data_6UT3 # _model_server_result.job_id rPAmNSlT55-hU2skqqr6Dw _model_server_result.datetime_utc '2025-07-02 07:13:57' _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 6ut3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":700}' # _entry.id 6UT3 # _exptl.entry_id 6UT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.335 _cell.angle_gamma 90 _cell.entry_id 6UT3 _cell.length_a 102.474 _cell.length_b 109.619 _cell.length_c 120.782 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 I N N ? 3 K N N ? 3 M N 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 37 B THR 222 1_555 G MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc2 G MG MG . B MG 701 1_555 H O2G GSP . C GSP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc3 G MG MG . B MG 701 1_555 H O2B GSP . C GSP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc4 G MG MG . B MG 701 1_555 H O1B GSP . C GSP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc5 C OG1 THR 37 C THR 222 1_555 J MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc6 I O3G GSP . C GSP 702 1_555 J MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc7 I O1B GSP . C GSP 702 1_555 J MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc8 D OG1 THR 37 D THR 222 1_555 L MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc9 D OD2 ASP 171 D ASP 356 1_555 L MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc10 D OE2 GLU 172 D GLU 357 1_555 L MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc11 K O3G GSP . D GSP 700 1_555 L MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc12 K O1B GSP . D GSP 700 1_555 L MG MG . D MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc13 E OG1 THR 37 E THR 222 1_555 N MG MG . E MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc14 E OD2 ASP 171 E ASP 356 1_555 N MG MG . E MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc15 M O2G GSP . E GSP 700 1_555 N MG MG . E MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc16 M O1B GSP . E GSP 700 1_555 N MG MG . E MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? metalc ? metalc17 M O2B GSP . E GSP 700 1_555 N MG MG . E MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 O3B GSP sing 116 n n PG S1G GSP doub 117 n n PG O2G GSP sing 118 n n PG O3G GSP sing 119 n n O3B PB GSP sing 120 n n O2G HOG2 GSP sing 121 n n O3G HOG3 GSP sing 122 n n PB O1B GSP doub 123 n n PB O2B GSP sing 124 n n PB O3A GSP sing 125 n n O2B HOB2 GSP sing 126 n n PA O1A GSP doub 127 n n PA O2A GSP sing 128 n n PA O3A GSP sing 129 n n PA O5' GSP sing 130 n n O2A HOA2 GSP sing 131 n n O5' C5' GSP sing 132 n n C5' C4' GSP sing 133 n n C5' "H5'1" GSP sing 134 n n C5' "H5'2" GSP sing 135 n n C4' O4' GSP sing 136 n n C4' C3' GSP sing 137 n n C4' H4' GSP sing 138 n n O4' C1' GSP sing 139 n n C3' O3' GSP sing 140 n n C3' C2' GSP sing 141 n n C3' H3' GSP sing 142 n n O3' HO3' GSP sing 143 n n C2' O2' GSP sing 144 n n C2' C1' GSP sing 145 n n C2' H2' GSP sing 146 n n O2' HO2' GSP sing 147 n n C1' N9 GSP sing 148 n n C1' H1' GSP sing 149 n n N9 C8 GSP sing 150 n y N9 C4 GSP sing 151 n y C8 N7 GSP doub 152 n y C8 H8 GSP sing 153 n n N7 C5 GSP sing 154 n y C5 C6 GSP sing 155 n n C5 C4 GSP doub 156 n y C6 O6 GSP doub 157 n n C6 N1 GSP sing 158 n n N1 C2 GSP sing 159 n n N1 HN1 GSP sing 160 n n C2 N2 GSP sing 161 n n C2 N3 GSP doub 162 n n N2 HN21 GSP sing 163 n n N2 HN22 GSP sing 164 n n N3 C4 GSP sing 165 n n # _atom_sites.entry_id 6UT3 _atom_sites.fract_transf_matrix[1][1] 0.009759 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003234 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009123 _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] 0.008722 _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 2 MG B 1 701 701 MG MG . H 3 GSP C 1 701 700 GSP GSP . I 3 GSP C 1 702 700 GSP GSP . J 2 MG C 1 703 701 MG MG . K 3 GSP D 1 700 700 GSP GSP . L 2 MG D 1 701 701 MG MG . M 3 GSP E 1 700 700 GSP GSP . N 2 MG E 1 701 701 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 PG GSP . . . M 3 -10.054 19.945 391.159 1 113.82 ? PG GSP 700 E 1 HETATM 2 O O3B GSP . . . M 3 -10.55 20.884 392.341 1 113.82 ? O3B GSP 700 E 1 HETATM 3 S S1G GSP . . . M 3 -11.449 19.683 389.871 1 113.82 ? S1G GSP 700 E 1 HETATM 4 O O2G GSP . . . M 3 -9.678 18.728 391.951 1 113.82 ? O2G GSP 700 E 1 HETATM 5 O O3G GSP . . . M 3 -8.837 20.652 390.653 1 113.82 ? O3G GSP 700 E 1 HETATM 6 P PB GSP . . . M 3 -11.284 20.422 393.675 1 113.82 ? PB GSP 700 E 1 HETATM 7 O O1B GSP . . . M 3 -12.668 20.006 393.343 1 113.82 ? O1B GSP 700 E 1 HETATM 8 O O2B GSP . . . M 3 -10.392 19.483 394.406 1 113.82 ? O2B GSP 700 E 1 HETATM 9 P PA GSP . . . M 3 -11.624 21.908 396.036 1 113.82 ? PA GSP 700 E 1 HETATM 10 O O1A GSP . . . M 3 -13.056 21.589 396.284 1 113.82 ? O1A GSP 700 E 1 HETATM 11 O O2A GSP . . . M 3 -10.6 21.087 396.739 1 113.82 ? O2A GSP 700 E 1 HETATM 12 O O3A GSP . . . M 3 -11.327 21.796 394.478 1 113.82 ? O3A GSP 700 E 1 HETATM 13 O O5' GSP . . . M 3 -11.347 23.452 396.321 1 113.82 ? O5' GSP 700 E 1 HETATM 14 C C5' GSP . . . M 3 -10.015 23.952 396.078 1 113.82 ? C5' GSP 700 E 1 HETATM 15 C C4' GSP . . . M 3 -9.723 25.032 397.087 1 113.82 ? C4' GSP 700 E 1 HETATM 16 O O4' GSP . . . M 3 -10.859 25.935 397.114 1 113.82 ? O4' GSP 700 E 1 HETATM 17 C C3' GSP . . . M 3 -9.547 24.566 398.539 1 113.82 ? C3' GSP 700 E 1 HETATM 18 O O3' GSP . . . M 3 -8.659 25.444 399.215 1 113.82 ? O3' GSP 700 E 1 HETATM 19 C C2' GSP . . . M 3 -10.953 24.778 399.098 1 113.82 ? C2' GSP 700 E 1 HETATM 20 O O2' GSP . . . M 3 -11.007 24.833 400.505 1 113.82 ? O2' GSP 700 E 1 HETATM 21 C C1' GSP . . . M 3 -11.273 26.113 398.446 1 113.82 ? C1' GSP 700 E 1 HETATM 22 N N9 GSP . . . M 3 -12.694 26.43 398.435 1 113.82 ? N9 GSP 700 E 1 HETATM 23 C C8 GSP . . . M 3 -13.53 26.374 397.351 1 113.82 ? C8 GSP 700 E 1 HETATM 24 N N7 GSP . . . M 3 -14.766 26.706 397.63 1 113.82 ? N7 GSP 700 E 1 HETATM 25 C C5 GSP . . . M 3 -14.743 26.987 398.988 1 113.82 ? C5 GSP 700 E 1 HETATM 26 C C6 GSP . . . M 3 -15.79 27.397 399.846 1 113.82 ? C6 GSP 700 E 1 HETATM 27 O O6 GSP . . . M 3 -16.978 27.592 399.562 1 113.82 ? O6 GSP 700 E 1 HETATM 28 N N1 GSP . . . M 3 -15.339 27.575 401.153 1 113.82 ? N1 GSP 700 E 1 HETATM 29 C C2 GSP . . . M 3 -14.048 27.384 401.576 1 113.82 ? C2 GSP 700 E 1 HETATM 30 N N2 GSP . . . M 3 -13.806 27.605 402.874 1 113.82 ? N2 GSP 700 E 1 HETATM 31 N N3 GSP . . . M 3 -13.057 26.999 400.773 1 113.82 ? N3 GSP 700 E 1 HETATM 32 C C4 GSP . . . M 3 -13.475 26.82 399.497 1 113.82 ? C4 GSP 700 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #