data_7AQJ # _model_server_result.job_id D2BVjoYZR0RUqUjFRAevJQ _model_server_result.datetime_utc '2025-07-27 12:44:14' _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 7aqj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7AQJ # _exptl.entry_id 7AQJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 299.28 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione _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 102.295 _cell.angle_gamma 90 _cell.entry_id 7AQJ _cell.length_a 113.661 _cell.length_b 53.75 _cell.length_c 44.88 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AQJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 145 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 145 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C06 _struct_conn.ptnr2_label_comp_id S7H _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id S7H _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id B _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id B _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 1.755 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H17 N3 O6' _chem_comp.formula_weight 299.28 _chem_comp.id S7H _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(2~{R})-2-oxidanylpropyl]-3-[[(2~{R})-oxiran-2-yl]methyl]-5-[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione _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 C05 C06 S7H sing 316 n n C05 O07 S7H sing 317 n n C05 C04 S7H sing 318 n n C04 N03 S7H sing 319 n n O01 C02 S7H doub 320 n n N03 C02 S7H sing 321 n n N03 C08 S7H sing 322 n n C02 N17 S7H sing 323 n n O09 C08 S7H doub 324 n n C08 N10 S7H sing 325 n n N17 C18 S7H sing 326 n n N17 C15 S7H sing 327 n n C18 C19 S7H sing 328 n n N10 C15 S7H sing 329 n n N10 C11 S7H sing 330 n n C20 C19 S7H sing 331 n n C20 O21 S7H sing 332 n n C15 O16 S7H doub 333 n n C19 O21 S7H sing 334 n n C11 C12 S7H sing 335 n n C13 C12 S7H sing 336 n n C13 O14 S7H sing 337 n n C12 O14 S7H sing 338 n n C11 H112 S7H sing 339 n n C11 H111 S7H sing 340 n n C12 H121 S7H sing 341 n n C13 H131 S7H sing 342 n n C13 H132 S7H sing 343 n n C18 H181 S7H sing 344 n n C18 H182 S7H sing 345 n n C19 H191 S7H sing 346 n n C20 H202 S7H sing 347 n n C20 H201 S7H sing 348 n n C04 H041 S7H sing 349 n n C04 H042 S7H sing 350 n n C05 H051 S7H sing 351 n n C06 H061 S7H sing 352 n n C06 H062 S7H sing 353 n n C06 H2 S7H sing 354 n n O07 H1 S7H sing 355 n n # _atom_sites.entry_id 7AQJ _atom_sites.fract_transf_matrix[1][1] 0.008798 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001917 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018605 _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] 0.022805 _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 B 2 S7H A 1 401 401 S7H LIG . C 3 RV8 A 1 402 501 RV8 LI2 . D 4 HOH A 1 501 5 HOH HOH . D 4 HOH A 2 502 8 HOH HOH . D 4 HOH A 3 503 16 HOH HOH . D 4 HOH A 4 504 19 HOH HOH . D 4 HOH A 5 505 13 HOH HOH . D 4 HOH A 6 506 1 HOH HOH . D 4 HOH A 7 507 15 HOH HOH . D 4 HOH A 8 508 2 HOH HOH . D 4 HOH A 9 509 11 HOH HOH . D 4 HOH A 10 510 12 HOH HOH . D 4 HOH A 11 511 7 HOH HOH . D 4 HOH A 12 512 4 HOH HOH . D 4 HOH A 13 513 10 HOH HOH . D 4 HOH A 14 514 18 HOH HOH . D 4 HOH A 15 515 14 HOH HOH . D 4 HOH A 16 516 3 HOH HOH . D 4 HOH A 17 517 9 HOH HOH . D 4 HOH A 18 518 6 HOH HOH . D 4 HOH A 19 519 21 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 17 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 N N10 S7H . B . B 2 7.538 -1.547 23.732 0.47 58.98 ? N10 S7H 401 A 1 HETATM 2 C C11 S7H . B . B 2 6.69 -2.1 24.923 0.47 57.41 ? C11 S7H 401 A 1 HETATM 3 C C12 S7H . B . B 2 5.82 -1.006 25.505 0.47 57.04 ? C12 S7H 401 A 1 HETATM 4 C C13 S7H . B . B 2 5.891 0.44 24.95 0.47 58.49 ? C13 S7H 401 A 1 HETATM 5 C C18 S7H . B . B 2 11.18 -0.195 23.069 0.47 55.94 ? C18 S7H 401 A 1 HETATM 6 C C19 S7H . B . B 2 11.37 0.823 24.219 0.47 58.2 ? C19 S7H 401 A 1 HETATM 7 C C20 S7H . B . B 2 10.875 2.27 23.941 0.47 57.89 ? C20 S7H 401 A 1 HETATM 8 C C02 S7H . B . B 2 9.12 -0.457 21.568 0.47 55.86 ? C02 S7H 401 A 1 HETATM 9 C C04 S7H . B . B 2 7.15 -0.632 19.872 0.47 55.04 ? C04 S7H 401 A 1 HETATM 10 C C05 S7H . B . B 2 7.045 -1.949 19.004 0.47 52.8 ? C05 S7H 401 A 1 HETATM 11 C C06 S7H . B . B 2 8.243 -2.907 19.257 0.47 50.61 ? C06 S7H 401 A 1 HETATM 12 C C08 S7H . B . B 2 6.957 -1.361 22.394 0.47 58.96 ? C08 S7H 401 A 1 HETATM 13 C C15 S7H . B . B 2 8.916 -1.154 23.952 0.47 59.28 ? C15 S7H 401 A 1 HETATM 14 N N03 S7H . B . B 2 7.751 -0.817 21.308 0.47 58.4 ? N03 S7H 401 A 1 HETATM 15 N N17 S7H . B . B 2 9.716 -0.617 22.864 0.47 57.66 ? N17 S7H 401 A 1 HETATM 16 O O01 S7H . B . B 2 9.811 0.006 20.658 0.47 53.65 ? O01 S7H 401 A 1 HETATM 17 O O07 S7H . B . B 2 5.851 -2.61 19.334 0.47 53.93 ? O07 S7H 401 A 1 HETATM 18 O O09 S7H . B . B 2 5.781 -1.671 22.176 0.47 60.56 ? O09 S7H 401 A 1 HETATM 19 O O14 S7H . B . B 2 6.565 0.079 26.2 0.47 57.58 ? O14 S7H 401 A 1 HETATM 20 O O16 S7H . B . B 2 9.416 -1.294 25.082 0.47 59.49 ? O16 S7H 401 A 1 HETATM 21 O O21 S7H . B . B 2 10.163 1.381 24.868 0.47 60.12 ? O21 S7H 401 A 1 HETATM 22 H H112 S7H . B . B 2 7.238 -2.483 25.626 0.47 69.05 ? H112 S7H 401 A 1 HETATM 23 H H111 S7H . B . B 2 6.133 -2.852 24.667 0.47 69.05 ? H111 S7H 401 A 1 HETATM 24 H H121 S7H . B . B 2 4.946 -1.198 25.878 0.47 68.6 ? H121 S7H 401 A 1 HETATM 25 H H131 S7H . B . B 2 5.118 1.014 25.064 0.47 70.34 ? H131 S7H 401 A 1 HETATM 26 H H132 S7H . B . B 2 6.491 0.619 24.209 0.47 70.34 ? H132 S7H 401 A 1 HETATM 27 H H181 S7H . B . B 2 11.55 0.163 22.247 0.47 67.29 ? H181 S7H 401 A 1 HETATM 28 H H182 S7H . B . B 2 11.74 -0.972 23.221 0.47 67.29 ? H182 S7H 401 A 1 HETATM 29 H H191 S7H . B . B 2 12.096 0.745 24.857 0.47 69.99 ? H191 S7H 401 A 1 HETATM 30 H H202 S7H . B . B 2 10.425 2.438 23.099 0.47 69.62 ? H202 S7H 401 A 1 HETATM 31 H H201 S7H . B . B 2 11.361 2.999 24.357 0.47 69.62 ? H201 S7H 401 A 1 HETATM 32 H H041 S7H . B . B 2 6.268 -0.231 19.917 0.47 66.21 ? H041 S7H 401 A 1 HETATM 33 H H042 S7H . B . B 2 7.659 0.021 19.367 0.47 66.21 ? H042 S7H 401 A 1 HETATM 34 H H051 S7H . B . B 2 7.014 -1.672 18.076 0.47 63.51 ? H051 S7H 401 A 1 HETATM 35 H H061 S7H . B . B 2 8.495 -2.954 20.188 0.47 60.88 ? H061 S7H 401 A 1 HETATM 36 H H062 S7H . B . B 2 9.047 -2.631 18.79 0.47 60.88 ? H062 S7H 401 A 1 HETATM 37 H H1 S7H . B . B 2 5.185 -2.178 19.007 0.47 64.87 ? H1 S7H 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 37 #