data_4MGZ # _model_server_result.job_id x9TWRayi_Lc0spXFbgKv1Q _model_server_result.datetime_utc '2025-01-11 07:54:10' _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 4mgz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 4MGZ # _exptl.entry_id 4MGZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.459 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide' _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 4MGZ _cell.length_a 125.228 _cell.length_b 147.088 _cell.length_c 226.74 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MGZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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' 8_554 x,-y,-z-1/2 1 0 0 0 -1 0 0 0 -1 0 0 -113.37 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # _chem_comp.formula 'C17 H18 N5 O5 P S2' _chem_comp.formula_weight 467.459 _chem_comp.id HR6 _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,4aR,6R,7R,7aS)-6-[6-amino-8-(benzylsulfanyl)-9H-purin-9-yl]-2-sulfanyltetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-7-ol 2-oxide' _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 O2P P HR6 doub 152 n n O5' C5' HR6 sing 153 n n O5' P HR6 sing 154 n n C5' C4' HR6 sing 155 n n P O3' HR6 sing 156 n n P S1P HR6 sing 157 n n C4' O4' HR6 sing 158 n n C4' C3' HR6 sing 159 n n O3' C3' HR6 sing 160 n n O4' C1' HR6 sing 161 n n C3' C2' HR6 sing 162 n n O2' C2' HR6 sing 163 n n C2' C1' HR6 sing 164 n n C1' N9 HR6 sing 165 n n N3 C4 HR6 doub 166 n y N3 C2 HR6 sing 167 n y N9 C4 HR6 sing 168 n y N9 C8 HR6 sing 169 n y C4 C5 HR6 sing 170 n y C2 N1 HR6 doub 171 n y S2 C8 HR6 sing 172 n n S2 C9 HR6 sing 173 n n C8 N7 HR6 doub 174 n y N1 C6 HR6 sing 175 n y C5 N7 HR6 sing 176 n y C5 C6 HR6 doub 177 n y C6 N6 HR6 sing 178 n n C15 C14 HR6 doub 179 n y C15 C10 HR6 sing 180 n y C14 C13 HR6 sing 181 n y C9 C10 HR6 sing 182 n n C10 C11 HR6 doub 183 n y C13 C12 HR6 doub 184 n y C11 C12 HR6 sing 185 n y S1P H1 HR6 sing 186 n n C5' H2 HR6 sing 187 n n C5' H3 HR6 sing 188 n n C3' H4 HR6 sing 189 n n C2' H5 HR6 sing 190 n n O2' H6 HR6 sing 191 n n C4' H7 HR6 sing 192 n n C1' H8 HR6 sing 193 n n C2 H9 HR6 sing 194 n n N6 H10 HR6 sing 195 n n N6 H11 HR6 sing 196 n n C9 H12 HR6 sing 197 n n C9 H13 HR6 sing 198 n n C15 H14 HR6 sing 199 n n C14 H15 HR6 sing 200 n n C11 H16 HR6 sing 201 n n C12 H17 HR6 sing 202 n n C13 H18 HR6 sing 203 n n # _atom_sites.entry_id 4MGZ _atom_sites.fract_transf_matrix[1][1] 0.007985 _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] 0.006799 _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] 0.00441 _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 HR6 E 1 1001 2 HR6 HR6 . D 3 HR6 E 1 1002 3 HR6 HR6 . E 4 SO4 R 1 201 1 SO4 SO4 . F 5 HOH E 1 1101 1 HOH HOH . F 5 HOH E 2 1102 2 HOH HOH . F 5 HOH E 3 1103 3 HOH HOH . F 5 HOH E 4 1104 4 HOH HOH . F 5 HOH E 5 1105 5 HOH HOH . F 5 HOH E 6 1106 6 HOH HOH . F 5 HOH E 7 1107 7 HOH HOH . F 5 HOH E 8 1108 8 HOH HOH . F 5 HOH E 9 1109 9 HOH HOH . F 5 HOH E 10 1110 10 HOH HOH . F 5 HOH E 11 1111 11 HOH HOH . F 5 HOH E 12 1112 12 HOH HOH . F 5 HOH E 13 1113 13 HOH HOH . F 5 HOH E 14 1114 14 HOH HOH . F 5 HOH E 15 1115 15 HOH HOH . F 5 HOH E 16 1116 17 HOH HOH . F 5 HOH E 17 1117 18 HOH HOH . F 5 HOH E 18 1118 19 HOH HOH . F 5 HOH E 19 1119 20 HOH HOH . F 5 HOH E 20 1120 21 HOH HOH . F 5 HOH E 21 1121 22 HOH HOH . F 5 HOH E 22 1122 23 HOH HOH . F 5 HOH E 23 1123 24 HOH HOH . F 5 HOH E 24 1124 25 HOH HOH . F 5 HOH E 25 1125 26 HOH HOH . F 5 HOH E 26 1126 28 HOH HOH . F 5 HOH E 27 1127 29 HOH HOH . F 5 HOH E 28 1128 30 HOH HOH . F 5 HOH E 29 1129 31 HOH HOH . F 5 HOH E 30 1130 32 HOH HOH . F 5 HOH E 31 1131 34 HOH HOH . F 5 HOH E 32 1132 35 HOH HOH . F 5 HOH E 33 1133 36 HOH HOH . F 5 HOH E 34 1134 37 HOH HOH . F 5 HOH E 35 1135 38 HOH HOH . F 5 HOH E 36 1136 39 HOH HOH . F 5 HOH E 37 1137 40 HOH HOH . F 5 HOH E 38 1138 41 HOH HOH . F 5 HOH E 39 1139 42 HOH HOH . F 5 HOH E 40 1140 43 HOH HOH . F 5 HOH E 41 1141 46 HOH HOH . F 5 HOH E 42 1142 47 HOH HOH . F 5 HOH E 43 1143 48 HOH HOH . F 5 HOH E 44 1144 49 HOH HOH . F 5 HOH E 45 1145 50 HOH HOH . F 5 HOH E 46 1146 51 HOH HOH . F 5 HOH E 47 1147 52 HOH HOH . F 5 HOH E 48 1148 53 HOH HOH . F 5 HOH E 49 1149 55 HOH HOH . F 5 HOH E 50 1150 56 HOH HOH . F 5 HOH E 51 1151 57 HOH HOH . F 5 HOH E 52 1152 58 HOH HOH . F 5 HOH E 53 1153 59 HOH HOH . F 5 HOH E 54 1154 60 HOH HOH . F 5 HOH E 55 1155 61 HOH HOH . F 5 HOH E 56 1156 62 HOH HOH . F 5 HOH E 57 1157 64 HOH HOH . F 5 HOH E 58 1158 65 HOH HOH . F 5 HOH E 59 1159 66 HOH HOH . F 5 HOH E 60 1160 67 HOH HOH . G 5 HOH R 1 301 16 HOH HOH . G 5 HOH R 2 302 27 HOH HOH . G 5 HOH R 3 303 33 HOH HOH . G 5 HOH R 4 304 44 HOH HOH . G 5 HOH R 5 305 45 HOH HOH . G 5 HOH R 6 306 54 HOH HOH . G 5 HOH R 7 307 63 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 S S1P HR6 . . . D 3 -2.887 -29.847 -61.89 1 77.66 ? S1P HR6 1002 E 1 HETATM 2 P P HR6 . . . D 3 -4.741 -30.414 -62.113 1 77.31 ? P HR6 1002 E 1 HETATM 3 O O2P HR6 . . . D 3 -5.064 -31.689 -61.189 1 77.27 ? O2P HR6 1002 E 1 HETATM 4 O O5' HR6 . . . D 3 -5.716 -29.166 -61.78 1 77.65 ? O5' HR6 1002 E 1 HETATM 5 C C5' HR6 . . . D 3 -5.858 -28.072 -62.699 1 78.01 ? C5' HR6 1002 E 1 HETATM 6 O O3' HR6 . . . D 3 -5.061 -30.729 -63.661 1 77.78 ? O3' HR6 1002 E 1 HETATM 7 C C3' HR6 . . . D 3 -5.071 -29.588 -64.51 1 78.32 ? C3' HR6 1002 E 1 HETATM 8 C C2' HR6 . . . D 3 -5.341 -29.772 -65.991 1 78.61 ? C2' HR6 1002 E 1 HETATM 9 O O2' HR6 . . . D 3 -6.281 -30.825 -66.231 1 78.65 ? O2' HR6 1002 E 1 HETATM 10 C C4' HR6 . . . D 3 -6.174 -28.647 -64.076 1 78.34 ? C4' HR6 1002 E 1 HETATM 11 O O4' HR6 . . . D 3 -6.229 -27.711 -65.153 1 78.72 ? O4' HR6 1002 E 1 HETATM 12 C C1' HR6 . . . D 3 -5.919 -28.406 -66.377 1 78.97 ? C1' HR6 1002 E 1 HETATM 13 N N9 HR6 . . . D 3 -4.967 -27.612 -67.219 1 79.56 ? N9 HR6 1002 E 1 HETATM 14 C C4 HR6 . . . D 3 -3.644 -27.426 -67.04 1 79.73 ? C4 HR6 1002 E 1 HETATM 15 N N3 HR6 . . . D 3 -2.73 -27.838 -66.12 1 79.87 ? N3 HR6 1002 E 1 HETATM 16 C C2 HR6 . . . D 3 -1.432 -27.487 -66.197 1 79.87 ? C2 HR6 1002 E 1 HETATM 17 N N1 HR6 . . . D 3 -0.934 -26.71 -67.174 1 79.83 ? N1 HR6 1002 E 1 HETATM 18 C C6 HR6 . . . D 3 -1.722 -26.224 -68.158 1 79.77 ? C6 HR6 1002 E 1 HETATM 19 N N6 HR6 . . . D 3 -1.145 -25.37 -69.223 1 79.98 ? N6 HR6 1002 E 1 HETATM 20 C C5 HR6 . . . D 3 -3.165 -26.566 -68.15 1 79.73 ? C5 HR6 1002 E 1 HETATM 21 N N7 HR6 . . . D 3 -4.222 -26.277 -68.933 1 79.84 ? N7 HR6 1002 E 1 HETATM 22 C C8 HR6 . . . D 3 -5.249 -26.918 -68.336 1 79.8 ? C8 HR6 1002 E 1 HETATM 23 S S2 HR6 . . . D 3 -6.856 -26.822 -69.021 1 79.86 ? S2 HR6 1002 E 1 HETATM 24 C C9 HR6 . . . D 3 -7.438 -28.018 -69.909 0 20 ? C9 HR6 1002 E 1 HETATM 25 C C10 HR6 . . . D 3 -8.234 -27.879 -71.226 0 20 ? C10 HR6 1002 E 1 HETATM 26 C C15 HR6 . . . D 3 -9.637 -28.096 -71.225 0 20 ? C15 HR6 1002 E 1 HETATM 27 C C14 HR6 . . . D 3 -10.361 -27.997 -72.426 0 20 ? C14 HR6 1002 E 1 HETATM 28 C C11 HR6 . . . D 3 -7.579 -27.583 -72.456 0 20 ? C11 HR6 1002 E 1 HETATM 29 C C12 HR6 . . . D 3 -8.303 -27.487 -73.656 0 20 ? C12 HR6 1002 E 1 HETATM 30 C C13 HR6 . . . D 3 -9.692 -27.695 -73.633 0 20 ? C13 HR6 1002 E 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 30 #