data_4TN1 # _model_server_result.job_id kHLkRHv2VX8s35L08Rn4aQ _model_server_result.datetime_utc '2024-11-27 04:18:50' _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 4tn1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":901}' # _entry.id 4TN1 # _exptl.entry_id 4TN1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 4TN1 _cell.length_a 115.69 _cell.length_b 115.69 _cell.length_c 119.8 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TN1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? Monomeric 1 author_and_software_defined_assembly 1 ? Monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 E 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 disulf ? disulf1 A SG CYS 14 B CYS 527 1_555 A SG CYS 99 B CYS 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc1 A OG1 THR 24 B THR 537 1_555 D MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc2 A OG1 THR 44 B THR 557 1_555 D MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 C O3G GSP . B GSP 901 1_555 D MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc4 C O2B GSP . B GSP 901 1_555 D MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.877 ? metalc ? metalc5 D MG MG . B MG 902 1_555 G O HOH . B HOH 1029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 D MG MG . B MG 902 1_555 G O HOH . B HOH 1030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc7 B OG1 THR 24 A THR 537 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc8 B OG1 THR 44 A THR 557 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc9 E O3G GSP . A GSP 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.893 ? metalc ? metalc10 E O2B GSP . A GSP 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc11 F MG MG . A MG 902 1_555 H O HOH . A HOH 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc12 F MG MG . A MG 902 1_555 H O HOH . A HOH 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? # _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 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 4TN1 _atom_sites.fract_transf_matrix[1][1] 0.008644 _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] 0.008644 _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] 0.008347 _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 2 GSP B 1 901 4014 GSP GSP . D 3 MG B 1 902 2 MG MG . E 2 GSP A 1 901 4015 GSP GSP . F 3 MG A 1 902 1 MG MG . G 4 HOH B 1 1001 29 HOH HOH . G 4 HOH B 2 1002 47 HOH HOH . G 4 HOH B 3 1003 1 HOH HOH . G 4 HOH B 4 1004 3 HOH HOH . G 4 HOH B 5 1005 5 HOH HOH . G 4 HOH B 6 1006 7 HOH HOH . G 4 HOH B 7 1007 9 HOH HOH . G 4 HOH B 8 1008 10 HOH HOH . G 4 HOH B 9 1009 12 HOH HOH . G 4 HOH B 10 1010 13 HOH HOH . G 4 HOH B 11 1011 14 HOH HOH . G 4 HOH B 12 1012 15 HOH HOH . G 4 HOH B 13 1013 16 HOH HOH . G 4 HOH B 14 1014 17 HOH HOH . G 4 HOH B 15 1015 18 HOH HOH . G 4 HOH B 16 1016 21 HOH HOH . G 4 HOH B 17 1017 23 HOH HOH . G 4 HOH B 18 1018 24 HOH HOH . G 4 HOH B 19 1019 27 HOH HOH . G 4 HOH B 20 1020 30 HOH HOH . G 4 HOH B 21 1021 33 HOH HOH . G 4 HOH B 22 1022 34 HOH HOH . G 4 HOH B 23 1023 37 HOH HOH . G 4 HOH B 24 1024 38 HOH HOH . G 4 HOH B 25 1025 40 HOH HOH . G 4 HOH B 26 1026 42 HOH HOH . G 4 HOH B 27 1027 43 HOH HOH . G 4 HOH B 28 1028 52 HOH HOH . G 4 HOH B 29 1029 53 HOH HOH . G 4 HOH B 30 1030 54 HOH HOH . G 4 HOH B 31 1031 55 HOH HOH . G 4 HOH B 32 1032 56 HOH HOH . H 4 HOH A 1 1001 39 HOH HOH . H 4 HOH A 2 1002 6 HOH HOH . H 4 HOH A 3 1003 4 HOH HOH . H 4 HOH A 4 1004 11 HOH HOH . H 4 HOH A 5 1005 19 HOH HOH . H 4 HOH A 6 1006 20 HOH HOH . H 4 HOH A 7 1007 22 HOH HOH . H 4 HOH A 8 1008 25 HOH HOH . H 4 HOH A 9 1009 26 HOH HOH . H 4 HOH A 10 1010 32 HOH HOH . H 4 HOH A 11 1011 36 HOH HOH . H 4 HOH A 12 1012 45 HOH HOH . H 4 HOH A 13 1013 48 HOH HOH . H 4 HOH A 14 1014 49 HOH HOH . H 4 HOH A 15 1015 50 HOH HOH . H 4 HOH A 16 1016 51 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 PG GSP . . . C 2 -15.816 -36.859 -22.898 1 52.47 ? PG GSP 901 B 1 HETATM 2 O O3B GSP . . . C 2 -16.3 -35.376 -23.283 1 25.38 ? O3B GSP 901 B 1 HETATM 3 S S1G GSP . . . C 2 -16.556 -37.979 -23.952 1 43.16 ? S1G GSP 901 B 1 HETATM 4 O O2G GSP . . . C 2 -16.218 -37.166 -21.445 1 38.45 ? O2G GSP 901 B 1 HETATM 5 O O3G GSP . . . C 2 -14.286 -36.918 -23.025 1 26.86 ? O3G GSP 901 B 1 HETATM 6 P PB GSP . . . C 2 -15.372 -34.088 -23.058 1 35.76 ? PB GSP 901 B 1 HETATM 7 O O1B GSP . . . C 2 -15.424 -33.648 -21.649 1 38.98 ? O1B GSP 901 B 1 HETATM 8 O O2B GSP . . . C 2 -13.987 -34.334 -23.509 1 41.73 ? O2B GSP 901 B 1 HETATM 9 P PA GSP . . . C 2 -15.764 -32.737 -25.503 1 50.42 ? PA GSP 901 B 1 HETATM 10 O O1A GSP . . . C 2 -14.522 -31.946 -25.641 1 34.53 ? O1A GSP 901 B 1 HETATM 11 O O2A GSP . . . C 2 -15.694 -34.008 -26.255 1 37.06 ? O2A GSP 901 B 1 HETATM 12 O O3A GSP . . . C 2 -16.105 -32.975 -23.951 1 49.39 ? O3A GSP 901 B 1 HETATM 13 O O5' GSP . . . C 2 -17.027 -31.843 -25.925 1 42.61 ? O5' GSP 901 B 1 HETATM 14 C C5' GSP . . . C 2 -18.313 -32.416 -26.001 1 35.64 ? C5' GSP 901 B 1 HETATM 15 C C4' GSP . . . C 2 -19.185 -31.55 -26.896 1 39.27 ? C4' GSP 901 B 1 HETATM 16 O O4' GSP . . . C 2 -19.462 -30.336 -26.222 1 42.4 ? O4' GSP 901 B 1 HETATM 17 C C3' GSP . . . C 2 -18.46 -31.206 -28.188 1 44.61 ? C3' GSP 901 B 1 HETATM 18 O O3' GSP . . . C 2 -19.318 -31.404 -29.289 1 38.09 ? O3' GSP 901 B 1 HETATM 19 C C2' GSP . . . C 2 -18.125 -29.737 -28.064 1 46.99 ? C2' GSP 901 B 1 HETATM 20 O O2' GSP . . . C 2 -18.318 -29.092 -29.299 1 59.96 ? O2' GSP 901 B 1 HETATM 21 C C1' GSP . . . C 2 -19.098 -29.222 -27.016 1 45.49 ? C1' GSP 901 B 1 HETATM 22 N N9 GSP . . . C 2 -18.449 -28.178 -26.201 1 44.98 ? N9 GSP 901 B 1 HETATM 23 C C8 GSP . . . C 2 -17.338 -28.338 -25.416 1 41.08 ? C8 GSP 901 B 1 HETATM 24 N N7 GSP . . . C 2 -17.046 -27.15 -24.839 1 40.83 ? N7 GSP 901 B 1 HETATM 25 C C5 GSP . . . C 2 -17.951 -26.231 -25.248 1 44.16 ? C5 GSP 901 B 1 HETATM 26 C C6 GSP . . . C 2 -18.111 -24.878 -24.966 1 45.98 ? C6 GSP 901 B 1 HETATM 27 O O6 GSP . . . C 2 -17.335 -24.299 -24.204 1 47.77 ? O6 GSP 901 B 1 HETATM 28 N N1 GSP . . . C 2 -19.154 -24.182 -25.539 1 47.33 ? N1 GSP 901 B 1 HETATM 29 C C2 GSP . . . C 2 -20.027 -24.829 -26.388 1 48.68 ? C2 GSP 901 B 1 HETATM 30 N N2 GSP . . . C 2 -21.032 -24.155 -26.941 1 49.16 ? N2 GSP 901 B 1 HETATM 31 N N3 GSP . . . C 2 -19.861 -26.172 -26.664 1 44.32 ? N3 GSP 901 B 1 HETATM 32 C C4 GSP . . . C 2 -18.84 -26.864 -26.105 1 41.7 ? C4 GSP 901 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #