data_1YHN # _model_server_result.job_id OcFdzVx2LW4kdh3wEc5huw _model_server_result.datetime_utc '2024-12-03 14:25:11' _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 1yhn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 1YHN # _exptl.entry_id 1YHN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 1YHN _cell.length_a 93.134 _cell.length_b 93.134 _cell.length_c 132.826 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YHN _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 66.413 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 OG1 THR 22 A THR 22 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 A OG1 THR 40 A THR 40 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc3 A OD1 ASP 63 A ASP 63 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc4 A OD2 ASP 63 A ASP 63 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.114 ? metalc ? metalc5 A O THR 64 A THR 64 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.068 ? metalc ? metalc6 D O1G GTP . A GTP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc7 D O3B GTP . A GTP 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 1YHN _atom_sites.fract_transf_matrix[1][1] 0.010737 _atom_sites.fract_transf_matrix[1][2] 0.006199 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012398 _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] 0.007529 _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 MG A 1 302 302 MG MG . D 4 GTP A 1 301 301 GTP GTP . E 5 HOH A 1 303 1 HOH WAT . E 5 HOH A 2 304 2 HOH WAT . E 5 HOH A 3 305 4 HOH WAT . E 5 HOH A 4 306 5 HOH WAT . E 5 HOH A 5 307 6 HOH WAT . E 5 HOH A 6 308 7 HOH WAT . E 5 HOH A 7 309 8 HOH WAT . E 5 HOH A 8 310 9 HOH WAT . E 5 HOH A 9 311 11 HOH WAT . E 5 HOH A 10 312 12 HOH WAT . E 5 HOH A 11 313 13 HOH WAT . E 5 HOH A 12 314 15 HOH WAT . E 5 HOH A 13 315 16 HOH WAT . E 5 HOH A 14 316 17 HOH WAT . E 5 HOH A 15 317 18 HOH WAT . E 5 HOH A 16 318 21 HOH WAT . E 5 HOH A 17 319 22 HOH WAT . E 5 HOH A 18 320 23 HOH WAT . E 5 HOH A 19 321 24 HOH WAT . E 5 HOH A 20 322 26 HOH WAT . E 5 HOH A 21 323 28 HOH WAT . E 5 HOH A 22 324 29 HOH WAT . E 5 HOH A 23 325 30 HOH WAT . E 5 HOH A 24 326 31 HOH WAT . E 5 HOH A 25 327 32 HOH WAT . E 5 HOH A 26 328 34 HOH WAT . E 5 HOH A 27 329 36 HOH WAT . F 5 HOH B 1 3 3 HOH WAT . F 5 HOH B 2 10 10 HOH WAT . F 5 HOH B 3 14 14 HOH WAT . F 5 HOH B 4 19 19 HOH WAT . F 5 HOH B 5 25 25 HOH WAT . F 5 HOH B 6 27 27 HOH WAT . F 5 HOH B 7 33 33 HOH WAT . # 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 PG GTP . . . D 4 16.842 65.886 32.24 1 46.92 ? PG GTP 301 A 1 HETATM 2 O O1G GTP . . . D 4 15.975 66.595 33.257 1 48.09 ? O1G GTP 301 A 1 HETATM 3 O O2G GTP . . . D 4 16.28 65.839 30.843 1 47.12 ? O2G GTP 301 A 1 HETATM 4 O O3G GTP . . . D 4 17.107 64.46 32.705 1 44.27 ? O3G GTP 301 A 1 HETATM 5 O O3B GTP . . . D 4 18.218 66.709 32.168 1 48.13 ? O3B GTP 301 A 1 HETATM 6 P PB GTP . . . D 4 19.373 66.561 33.226 1 46.81 ? PB GTP 301 A 1 HETATM 7 O O1B GTP . . . D 4 20.579 67.333 32.965 1 47.4 ? O1B GTP 301 A 1 HETATM 8 O O2B GTP . . . D 4 19.66 65.161 33.351 1 50.04 ? O2B GTP 301 A 1 HETATM 9 O O3A GTP . . . D 4 18.841 66.944 34.621 1 47.69 ? O3A GTP 301 A 1 HETATM 10 P PA GTP . . . D 4 19.341 67.799 35.866 1 48.63 ? PA GTP 301 A 1 HETATM 11 O O1A GTP . . . D 4 18.153 67.849 36.784 1 51.23 ? O1A GTP 301 A 1 HETATM 12 O O2A GTP . . . D 4 19.953 69.074 35.406 1 48.48 ? O2A GTP 301 A 1 HETATM 13 O O5' GTP . . . D 4 20.316 66.856 36.668 1 46.06 ? O5' GTP 301 A 1 HETATM 14 C C5' GTP . . . D 4 21.462 66.159 36.292 1 47.28 ? C5' GTP 301 A 1 HETATM 15 C C4' GTP . . . D 4 21.938 65.397 37.557 1 46.8 ? C4' GTP 301 A 1 HETATM 16 O O4' GTP . . . D 4 23.377 65.465 37.708 1 47 ? O4' GTP 301 A 1 HETATM 17 C C3' GTP . . . D 4 21.403 65.91 38.925 1 46.13 ? C3' GTP 301 A 1 HETATM 18 O O3' GTP . . . D 4 21.173 64.84 39.835 1 43.78 ? O3' GTP 301 A 1 HETATM 19 C C2' GTP . . . D 4 22.461 66.858 39.38 1 46 ? C2' GTP 301 A 1 HETATM 20 O O2' GTP . . . D 4 22.549 66.873 40.807 1 46.15 ? O2' GTP 301 A 1 HETATM 21 C C1' GTP . . . D 4 23.729 66.338 38.801 1 46.18 ? C1' GTP 301 A 1 HETATM 22 N N9 GTP . . . D 4 24.626 67.359 38.237 1 46.11 ? N9 GTP 301 A 1 HETATM 23 C C8 GTP . . . D 4 24.296 68.32 37.308 1 45.75 ? C8 GTP 301 A 1 HETATM 24 N N7 GTP . . . D 4 25.281 69.1 36.995 1 46.29 ? N7 GTP 301 A 1 HETATM 25 C C5 GTP . . . D 4 26.336 68.643 37.767 1 46.38 ? C5 GTP 301 A 1 HETATM 26 C C6 GTP . . . D 4 27.694 69.09 37.868 1 47 ? C6 GTP 301 A 1 HETATM 27 O O6 GTP . . . D 4 28.263 70.024 37.292 1 47.96 ? O6 GTP 301 A 1 HETATM 28 N N1 GTP . . . D 4 28.44 68.329 38.785 1 47.08 ? N1 GTP 301 A 1 HETATM 29 C C2 GTP . . . D 4 27.942 67.26 39.505 1 46.96 ? C2 GTP 301 A 1 HETATM 30 N N2 GTP . . . D 4 28.817 66.664 40.321 1 47.9 ? N2 GTP 301 A 1 HETATM 31 N N3 GTP . . . D 4 26.688 66.832 39.417 1 46.26 ? N3 GTP 301 A 1 HETATM 32 C C4 GTP . . . D 4 25.938 67.569 38.535 1 46.31 ? C4 GTP 301 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #