data_5C46 # _model_server_result.job_id AVSQnA5sWTF9sjDaLRM4Zg _model_server_result.datetime_utc '2024-11-08 15:34:03' _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 5c46 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2000}' # _entry.id 5C46 # _exptl.entry_id 5C46 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 5C46 _cell.length_a 48.94 _cell.length_b 97.95 _cell.length_c 190.43 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C46 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 4 _struct_asym.id E _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 B OG SER 28 F SER 25 1_555 F MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 B OG1 THR 46 F THR 43 1_555 F MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc3 E O3G GSP . F GSP 2000 1_555 F MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc4 E O2B GSP . F GSP 2000 1_555 F MG MG . F MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? # _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 5C46 _atom_sites.fract_transf_matrix[1][1] 0.020433 _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] 0.010209 _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] 0.005251 _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 SO4 E 1 801 2 SO4 SO4 . D 3 SO4 E 1 802 3 SO4 SO4 . E 4 GSP F 1 2000 2000 GSP GSP . F 5 MG F 1 2001 2001 MG MG . G 6 HOH E 1 901 1 HOH HOH . G 6 HOH E 2 902 4 HOH HOH . G 6 HOH E 3 903 3 HOH HOH . H 6 HOH F 1 2101 5 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 . . . E 4 -6.959 5.753 18.415 1 129.21 ? PG GSP 2000 F 1 HETATM 2 O O3B GSP . . . E 4 -8.133 5.884 17.319 1 61.67 ? O3B GSP 2000 F 1 HETATM 3 S S1G GSP . . . E 4 -5.444 5.71 17.647 1 106.34 ? S1G GSP 2000 F 1 HETATM 4 O O2G GSP . . . E 4 -7.164 4.475 19.248 1 130.15 ? O2G GSP 2000 F 1 HETATM 5 O O3G GSP . . . E 4 -7.017 6.967 19.359 1 131.08 ? O3G GSP 2000 F 1 HETATM 6 P PB GSP . . . E 4 -9.676 5.947 17.782 1 55.19 ? PB GSP 2000 F 1 HETATM 7 O O1B GSP . . . E 4 -10.099 4.636 18.327 1 58.95 ? O1B GSP 2000 F 1 HETATM 8 O O2B GSP . . . E 4 -9.876 7.043 18.762 1 64.64 ? O2B GSP 2000 F 1 HETATM 9 P PA GSP . . . E 4 -10.955 7.709 16.003 1 57.15 ? PA GSP 2000 F 1 HETATM 10 O O1A GSP . . . E 4 -9.8 8.61 15.792 1 55.76 ? O1A GSP 2000 F 1 HETATM 11 O O2A GSP . . . E 4 -11.889 8.252 17.013 1 62.93 ? O2A GSP 2000 F 1 HETATM 12 O O3A GSP . . . E 4 -10.49 6.228 16.424 1 72.82 ? O3A GSP 2000 F 1 HETATM 13 O O5' GSP . . . E 4 -11.743 7.404 14.635 1 67.44 ? O5' GSP 2000 F 1 HETATM 14 C C5' GSP . . . E 4 -11.054 6.923 13.502 1 62.29 ? C5' GSP 2000 F 1 HETATM 15 C C4' GSP . . . E 4 -11.788 7.369 12.246 1 57.16 ? C4' GSP 2000 F 1 HETATM 16 O O4' GSP . . . E 4 -13.048 6.722 12.189 1 55.36 ? O4' GSP 2000 F 1 HETATM 17 C C3' GSP . . . E 4 -12.035 8.867 12.27 1 63.51 ? C3' GSP 2000 F 1 HETATM 18 O O3' GSP . . . E 4 -11.613 9.434 11.053 1 73.46 ? O3' GSP 2000 F 1 HETATM 19 C C2' GSP . . . E 4 -13.533 9.015 12.415 1 67.3 ? C2' GSP 2000 F 1 HETATM 20 O O2' GSP . . . E 4 -14.013 9.975 11.511 1 77.71 ? O2' GSP 2000 F 1 HETATM 21 C C1' GSP . . . E 4 -14.101 7.657 12.05 1 63.11 ? C1' GSP 2000 F 1 HETATM 22 N N9 GSP . . . E 4 -15.22 7.34 12.955 1 70.62 ? N9 GSP 2000 F 1 HETATM 23 C C8 GSP . . . E 4 -15.159 7.289 14.322 1 72.49 ? C8 GSP 2000 F 1 HETATM 24 N N7 GSP . . . E 4 -16.386 6.972 14.796 1 72.57 ? N7 GSP 2000 F 1 HETATM 25 C C5 GSP . . . E 4 -17.232 6.824 13.753 1 77.14 ? C5 GSP 2000 F 1 HETATM 26 C C6 GSP . . . E 4 -18.584 6.506 13.68 1 82 ? C6 GSP 2000 F 1 HETATM 27 O O6 GSP . . . E 4 -19.23 6.298 14.706 1 81.35 ? O6 GSP 2000 F 1 HETATM 28 N N1 GSP . . . E 4 -19.197 6.421 12.447 1 85.6 ? N1 GSP 2000 F 1 HETATM 29 C C2 GSP . . . E 4 -18.466 6.653 11.299 1 80.4 ? C2 GSP 2000 F 1 HETATM 30 N N2 GSP . . . E 4 -19.057 6.572 10.11 1 79.19 ? N2 GSP 2000 F 1 HETATM 31 N N3 GSP . . . E 4 -17.124 6.969 11.38 1 75.59 ? N3 GSP 2000 F 1 HETATM 32 C C4 GSP . . . E 4 -16.513 7.054 12.587 1 75.25 ? C4 GSP 2000 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #