data_5FV7 # _model_server_result.job_id pT3TXTxb0iqwm_3WlafndQ _model_server_result.datetime_utc '2025-01-11 04:48:49' _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 5fv7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1338}' # _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 . . . H 3 6.281 13.649 40.436 1 39.63 ? C1 R3Z 1338 B 1 HETATM 2 C C2 R3Z . . . H 3 6.492 13.813 41.802 1 40.31 ? C2 R3Z 1338 B 1 HETATM 3 C C3 R3Z . . . H 3 5.926 12.941 42.725 1 39.65 ? C3 R3Z 1338 B 1 HETATM 4 C C4 R3Z . . . H 3 5.14 11.886 42.276 1 39.8 ? C4 R3Z 1338 B 1 HETATM 5 C C5 R3Z . . . H 3 4.923 11.725 40.889 1 39.81 ? C5 R3Z 1338 B 1 HETATM 6 C C6 R3Z . . . H 3 5.496 12.606 39.975 1 39.05 ? C6 R3Z 1338 B 1 HETATM 7 O O7 R3Z . . . H 3 4.15 10.701 40.42 1 38.98 ? O7 R3Z 1338 B 1 HETATM 8 C C8 R3Z . . . H 3 3.304 10.069 41.395 1 38.57 ? C8 R3Z 1338 B 1 HETATM 9 C C9 R3Z . . . H 3 4.095 9.769 42.689 1 38.83 ? C9 R3Z 1338 B 1 HETATM 10 O O10 R3Z . . . H 3 4.586 11.029 43.194 1 39.2 ? O10 R3Z 1338 B 1 HETATM 11 C C11 R3Z . . . H 3 3.251 9.004 43.729 1 38.43 ? C11 R3Z 1338 B 1 HETATM 12 N N12 R3Z . . . H 3 1.876 9.522 43.838 1 39.55 ? N12 R3Z 1338 B 1 HETATM 13 C C13 R3Z . . . H 3 1.603 10.588 44.723 1 41.24 ? C13 R3Z 1338 B 1 HETATM 14 C C14 R3Z . . . H 3 2.45 11.282 45.583 1 42.39 ? C14 R3Z 1338 B 1 HETATM 15 C C15 R3Z . . . H 3 1.892 12.258 46.297 1 42.35 ? C15 R3Z 1338 B 1 HETATM 16 S S16 R3Z . . . H 3 0.229 12.394 45.959 1 41.5 ? S16 R3Z 1338 B 1 HETATM 17 C C17 R3Z . . . H 3 0.303 11.071 44.8 1 41.46 ? C17 R3Z 1338 B 1 HETATM 18 C C18 R3Z . . . H 3 -0.707 10.477 43.992 1 40.85 ? C18 R3Z 1338 B 1 HETATM 19 O O19 R3Z . . . H 3 -1.857 10.885 44.045 1 41.97 ? O19 R3Z 1338 B 1 HETATM 20 N N20 R3Z . . . H 3 -0.394 9.456 43.167 1 38.96 ? N20 R3Z 1338 B 1 HETATM 21 C C21 R3Z . . . H 3 0.873 8.992 43.096 1 38.48 ? C21 R3Z 1338 B 1 HETATM 22 O O22 R3Z . . . H 3 1.091 8.071 42.329 1 37.11 ? O22 R3Z 1338 B 1 HETATM 23 O O23 R3Z . . . H 3 -1.409 8.877 42.367 1 36.03 ? O23 R3Z 1338 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #