2 43.858 26.875 3.892 0 20.88 ? HN22 PGP 105 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 41 #