data_5FV7 # _model_server_result.job_id eT27Fo7KpbphHlpSyFoxcA _model_server_result.datetime_utc '2025-01-11 04:46:15' _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 5fv7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1341}' # _entry.id 5FV7 # _exptl.entry_id 5FV7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.331 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 102.06 _cell.angle_beta 94.01 _cell.angle_gamma 90.74 _cell.entry_id 5FV7 _cell.length_a 43.339 _cell.length_b 50.193 _cell.length_c 66.945 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FV7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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,E,I 1 1 B,F,G,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 ? 3 E N N ? 3 H 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 OE1 GLU 160 A GLU 160 1_555 C MG MG . A MG 1339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc2 A OE2 GLU 160 A GLU 160 1_555 D MG MG . A MG 1340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc3 A OD2 ASP 179 A ASP 179 1_555 D MG MG . A MG 1340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc4 A OD1 ASP 181 A ASP 181 1_555 D MG MG . A MG 1340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc5 A OD2 ASP 181 A ASP 181 1_555 D MG MG . A MG 1340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc6 C MG MG . A MG 1339 1_555 E O19 R3Z . A R3Z 1341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc7 C MG MG . A MG 1339 1_555 E O23 R3Z . A R3Z 1341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc8 D MG MG . A MG 1340 1_555 E O22 R3Z . A R3Z 1341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc9 D MG MG . A MG 1340 1_555 E O23 R3Z . A R3Z 1341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc10 B OE1 GLU 160 B GLU 160 1_555 F MG MG . B MG 1336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? metalc ? metalc11 B OE2 GLU 160 B GLU 160 1_555 G MG MG . B MG 1337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc12 B OD2 ASP 179 B ASP 179 1_555 G MG MG . B MG 1337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc13 B OD2 ASP 181 B ASP 181 1_555 G MG MG . B MG 1337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc14 F MG MG . B MG 1336 1_555 H O19 R3Z . B R3Z 1338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc15 F MG MG . B MG 1336 1_555 H O23 R3Z . B R3Z 1338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc16 G MG MG . B MG 1337 1_555 H O23 R3Z . B R3Z 1338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc17 G MG MG . B MG 1337 1_555 H O22 R3Z . B R3Z 1338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _chem_comp.formula 'C15 H12 N2 O5 S' _chem_comp.formula_weight 332.331 _chem_comp.id R3Z _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione _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 C1 C2 R3Z doub 277 n y C1 C6 R3Z sing 278 n y C2 C3 R3Z sing 279 n y C3 C4 R3Z doub 280 n y C4 C5 R3Z sing 281 n y C4 O10 R3Z sing 282 n n C5 C6 R3Z doub 283 n y C5 O7 R3Z sing 284 n n O7 C8 R3Z sing 285 n n C8 C9 R3Z sing 286 n n C9 O10 R3Z sing 287 n n C9 C11 R3Z sing 288 n n C11 N12 R3Z sing 289 n n N12 C13 R3Z sing 290 n n N12 C21 R3Z sing 291 n n C13 C14 R3Z sing 292 n y C13 C17 R3Z doub 293 n y C14 C15 R3Z doub 294 n y C15 S16 R3Z sing 295 n y S16 C17 R3Z sing 296 n y C17 C18 R3Z sing 297 n n C18 O19 R3Z doub 298 n n C18 N20 R3Z sing 299 n n N20 C21 R3Z sing 300 n n N20 O23 R3Z sing 301 n n C21 O22 R3Z doub 302 n n C1 H1 R3Z sing 303 n n C2 H2 R3Z sing 304 n n C3 H3 R3Z sing 305 n n C6 H6 R3Z sing 306 n n C8 H8 R3Z sing 307 n n C8 H8A R3Z sing 308 n n C9 H9 R3Z sing 309 n n C11 H11 R3Z sing 310 n n C11 H11A R3Z sing 311 n n C14 H14 R3Z sing 312 n n C15 H15 R3Z sing 313 n n O23 HO23 R3Z sing 314 n n # _atom_sites.entry_id 5FV7 _atom_sites.fract_transf_matrix[1][1] 0.023074 _atom_sites.fract_transf_matrix[1][2] 0.000298 _atom_sites.fract_transf_matrix[1][3] 0.001719 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019925 _atom_sites.fract_transf_matrix[2][3] 0.004288 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015317 _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 MG A 1 1339 1339 MG MG . D 2 MG A 1 1340 1340 MG MG . E 3 R3Z A 1 1341 1341 R3Z R3Z . F 2 MG B 1 1336 1336 MG MG . G 2 MG B 1 1337 1337 MG MG . H 3 R3Z B 1 1338 1338 R3Z R3Z . I 4 HOH A 1 2001 2001 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 C C1 R3Z . . . E 3 -13.869 -8.134 -1.11 1 47.57 ? C1 R3Z 1341 A 1 HETATM 2 C C2 R3Z . . . E 3 -14.944 -8.084 -1.991 1 47.5 ? C2 R3Z 1341 A 1 HETATM 3 C C3 R3Z . . . E 3 -15.844 -7.025 -1.942 1 47.52 ? C3 R3Z 1341 A 1 HETATM 4 C C4 R3Z . . . E 3 -15.68 -6.003 -1.005 1 47.48 ? C4 R3Z 1341 A 1 HETATM 5 C C5 R3Z . . . E 3 -14.597 -6.062 -0.118 1 47.13 ? C5 R3Z 1341 A 1 HETATM 6 C C6 R3Z . . . E 3 -13.695 -7.125 -0.171 1 47.7 ? C6 R3Z 1341 A 1 HETATM 7 O O7 R3Z . . . E 3 -14.417 -5.076 0.802 1 46.9 ? O7 R3Z 1341 A 1 HETATM 8 C C8 R3Z . . . E 3 -15.568 -4.282 1.129 1 46.86 ? C8 R3Z 1341 A 1 HETATM 9 C C9 R3Z . . . E 3 -16.28 -3.809 -0.156 1 46.67 ? C9 R3Z 1341 A 1 HETATM 10 O O10 R3Z . . . E 3 -16.582 -4.964 -0.963 1 47.35 ? O10 R3Z 1341 A 1 HETATM 11 C C11 R3Z . . . E 3 -17.549 -2.98 0.153 1 46.39 ? C11 R3Z 1341 A 1 HETATM 12 N N12 R3Z . . . E 3 -18.362 -3.489 1.286 1 46.16 ? N12 R3Z 1341 A 1 HETATM 13 C C13 R3Z . . . E 3 -19.292 -4.521 1.051 1 45.76 ? C13 R3Z 1341 A 1 HETATM 14 C C14 R3Z . . . E 3 -19.601 -5.185 -0.132 1 45.64 ? C14 R3Z 1341 A 1 HETATM 15 C C15 R3Z . . . E 3 -20.536 -6.123 -0.031 1 46.43 ? C15 R3Z 1341 A 1 HETATM 16 S S16 R3Z . . . E 3 -21.118 -6.262 1.566 1 45.14 ? S16 R3Z 1341 A 1 HETATM 17 C C17 R3Z . . . E 3 -20.048 -4.986 2.122 1 45.04 ? C17 R3Z 1341 A 1 HETATM 18 C C18 R3Z . . . E 3 -19.87 -4.415 3.414 1 44.4 ? C18 R3Z 1341 A 1 HETATM 19 O O19 R3Z . . . E 3 -20.527 -4.816 4.364 1 42.97 ? O19 R3Z 1341 A 1 HETATM 20 N N20 R3Z . . . E 3 -18.971 -3.424 3.584 1 43.72 ? N20 R3Z 1341 A 1 HETATM 21 C C21 R3Z . . . E 3 -18.238 -2.974 2.538 1 44.6 ? C21 R3Z 1341 A 1 HETATM 22 O O22 R3Z . . . E 3 -17.438 -2.078 2.744 1 46.48 ? O22 R3Z 1341 A 1 HETATM 23 O O23 R3Z . . . E 3 -18.803 -2.86 4.876 1 41.69 ? O23 R3Z 1341 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #