data_4GZM # _model_server_result.job_id 4IZDZHSNKXkIj4-VDeAdWw _model_server_result.datetime_utc '2024-12-03 13:10:49' _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 4gzm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1000}' # _entry.id 4GZM # _exptl.entry_id 4GZM _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 90.21 _cell.angle_gamma 90 _cell.entry_id 4GZM _cell.length_a 40.094 _cell.length_b 98.807 _cell.length_c 51.994 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GZM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA 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 1 1 B,E,F 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 metalc ? metalc1 A OG1 THR 44 A THR 17 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc2 A OG1 THR 62 A THR 35 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 C O3G GSP . A GSP 1000 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc4 C O2B GSP . A GSP 1000 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc5 B OG1 THR 44 B THR 17 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc6 B OG1 THR 62 B THR 35 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc7 B OD1 ASP 84 B ASP 57 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc8 E O3G GSP . B GSP 1000 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc9 E O2B GSP . B GSP 1000 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc10 E O2G GSP . B GSP 1000 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? # _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 4GZM _atom_sites.fract_transf_matrix[1][1] 0.024941 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000091 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010121 _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] 0.019233 _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 A 1 1000 1000 GSP GSP . D 3 MG A 1 1001 1001 MG MG . E 2 GSP B 1 1000 1000 GSP GSP . F 3 MG B 1 1001 1001 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 . . . E 2 -12.443 39.734 -3.871 1 129.9 ? PG GSP 1000 B 1 HETATM 2 O O3B GSP . . . E 2 -12.797 38.405 -3.034 1 127.69 ? O3B GSP 1000 B 1 HETATM 3 S S1G GSP . . . E 2 -13.649 39.844 -5.396 1 128.46 ? S1G GSP 1000 B 1 HETATM 4 O O2G GSP . . . E 2 -12.633 41.014 -2.912 1 125.04 ? O2G GSP 1000 B 1 HETATM 5 O O3G GSP . . . E 2 -10.925 39.669 -4.408 1 127.08 ? O3G GSP 1000 B 1 HETATM 6 P PB GSP . . . E 2 -11.663 37.57 -2.253 1 126.24 ? PB GSP 1000 B 1 HETATM 7 O O1B GSP . . . E 2 -11.215 36.44 -3.151 1 125.39 ? O1B GSP 1000 B 1 HETATM 8 O O2B GSP . . . E 2 -10.635 38.523 -1.687 1 124.07 ? O2B GSP 1000 B 1 HETATM 9 P PA GSP . . . E 2 -12.781 37.835 0.29 1 106.5 ? PA GSP 1000 B 1 HETATM 10 O O1A GSP . . . E 2 -13.416 39.14 -0.127 1 104.56 ? O1A GSP 1000 B 1 HETATM 11 O O2A GSP . . . E 2 -11.499 37.851 1.095 1 102.32 ? O2A GSP 1000 B 1 HETATM 12 O O3A GSP . . . E 2 -12.517 36.959 -1.034 1 115.14 ? O3A GSP 1000 B 1 HETATM 13 O O5' GSP . . . E 2 -13.887 36.955 1.068 1 107.86 ? O5' GSP 1000 B 1 HETATM 14 C C5' GSP . . . E 2 -14.961 36.312 0.375 1 105.92 ? C5' GSP 1000 B 1 HETATM 15 C C4' GSP . . . E 2 -15.969 35.684 1.337 1 104.78 ? C4' GSP 1000 B 1 HETATM 16 O O4' GSP . . . E 2 -15.561 34.352 1.662 1 105.03 ? O4' GSP 1000 B 1 HETATM 17 C C3' GSP . . . E 2 -16.126 36.452 2.645 1 108.04 ? C3' GSP 1000 B 1 HETATM 18 O O3' GSP . . . E 2 -17.399 37.103 2.701 1 110.95 ? O3' GSP 1000 B 1 HETATM 19 C C2' GSP . . . E 2 -15.998 35.422 3.753 1 109.45 ? C2' GSP 1000 B 1 HETATM 20 O O2' GSP . . . E 2 -17.219 35.254 4.479 1 113.43 ? O2' GSP 1000 B 1 HETATM 21 C C1' GSP . . . E 2 -15.627 34.117 3.071 1 109.03 ? C1' GSP 1000 B 1 HETATM 22 N N9 GSP . . . E 2 -14.303 33.71 3.596 1 112.62 ? N9 GSP 1000 B 1 HETATM 23 C C8 GSP . . . E 2 -13.109 34.236 3.258 1 115.62 ? C8 GSP 1000 B 1 HETATM 24 N N7 GSP . . . E 2 -12.095 33.637 3.934 1 113.86 ? N7 GSP 1000 B 1 HETATM 25 C C5 GSP . . . E 2 -12.646 32.706 4.728 1 113.15 ? C5 GSP 1000 B 1 HETATM 26 C C6 GSP . . . E 2 -12.149 31.712 5.705 1 115.01 ? C6 GSP 1000 B 1 HETATM 27 O O6 GSP . . . E 2 -10.929 31.605 5.946 1 114.53 ? O6 GSP 1000 B 1 HETATM 28 N N1 GSP . . . E 2 -13.051 30.931 6.318 1 118.77 ? N1 GSP 1000 B 1 HETATM 29 C C2 GSP . . . E 2 -14.377 31.023 6.072 1 117.32 ? C2 GSP 1000 B 1 HETATM 30 N N2 GSP . . . E 2 -15.221 30.198 6.735 1 117.75 ? N2 GSP 1000 B 1 HETATM 31 N N3 GSP . . . E 2 -14.904 31.912 5.188 1 114.02 ? N3 GSP 1000 B 1 HETATM 32 C C4 GSP . . . E 2 -14.101 32.76 4.503 1 113.54 ? C4 GSP 1000 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 495 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #