data_9BYS # _model_server_result.job_id sZ7cSLm-vj8VelKyakDN0Q _model_server_result.datetime_utc '2025-06-27 20:17:01' _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 9bys # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 9BYS # _exptl.entry_id 9BYS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.294 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _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 90 _cell.angle_gamma 90 _cell.entry_id 9BYS _cell.length_a 111.35 _cell.length_b 111.35 _cell.length_c 206.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BYS _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 99 A CYS 98 1_555 A SG CYS 162 A CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 201 A CYS 200 1_555 A SG CYS 257 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 B SG CYS 24 AAAB CYS 23 1_555 B SG CYS 92 AAAB CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 145 AAAB CYS 144 1_555 B SG CYS 210 AAAB CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 171 AAAB CYS 170 1_555 C SG CYS 158 AAAC CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 23 AAAC CYS 22 1_555 C SG CYS 89 AAAC CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 D SG CYS 26 AAAD CYS 25 1_555 D SG CYS 81 AAAD CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A NZ LYS 44 A LYS 43 1_555 E C1 Q87 . A Q87 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _chem_comp.formula 'C12 H18 N4 O7' _chem_comp.formula_weight 330.294 _chem_comp.id Q87 _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol _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 Q87 sing 290 n n C1 C Q87 sing 291 n n O6 C11 Q87 doub 292 n n C2 N Q87 doub 293 n n C11 C3 Q87 sing 294 n n C11 N3 Q87 sing 295 n n N C3 Q87 sing 296 n n C3 C4 Q87 doub 297 n n N3 C10 Q87 sing 298 n n C4 N1 Q87 sing 299 n n C4 N2 Q87 sing 300 n n C10 N2 Q87 sing 301 n n C10 O5 Q87 doub 302 n n O3 C8 Q87 sing 303 n n O1 C6 Q87 sing 304 n n N1 C5 Q87 sing 305 n n C8 C7 Q87 sing 306 n n C8 C9 Q87 sing 307 n n C7 C6 Q87 sing 308 n n C7 O2 Q87 sing 309 n n C6 C5 Q87 sing 310 n n O4 C9 Q87 sing 311 n n C5 H1 Q87 sing 312 n n C5 H2 Q87 sing 313 n n C6 H3 Q87 sing 314 n n C8 H4 Q87 sing 315 n n N1 H5 Q87 sing 316 n n N3 H6 Q87 sing 317 n n C2 H7 Q87 sing 318 n n O2 H8 Q87 sing 319 n n C H9 Q87 sing 320 n n C H10 Q87 sing 321 n n C H11 Q87 sing 322 n n C7 H15 Q87 sing 323 n n C9 H16 Q87 sing 324 n n C9 H17 Q87 sing 325 n n O1 H18 Q87 sing 326 n n O3 H19 Q87 sing 327 n n O4 H20 Q87 sing 328 n n C1 O7 Q87 doub 329 n n N2 H12 Q87 sing 330 n n # _atom_sites.entry_id 9BYS _atom_sites.fract_transf_matrix[1][1] 0.008981 _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] 0.008981 _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] 0.004844 _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 E 5 Q87 A 1 301 301 Q87 5OU . F 6 GOL A 1 302 1 GOL GOL . G 6 GOL A 1 303 2 GOL GOL . H 6 GOL A 1 304 3 GOL GOL . I 7 HOH A 1 401 31 HOH HOH . I 7 HOH A 2 402 82 HOH HOH . I 7 HOH A 3 403 7 HOH HOH . I 7 HOH A 4 404 99 HOH HOH . I 7 HOH A 5 405 14 HOH HOH . I 7 HOH A 6 406 37 HOH HOH . I 7 HOH A 7 407 87 HOH HOH . I 7 HOH A 8 408 16 HOH HOH . I 7 HOH A 9 409 8 HOH HOH . I 7 HOH A 10 410 17 HOH HOH . I 7 HOH A 11 411 1 HOH HOH . I 7 HOH A 12 412 98 HOH HOH . I 7 HOH A 13 413 28 HOH HOH . I 7 HOH A 14 414 4 HOH HOH . I 7 HOH A 15 415 94 HOH HOH . I 7 HOH A 16 416 104 HOH HOH . I 7 HOH A 17 417 55 HOH HOH . I 7 HOH A 18 418 71 HOH HOH . I 7 HOH A 19 419 12 HOH HOH . I 7 HOH A 20 420 29 HOH HOH . I 7 HOH A 21 421 78 HOH HOH . I 7 HOH A 22 422 83 HOH HOH . I 7 HOH A 23 423 36 HOH HOH . I 7 HOH A 24 424 5 HOH HOH . I 7 HOH A 25 425 3 HOH HOH . I 7 HOH A 26 426 97 HOH HOH . I 7 HOH A 27 427 18 HOH HOH . I 7 HOH A 28 428 90 HOH HOH . I 7 HOH A 29 429 93 HOH HOH . I 7 HOH A 30 430 44 HOH HOH . I 7 HOH A 31 431 67 HOH HOH . I 7 HOH A 32 432 15 HOH HOH . I 7 HOH A 33 433 89 HOH HOH . I 7 HOH A 34 434 45 HOH HOH . I 7 HOH A 35 435 106 HOH HOH . I 7 HOH A 36 436 53 HOH HOH . I 7 HOH A 37 437 51 HOH HOH . I 7 HOH A 38 438 63 HOH HOH . I 7 HOH A 39 439 62 HOH HOH . I 7 HOH A 40 440 48 HOH HOH . I 7 HOH A 41 441 41 HOH HOH . I 7 HOH A 42 442 64 HOH HOH . I 7 HOH A 43 443 13 HOH HOH . I 7 HOH A 44 444 102 HOH HOH . I 7 HOH A 45 445 11 HOH HOH . I 7 HOH A 46 446 68 HOH HOH . I 7 HOH A 47 447 34 HOH HOH . I 7 HOH A 48 448 35 HOH HOH . I 7 HOH A 49 449 38 HOH HOH . I 7 HOH A 50 450 46 HOH HOH . I 7 HOH A 51 451 27 HOH HOH . I 7 HOH A 52 452 61 HOH HOH . I 7 HOH A 53 453 88 HOH HOH . I 7 HOH A 54 454 84 HOH HOH . I 7 HOH A 55 455 40 HOH HOH . I 7 HOH A 56 456 73 HOH HOH . I 7 HOH A 57 457 103 HOH HOH . I 7 HOH A 58 458 49 HOH HOH . I 7 HOH A 59 459 86 HOH HOH . I 7 HOH A 60 460 69 HOH HOH . I 7 HOH A 61 461 19 HOH HOH . I 7 HOH A 62 462 32 HOH HOH . I 7 HOH A 63 463 81 HOH HOH . I 7 HOH A 64 464 72 HOH HOH . I 7 HOH A 65 465 85 HOH HOH . I 7 HOH A 66 466 47 HOH HOH . I 7 HOH A 67 467 65 HOH HOH . I 7 HOH A 68 468 33 HOH HOH . J 7 HOH AAAB 1 301 100 HOH HOH . J 7 HOH AAAB 2 302 95 HOH HOH . J 7 HOH AAAB 3 303 79 HOH HOH . J 7 HOH AAAB 4 304 101 HOH HOH . J 7 HOH AAAB 5 305 52 HOH HOH . J 7 HOH AAAB 6 306 66 HOH HOH . J 7 HOH AAAB 7 307 30 HOH HOH . K 7 HOH AAAC 1 301 21 HOH HOH . K 7 HOH AAAC 2 302 23 HOH HOH . K 7 HOH AAAC 3 303 56 HOH HOH . K 7 HOH AAAC 4 304 10 HOH HOH . K 7 HOH AAAC 5 305 75 HOH HOH . K 7 HOH AAAC 6 306 24 HOH HOH . K 7 HOH AAAC 7 307 6 HOH HOH . K 7 HOH AAAC 8 308 80 HOH HOH . K 7 HOH AAAC 9 309 2 HOH HOH . K 7 HOH AAAC 10 310 9 HOH HOH . K 7 HOH AAAC 11 311 22 HOH HOH . K 7 HOH AAAC 12 312 20 HOH HOH . K 7 HOH AAAC 13 313 59 HOH HOH . K 7 HOH AAAC 14 314 91 HOH HOH . K 7 HOH AAAC 15 315 76 HOH HOH . K 7 HOH AAAC 16 316 60 HOH HOH . K 7 HOH AAAC 17 317 43 HOH HOH . K 7 HOH AAAC 18 318 58 HOH HOH . K 7 HOH AAAC 19 319 74 HOH HOH . K 7 HOH AAAC 20 320 39 HOH HOH . K 7 HOH AAAC 21 321 57 HOH HOH . L 7 HOH AAAD 1 101 96 HOH HOH . L 7 HOH AAAD 2 102 25 HOH HOH . L 7 HOH AAAD 3 103 26 HOH HOH . L 7 HOH AAAD 4 104 105 HOH HOH . L 7 HOH AAAD 5 105 50 HOH HOH . L 7 HOH AAAD 6 106 77 HOH HOH . L 7 HOH AAAD 7 107 70 HOH HOH . L 7 HOH AAAD 8 108 42 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 C4 Q87 . . . E 5 119.701 12.007 230.436 1 44.5 ? C4 Q87 301 A 1 HETATM 2 C C5 Q87 . . . E 5 121.1 13.927 229.744 1 39.6 ? C5 Q87 301 A 1 HETATM 3 C C6 Q87 . . . E 5 120.456 15.292 229.975 1 38.74 ? C6 Q87 301 A 1 HETATM 4 C C8 Q87 . . . E 5 118.545 16.768 229.148 1 38.18 ? C8 Q87 301 A 1 HETATM 5 N N1 Q87 . . . E 5 120.701 12.911 230.709 1 40.83 ? N1 Q87 301 A 1 HETATM 6 N N3 Q87 . . . E 5 117.699 10.269 229.739 1 44.49 ? N3 Q87 301 A 1 HETATM 7 O O6 Q87 . . . E 5 117.849 9.106 231.672 1 45.84 ? O6 Q87 301 A 1 HETATM 8 C C2 Q87 . . . E 5 119.882 10.134 233.423 1 48.53 ? C2 Q87 301 A 1 HETATM 9 O O2 Q87 . . . E 5 118.981 14.607 228.2 1 39.68 ? O2 Q87 301 A 1 HETATM 10 N N Q87 . . . E 5 120.072 11.014 232.508 1 51.23 ? N Q87 301 A 1 HETATM 11 C C Q87 . . . E 5 121.993 10.96 234.507 1 45.18 ? C Q87 301 A 1 HETATM 12 C C1 Q87 . . . E 5 120.701 10.203 234.627 1 43.98 ? C1 Q87 301 A 1 HETATM 13 C C10 Q87 . . . E 5 118.045 11.254 228.85 1 43.28 ? C10 Q87 301 A 1 HETATM 14 C C11 Q87 . . . E 5 118.254 10.044 230.987 1 44.63 ? C11 Q87 301 A 1 HETATM 15 C C3 Q87 . . . E 5 119.317 10.993 231.336 1 47.76 ? C3 Q87 301 A 1 HETATM 16 C C7 Q87 . . . E 5 119.034 15.345 229.416 1 39.21 ? C7 Q87 301 A 1 HETATM 17 C C9 Q87 . . . E 5 119.399 17.472 228.112 1 37.05 ? C9 Q87 301 A 1 HETATM 18 N N2 Q87 . . . E 5 119.051 12.095 229.244 1 43.77 ? N2 Q87 301 A 1 HETATM 19 O O1 Q87 . . . E 5 120.444 15.616 231.366 1 38.72 ? O1 Q87 301 A 1 HETATM 20 O O3 Q87 . . . E 5 117.196 16.721 228.684 1 38.76 ? O3 Q87 301 A 1 HETATM 21 O O4 Q87 . . . E 5 118.858 18.742 227.777 1 39.3 ? O4 Q87 301 A 1 HETATM 22 O O5 Q87 . . . E 5 117.49 11.372 227.761 1 44.19 ? O5 Q87 301 A 1 # _model_server_stats.io_time_ms 95 _model_server_stats.parse_time_ms 62 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 22 #