data_8I6D # _model_server_result.job_id ziyIyc8X_CF4hssAN3x2Mw _model_server_result.datetime_utc '2024-11-08 08:49:48' _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 8i6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 8I6D # _exptl.entry_id 8I6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 128.086 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-oxidanyl-1~{H}-pyrimidine-2,4-dione _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.02 _cell.angle_gamma 90 _cell.entry_id 8I6D _cell.length_a 45.98 _cell.length_b 77.99 _cell.length_c 59.37 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,H 1 1 B,F,G,I 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 ? 2 C N N ? 2 D N N ? 2 F N N # _chem_comp.formula 'C4 H4 N2 O3' _chem_comp.formula_weight 128.086 _chem_comp.id ODF _chem_comp.mon_nstd_flag . _chem_comp.name 5-oxidanyl-1~{H}-pyrimidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-Hydroxy-2,4(1H,3H)-pyrimidinedion # 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 O1 C1 ODF sing 246 n n O2 C2 ODF doub 247 n n C1 C2 ODF sing 248 n n C1 C3 ODF doub 249 n n C2 N1 ODF sing 250 n n C3 N2 ODF sing 251 n n N1 C4 ODF sing 252 n n N2 C4 ODF sing 253 n n C4 O3 ODF doub 254 n n N1 H1 ODF sing 255 n n C3 H2 ODF sing 256 n n O1 H4 ODF sing 257 n n N2 H5 ODF sing 258 n n # _atom_sites.entry_id 8I6D _atom_sites.fract_transf_matrix[1][1] 0.021749 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004631 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012822 _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] 0.017221 _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 ODF A 1 301 301 ODF UNL . D 2 ODF A 1 302 401 ODF UNL . E 3 EDO A 1 303 501 EDO EDO . F 2 ODF B 1 301 301 ODF UNL . G 4 PEG B 1 302 401 PEG PEG . H 5 HOH A 1 401 21 HOH HOH . H 5 HOH A 2 402 133 HOH HOH . H 5 HOH A 3 403 65 HOH HOH . H 5 HOH A 4 404 121 HOH HOH . H 5 HOH A 5 405 117 HOH HOH . H 5 HOH A 6 406 118 HOH HOH . H 5 HOH A 7 407 71 HOH HOH . H 5 HOH A 8 408 46 HOH HOH . H 5 HOH A 9 409 37 HOH HOH . H 5 HOH A 10 410 124 HOH HOH . H 5 HOH A 11 411 82 HOH HOH . H 5 HOH A 12 412 9 HOH HOH . H 5 HOH A 13 413 3 HOH HOH . H 5 HOH A 14 414 123 HOH HOH . H 5 HOH A 15 415 16 HOH HOH . H 5 HOH A 16 416 15 HOH HOH . H 5 HOH A 17 417 43 HOH HOH . H 5 HOH A 18 418 31 HOH HOH . H 5 HOH A 19 419 92 HOH HOH . H 5 HOH A 20 420 137 HOH HOH . H 5 HOH A 21 421 98 HOH HOH . H 5 HOH A 22 422 8 HOH HOH . H 5 HOH A 23 423 50 HOH HOH . H 5 HOH A 24 424 33 HOH HOH . H 5 HOH A 25 425 94 HOH HOH . H 5 HOH A 26 426 7 HOH HOH . H 5 HOH A 27 427 130 HOH HOH . H 5 HOH A 28 428 30 HOH HOH . H 5 HOH A 29 429 68 HOH HOH . H 5 HOH A 30 430 88 HOH HOH . H 5 HOH A 31 431 5 HOH HOH . H 5 HOH A 32 432 97 HOH HOH . H 5 HOH A 33 433 141 HOH HOH . H 5 HOH A 34 434 38 HOH HOH . H 5 HOH A 35 435 87 HOH HOH . H 5 HOH A 36 436 128 HOH HOH . H 5 HOH A 37 437 90 HOH HOH . H 5 HOH A 38 438 1 HOH HOH . H 5 HOH A 39 439 39 HOH HOH . H 5 HOH A 40 440 12 HOH HOH . H 5 HOH A 41 441 89 HOH HOH . H 5 HOH A 42 442 47 HOH HOH . H 5 HOH A 43 443 113 HOH HOH . H 5 HOH A 44 444 80 HOH HOH . H 5 HOH A 45 445 61 HOH HOH . H 5 HOH A 46 446 55 HOH HOH . H 5 HOH A 47 447 34 HOH HOH . H 5 HOH A 48 448 53 HOH HOH . H 5 HOH A 49 449 84 HOH HOH . H 5 HOH A 50 450 42 HOH HOH . H 5 HOH A 51 451 73 HOH HOH . H 5 HOH A 52 452 91 HOH HOH . H 5 HOH A 53 453 48 HOH HOH . H 5 HOH A 54 454 70 HOH HOH . H 5 HOH A 55 455 85 HOH HOH . H 5 HOH A 56 456 14 HOH HOH . H 5 HOH A 57 457 134 HOH HOH . H 5 HOH A 58 458 56 HOH HOH . H 5 HOH A 59 459 25 HOH HOH . H 5 HOH A 60 460 11 HOH HOH . H 5 HOH A 61 461 127 HOH HOH . H 5 HOH A 62 462 32 HOH HOH . H 5 HOH A 63 463 27 HOH HOH . H 5 HOH A 64 464 72 HOH HOH . H 5 HOH A 65 465 13 HOH HOH . H 5 HOH A 66 466 18 HOH HOH . H 5 HOH A 67 467 66 HOH HOH . H 5 HOH A 68 468 81 HOH HOH . H 5 HOH A 69 469 45 HOH HOH . H 5 HOH A 70 470 52 HOH HOH . H 5 HOH A 71 471 107 HOH HOH . H 5 HOH A 72 472 57 HOH HOH . H 5 HOH A 73 473 105 HOH HOH . H 5 HOH A 74 474 24 HOH HOH . H 5 HOH A 75 475 69 HOH HOH . H 5 HOH A 76 476 104 HOH HOH . H 5 HOH A 77 477 2 HOH HOH . H 5 HOH A 78 478 140 HOH HOH . H 5 HOH A 79 479 136 HOH HOH . H 5 HOH A 80 480 106 HOH HOH . I 5 HOH B 1 401 125 HOH HOH . I 5 HOH B 2 402 131 HOH HOH . I 5 HOH B 3 403 63 HOH HOH . I 5 HOH B 4 404 112 HOH HOH . I 5 HOH B 5 405 126 HOH HOH . I 5 HOH B 6 406 77 HOH HOH . I 5 HOH B 7 407 114 HOH HOH . I 5 HOH B 8 408 40 HOH HOH . I 5 HOH B 9 409 62 HOH HOH . I 5 HOH B 10 410 144 HOH HOH . I 5 HOH B 11 411 44 HOH HOH . I 5 HOH B 12 412 26 HOH HOH . I 5 HOH B 13 413 76 HOH HOH . I 5 HOH B 14 414 119 HOH HOH . I 5 HOH B 15 415 120 HOH HOH . I 5 HOH B 16 416 86 HOH HOH . I 5 HOH B 17 417 74 HOH HOH . I 5 HOH B 18 418 146 HOH HOH . I 5 HOH B 19 419 58 HOH HOH . I 5 HOH B 20 420 135 HOH HOH . I 5 HOH B 21 421 41 HOH HOH . I 5 HOH B 22 422 129 HOH HOH . I 5 HOH B 23 423 49 HOH HOH . I 5 HOH B 24 424 20 HOH HOH . I 5 HOH B 25 425 4 HOH HOH . I 5 HOH B 26 426 116 HOH HOH . I 5 HOH B 27 427 142 HOH HOH . I 5 HOH B 28 428 60 HOH HOH . I 5 HOH B 29 429 75 HOH HOH . I 5 HOH B 30 430 110 HOH HOH . I 5 HOH B 31 431 28 HOH HOH . I 5 HOH B 32 432 109 HOH HOH . I 5 HOH B 33 433 6 HOH HOH . I 5 HOH B 34 434 29 HOH HOH . I 5 HOH B 35 435 36 HOH HOH . I 5 HOH B 36 436 122 HOH HOH . I 5 HOH B 37 437 138 HOH HOH . I 5 HOH B 38 438 35 HOH HOH . I 5 HOH B 39 439 99 HOH HOH . I 5 HOH B 40 440 115 HOH HOH . I 5 HOH B 41 441 96 HOH HOH . I 5 HOH B 42 442 19 HOH HOH . I 5 HOH B 43 443 143 HOH HOH . I 5 HOH B 44 444 83 HOH HOH . I 5 HOH B 45 445 132 HOH HOH . I 5 HOH B 46 446 145 HOH HOH . I 5 HOH B 47 447 111 HOH HOH . I 5 HOH B 48 448 78 HOH HOH . I 5 HOH B 49 449 59 HOH HOH . I 5 HOH B 50 450 64 HOH HOH . I 5 HOH B 51 451 79 HOH HOH . I 5 HOH B 52 452 139 HOH HOH . I 5 HOH B 53 453 51 HOH HOH . I 5 HOH B 54 454 22 HOH HOH . I 5 HOH B 55 455 103 HOH HOH . I 5 HOH B 56 456 95 HOH HOH . I 5 HOH B 57 457 10 HOH HOH . I 5 HOH B 58 458 17 HOH HOH . I 5 HOH B 59 459 54 HOH HOH . I 5 HOH B 60 460 100 HOH HOH . I 5 HOH B 61 461 102 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 O O3 ODF . . . F 2 2.396 -47.705 -47.692 1 19.68 ? O3 ODF 301 B 1 HETATM 2 C C4 ODF . . . F 2 2.946 -48.528 -47.036 1 20.37 ? C4 ODF 301 B 1 HETATM 3 N N1 ODF . . . F 2 3.64 -48.236 -45.821 1 19.98 ? N1 ODF 301 B 1 HETATM 4 C C2 ODF . . . F 2 4.277 -49.278 -45.083 1 20.09 ? C2 ODF 301 B 1 HETATM 5 O O2 ODF . . . F 2 4.864 -49.11 -44.063 1 18.58 ? O2 ODF 301 B 1 HETATM 6 N N2 ODF . . . F 2 2.888 -49.886 -47.5 1 21.07 ? N2 ODF 301 B 1 HETATM 7 C C3 ODF . . . F 2 3.534 -50.974 -46.726 1 20.46 ? C3 ODF 301 B 1 HETATM 8 C C1 ODF . . . F 2 4.191 -50.691 -45.607 1 19.86 ? C1 ODF 301 B 1 HETATM 9 O O1 ODF . . . F 2 4.814 -51.682 -44.898 1 20.07 ? O1 ODF 301 B 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #