data_8BOS # _model_server_result.job_id Gim0Vi23FQ2oiosseZdEPA _model_server_result.datetime_utc '2024-12-22 01:40:11' _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 8bos # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 8BOS # _exptl.entry_id 8BOS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 109.25 _cell.angle_gamma 90 _cell.entry_id 8BOS _cell.length_a 71.832 _cell.length_b 41.558 _cell.length_c 89.674 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BOS _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 B SG CYS 60 G CYS 771 1_555 B SG CYS 165 G CYS 876 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc1 A OG SER 17 R SER 17 1_555 E MG MG . R MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc2 A OG1 THR 35 R THR 35 1_555 E MG MG . R MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc3 C O3B GDP . R GDP 201 1_555 D MG MGF . R MGF 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc4 C O1B GDP . R GDP 201 1_555 E MG MG . R MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc5 D MG MGF . R MGF 202 1_555 G O HOH . R HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc6 E MG MG . R MG 203 1_555 G O HOH . R HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc7 E MG MG . R MG 203 1_555 G O HOH . R HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? # _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 91 n n PB O2B GDP sing 92 n n PB O3B GDP sing 93 n n PB O3A GDP sing 94 n n O2B HOB2 GDP sing 95 n n O3B HOB3 GDP sing 96 n n O3A PA GDP sing 97 n n PA O1A GDP doub 98 n n PA O2A GDP sing 99 n n PA O5' GDP sing 100 n n O2A HOA2 GDP sing 101 n n O5' C5' GDP sing 102 n n C5' C4' GDP sing 103 n n C5' H5' GDP sing 104 n n C5' "H5''" GDP sing 105 n n C4' O4' GDP sing 106 n n C4' C3' GDP sing 107 n n C4' H4' GDP sing 108 n n O4' C1' GDP sing 109 n n C3' O3' GDP sing 110 n n C3' C2' GDP sing 111 n n C3' H3' GDP sing 112 n n O3' HO3' GDP sing 113 n n C2' O2' GDP sing 114 n n C2' C1' GDP sing 115 n n C2' H2' GDP sing 116 n n O2' HO2' GDP sing 117 n n C1' N9 GDP sing 118 n n C1' H1' GDP sing 119 n n N9 C8 GDP sing 120 n y N9 C4 GDP sing 121 n y C8 N7 GDP doub 122 n y C8 H8 GDP sing 123 n n N7 C5 GDP sing 124 n y C5 C6 GDP sing 125 n n C5 C4 GDP doub 126 n y C6 O6 GDP doub 127 n n C6 N1 GDP sing 128 n n N1 C2 GDP sing 129 n n N1 HN1 GDP sing 130 n n C2 N2 GDP sing 131 n n C2 N3 GDP doub 132 n n N2 HN21 GDP sing 133 n n N2 HN22 GDP sing 134 n n N3 C4 GDP sing 135 n n # _atom_sites.entry_id 8BOS _atom_sites.fract_transf_matrix[1][1] 0.013921 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004862 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024063 _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] 0.011812 _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 C 3 GDP R 1 201 201 GDP GDP . D 4 MGF R 1 202 202 MGF MGF . E 5 MG R 1 203 1 MG MG . F 6 GAI G 1 1101 1101 GAI GAI . G 7 HOH R 1 301 30 HOH HOH . G 7 HOH R 2 302 55 HOH HOH . G 7 HOH R 3 303 58 HOH HOH . G 7 HOH R 4 304 40 HOH HOH . G 7 HOH R 5 305 26 HOH HOH . G 7 HOH R 6 306 27 HOH HOH . G 7 HOH R 7 307 56 HOH HOH . G 7 HOH R 8 308 12 HOH HOH . G 7 HOH R 9 309 2 HOH HOH . G 7 HOH R 10 310 32 HOH HOH . G 7 HOH R 11 311 25 HOH HOH . G 7 HOH R 12 312 34 HOH HOH . G 7 HOH R 13 313 11 HOH HOH . G 7 HOH R 14 314 9 HOH HOH . G 7 HOH R 15 315 1 HOH HOH . G 7 HOH R 16 316 7 HOH HOH . G 7 HOH R 17 317 59 HOH HOH . G 7 HOH R 18 318 42 HOH HOH . G 7 HOH R 19 319 57 HOH HOH . H 7 HOH G 1 1201 5 HOH HOH . H 7 HOH G 2 1202 46 HOH HOH . H 7 HOH G 3 1203 17 HOH HOH . H 7 HOH G 4 1204 33 HOH HOH . H 7 HOH G 5 1205 43 HOH HOH . H 7 HOH G 6 1206 47 HOH HOH . H 7 HOH G 7 1207 13 HOH HOH . H 7 HOH G 8 1208 44 HOH HOH . H 7 HOH G 9 1209 4 HOH HOH . H 7 HOH G 10 1210 6 HOH HOH . H 7 HOH G 11 1211 51 HOH HOH . H 7 HOH G 12 1212 54 HOH HOH . H 7 HOH G 13 1213 21 HOH HOH . H 7 HOH G 14 1214 41 HOH HOH . H 7 HOH G 15 1215 50 HOH HOH . H 7 HOH G 16 1216 14 HOH HOH . H 7 HOH G 17 1217 45 HOH HOH . H 7 HOH G 18 1218 37 HOH HOH . H 7 HOH G 19 1219 31 HOH HOH . H 7 HOH G 20 1220 8 HOH HOH . H 7 HOH G 21 1221 22 HOH HOH . H 7 HOH G 22 1222 20 HOH HOH . H 7 HOH G 23 1223 15 HOH HOH . H 7 HOH G 24 1224 38 HOH HOH . H 7 HOH G 25 1225 10 HOH HOH . H 7 HOH G 26 1226 3 HOH HOH . H 7 HOH G 27 1227 48 HOH HOH . H 7 HOH G 28 1228 61 HOH HOH . H 7 HOH G 29 1229 19 HOH HOH . H 7 HOH G 30 1230 18 HOH HOH . H 7 HOH G 31 1231 16 HOH HOH . H 7 HOH G 32 1232 28 HOH HOH . H 7 HOH G 33 1233 49 HOH HOH . H 7 HOH G 34 1234 39 HOH HOH . H 7 HOH G 35 1235 35 HOH HOH . H 7 HOH G 36 1236 62 HOH HOH . H 7 HOH G 37 1237 36 HOH HOH . H 7 HOH G 38 1238 60 HOH HOH . H 7 HOH G 39 1239 52 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 PB GDP . . . C 3 18.731 8.096 19.458 1 29.66 ? PB GDP 201 R 1 HETATM 2 O O1B GDP . . . C 3 19.716 8.375 18.323 1 25.97 ? O1B GDP 201 R 1 HETATM 3 O O2B GDP . . . C 3 19.411 7.846 20.786 1 25.47 ? O2B GDP 201 R 1 HETATM 4 O O3B GDP . . . C 3 17.738 6.945 19.14 1 29.28 ? O3B GDP 201 R 1 HETATM 5 O O3A GDP . . . C 3 17.998 9.559 19.553 1 27.22 ? O3A GDP 201 R 1 HETATM 6 P PA GDP . . . C 3 18.195 10.836 18.582 1 30.14 ? PA GDP 201 R 1 HETATM 7 O O1A GDP . . . C 3 17.577 10.481 17.261 1 30.95 ? O1A GDP 201 R 1 HETATM 8 O O2A GDP . . . C 3 19.629 11.235 18.481 1 30.88 ? O2A GDP 201 R 1 HETATM 9 O O5' GDP . . . C 3 17.35 11.994 19.322 1 28.98 ? O5' GDP 201 R 1 HETATM 10 C C5' GDP . . . C 3 16.107 11.576 19.935 1 35.17 ? C5' GDP 201 R 1 HETATM 11 C C4' GDP . . . C 3 15.183 12.75 20.169 1 40.62 ? C4' GDP 201 R 1 HETATM 12 O O4' GDP . . . C 3 15.656 13.464 21.334 1 43.11 ? O4' GDP 201 R 1 HETATM 13 C C3' GDP . . . C 3 15.078 13.826 19.073 1 46.02 ? C3' GDP 201 R 1 HETATM 14 O O3' GDP . . . C 3 13.797 14.45 19.105 1 44.99 ? O3' GDP 201 R 1 HETATM 15 C C2' GDP . . . C 3 16.221 14.773 19.461 1 46.77 ? C2' GDP 201 R 1 HETATM 16 O O2' GDP . . . C 3 16.16 16.116 19.021 1 46.9 ? O2' GDP 201 R 1 HETATM 17 C C1' GDP . . . C 3 16.042 14.768 20.969 1 44.71 ? C1' GDP 201 R 1 HETATM 18 N N9 GDP . . . C 3 17.265 15.109 21.677 1 43.55 ? N9 GDP 201 R 1 HETATM 19 C C8 GDP . . . C 3 18.506 14.556 21.513 1 42.05 ? C8 GDP 201 R 1 HETATM 20 N N7 GDP . . . C 3 19.409 15.089 22.295 1 42.71 ? N7 GDP 201 R 1 HETATM 21 C C5 GDP . . . C 3 18.716 16.058 23.005 1 43.4 ? C5 GDP 201 R 1 HETATM 22 C C6 GDP . . . C 3 19.171 16.95 24.01 1 43.94 ? C6 GDP 201 R 1 HETATM 23 O O6 GDP . . . C 3 20.321 17.055 24.474 1 41.78 ? O6 GDP 201 R 1 HETATM 24 N N1 GDP . . . C 3 18.12 17.758 24.474 1 41.97 ? N1 GDP 201 R 1 HETATM 25 C C2 GDP . . . C 3 16.814 17.715 24.025 1 41.48 ? C2 GDP 201 R 1 HETATM 26 N N2 GDP . . . C 3 15.949 18.574 24.58 1 38.8 ? N2 GDP 201 R 1 HETATM 27 N N3 GDP . . . C 3 16.385 16.87 23.084 1 37.86 ? N3 GDP 201 R 1 HETATM 28 C C4 GDP . . . C 3 17.392 16.088 22.621 1 40.5 ? C4 GDP 201 R 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #