data_5IOS # _model_server_result.job_id FnEyQhtVeHsZpRHblxqokA _model_server_result.datetime_utc '2024-11-24 21:03:44' _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 5ios # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 5IOS # _exptl.entry_id 5IOS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5IOS _cell.length_a 54.071 _cell.length_b 116.217 _cell.length_c 141.007 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IOS _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _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,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 449 n n N1 C6 UMP sing 450 n n N1 C1' UMP sing 451 n n C2 N3 UMP sing 452 n n C2 O2 UMP doub 453 n n N3 C4 UMP sing 454 n n N3 HN3 UMP sing 455 n n C4 C5 UMP sing 456 n n C4 O4 UMP doub 457 n n C5 C6 UMP doub 458 n n C5 H5 UMP sing 459 n n C6 H6 UMP sing 460 n n C1' C2' UMP sing 461 n n C1' O4' UMP sing 462 n n C1' H1' UMP sing 463 n n C2' C3' UMP sing 464 n n C2' H2' UMP sing 465 n n C2' "H2''" UMP sing 466 n n C3' C4' UMP sing 467 n n C3' O3' UMP sing 468 n n C3' H3' UMP sing 469 n n C4' O4' UMP sing 470 n n C4' C5' UMP sing 471 n n C4' H4' UMP sing 472 n n O3' HO3' UMP sing 473 n n C5' O5' UMP sing 474 n n C5' H5' UMP sing 475 n n C5' "H5''" UMP sing 476 n n O5' P UMP sing 477 n n P OP1 UMP doub 478 n n P OP2 UMP sing 479 n n P OP3 UMP sing 480 n n OP2 HOP2 UMP sing 481 n n OP3 HOP3 UMP sing 482 n n # _atom_sites.entry_id 5IOS _atom_sites.fract_transf_matrix[1][1] 0.018494 _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] 0.008605 _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] 0.007092 _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 2 FAD A 1 301 1 FAD FAD . F 3 UMP A 1 302 1 UMP UMP . G 3 UMP A 1 303 1 UMP UMP . H 2 FAD B 1 301 1 FAD FAD . I 2 FAD C 1 301 1 FAD FAD . J 3 UMP C 1 302 1 UMP UMP . K 2 FAD D 1 301 1 FAD FAD . L 3 UMP D 1 302 1 UMP UMP . M 4 HOH A 1 401 127 HOH HOH . M 4 HOH A 2 402 94 HOH HOH . M 4 HOH A 3 403 95 HOH HOH . M 4 HOH A 4 404 136 HOH HOH . M 4 HOH A 5 405 98 HOH HOH . M 4 HOH A 6 406 67 HOH HOH . M 4 HOH A 7 407 17 HOH HOH . M 4 HOH A 8 408 40 HOH HOH . M 4 HOH A 9 409 21 HOH HOH . M 4 HOH A 10 410 71 HOH HOH . M 4 HOH A 11 411 49 HOH HOH . M 4 HOH A 12 412 100 HOH HOH . M 4 HOH A 13 413 128 HOH HOH . M 4 HOH A 14 414 62 HOH HOH . M 4 HOH A 15 415 77 HOH HOH . M 4 HOH A 16 416 7 HOH HOH . M 4 HOH A 17 417 78 HOH HOH . M 4 HOH A 18 418 57 HOH HOH . M 4 HOH A 19 419 22 HOH HOH . M 4 HOH A 20 420 25 HOH HOH . M 4 HOH A 21 421 16 HOH HOH . M 4 HOH A 22 422 15 HOH HOH . M 4 HOH A 23 423 72 HOH HOH . M 4 HOH A 24 424 80 HOH HOH . M 4 HOH A 25 425 137 HOH HOH . M 4 HOH A 26 426 88 HOH HOH . M 4 HOH A 27 427 37 HOH HOH . M 4 HOH A 28 428 101 HOH HOH . M 4 HOH A 29 429 31 HOH HOH . M 4 HOH A 30 430 97 HOH HOH . M 4 HOH A 31 431 140 HOH HOH . M 4 HOH A 32 432 141 HOH HOH . M 4 HOH A 33 433 48 HOH HOH . M 4 HOH A 34 434 142 HOH HOH . M 4 HOH A 35 435 89 HOH HOH . M 4 HOH A 36 436 90 HOH HOH . M 4 HOH A 37 437 143 HOH HOH . N 4 HOH B 1 401 139 HOH HOH . N 4 HOH B 2 402 144 HOH HOH . N 4 HOH B 3 403 70 HOH HOH . N 4 HOH B 4 404 121 HOH HOH . N 4 HOH B 5 405 52 HOH HOH . N 4 HOH B 6 406 122 HOH HOH . N 4 HOH B 7 407 20 HOH HOH . N 4 HOH B 8 408 11 HOH HOH . N 4 HOH B 9 409 130 HOH HOH . N 4 HOH B 10 410 112 HOH HOH . N 4 HOH B 11 411 73 HOH HOH . N 4 HOH B 12 412 138 HOH HOH . N 4 HOH B 13 413 18 HOH HOH . N 4 HOH B 14 414 13 HOH HOH . N 4 HOH B 15 415 14 HOH HOH . N 4 HOH B 16 416 91 HOH HOH . N 4 HOH B 17 417 109 HOH HOH . N 4 HOH B 18 418 9 HOH HOH . N 4 HOH B 19 419 34 HOH HOH . N 4 HOH B 20 420 43 HOH HOH . N 4 HOH B 21 421 32 HOH HOH . N 4 HOH B 22 422 64 HOH HOH . N 4 HOH B 23 423 55 HOH HOH . N 4 HOH B 24 424 24 HOH HOH . N 4 HOH B 25 425 145 HOH HOH . N 4 HOH B 26 426 3 HOH HOH . N 4 HOH B 27 427 126 HOH HOH . N 4 HOH B 28 428 105 HOH HOH . N 4 HOH B 29 429 125 HOH HOH . O 4 HOH C 1 401 129 HOH HOH . O 4 HOH C 2 402 106 HOH HOH . O 4 HOH C 3 403 39 HOH HOH . O 4 HOH C 4 404 29 HOH HOH . O 4 HOH C 5 405 28 HOH HOH . O 4 HOH C 6 406 82 HOH HOH . O 4 HOH C 7 407 35 HOH HOH . O 4 HOH C 8 408 12 HOH HOH . O 4 HOH C 9 409 115 HOH HOH . O 4 HOH C 10 410 114 HOH HOH . O 4 HOH C 11 411 116 HOH HOH . O 4 HOH C 12 412 99 HOH HOH . O 4 HOH C 13 413 33 HOH HOH . O 4 HOH C 14 414 54 HOH HOH . O 4 HOH C 15 415 74 HOH HOH . O 4 HOH C 16 416 38 HOH HOH . O 4 HOH C 17 417 50 HOH HOH . O 4 HOH C 18 418 6 HOH HOH . O 4 HOH C 19 419 4 HOH HOH . O 4 HOH C 20 420 41 HOH HOH . O 4 HOH C 21 421 61 HOH HOH . O 4 HOH C 22 422 107 HOH HOH . O 4 HOH C 23 423 19 HOH HOH . O 4 HOH C 24 424 36 HOH HOH . O 4 HOH C 25 425 30 HOH HOH . O 4 HOH C 26 426 118 HOH HOH . O 4 HOH C 27 427 123 HOH HOH . O 4 HOH C 28 428 124 HOH HOH . O 4 HOH C 29 429 108 HOH HOH . O 4 HOH C 30 430 96 HOH HOH . O 4 HOH C 31 431 75 HOH HOH . O 4 HOH C 32 432 131 HOH HOH . O 4 HOH C 33 433 79 HOH HOH . O 4 HOH C 34 434 93 HOH HOH . O 4 HOH C 35 435 132 HOH HOH . O 4 HOH C 36 436 58 HOH HOH . O 4 HOH C 37 437 111 HOH HOH . O 4 HOH C 38 438 110 HOH HOH . O 4 HOH C 39 439 68 HOH HOH . O 4 HOH C 40 440 92 HOH HOH . O 4 HOH C 41 441 65 HOH HOH . P 4 HOH D 1 401 42 HOH HOH . P 4 HOH D 2 402 81 HOH HOH . P 4 HOH D 3 403 117 HOH HOH . P 4 HOH D 4 404 60 HOH HOH . P 4 HOH D 5 405 5 HOH HOH . P 4 HOH D 6 406 76 HOH HOH . P 4 HOH D 7 407 23 HOH HOH . P 4 HOH D 8 408 10 HOH HOH . P 4 HOH D 9 409 133 HOH HOH . P 4 HOH D 10 410 87 HOH HOH . P 4 HOH D 11 411 135 HOH HOH . P 4 HOH D 12 412 8 HOH HOH . P 4 HOH D 13 413 56 HOH HOH . P 4 HOH D 14 414 119 HOH HOH . P 4 HOH D 15 415 26 HOH HOH . P 4 HOH D 16 416 46 HOH HOH . P 4 HOH D 17 417 27 HOH HOH . P 4 HOH D 18 418 134 HOH HOH . P 4 HOH D 19 419 47 HOH HOH . P 4 HOH D 20 420 113 HOH HOH . P 4 HOH D 21 421 66 HOH HOH . P 4 HOH D 22 422 103 HOH HOH . P 4 HOH D 23 423 120 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 N1 UMP . . . F 3 -2.49 8.329 10.699 1 26.22 ? N1 UMP 302 A 1 HETATM 2 C C2 UMP . . . F 3 -2.603 7.477 11.791 1 24.7 ? C2 UMP 302 A 1 HETATM 3 N N3 UMP . . . F 3 -3.652 6.646 11.844 1 25.57 ? N3 UMP 302 A 1 HETATM 4 C C4 UMP . . . F 3 -4.604 6.623 10.924 1 27.31 ? C4 UMP 302 A 1 HETATM 5 C C5 UMP . . . F 3 -4.517 7.478 9.835 1 28.01 ? C5 UMP 302 A 1 HETATM 6 C C6 UMP . . . F 3 -3.433 8.336 9.746 1 28.19 ? C6 UMP 302 A 1 HETATM 7 O O2 UMP . . . F 3 -1.708 7.492 12.66 1 24.09 ? O2 UMP 302 A 1 HETATM 8 O O4 UMP . . . F 3 -5.566 5.824 11.043 1 28.97 ? O4 UMP 302 A 1 HETATM 9 C C1' UMP . . . F 3 -1.336 9.21 10.653 1 26.57 ? C1' UMP 302 A 1 HETATM 10 C C2' UMP . . . F 3 -0.065 8.424 10.371 1 26.75 ? C2' UMP 302 A 1 HETATM 11 C C3' UMP . . . F 3 0.638 9.261 9.319 1 28.19 ? C3' UMP 302 A 1 HETATM 12 C C4' UMP . . . F 3 -0.495 10.05 8.651 1 27.22 ? C4' UMP 302 A 1 HETATM 13 O O3' UMP . . . F 3 1.58 10.123 9.958 1 28.46 ? O3' UMP 302 A 1 HETATM 14 O O4' UMP . . . F 3 -1.559 10.136 9.598 1 26.76 ? O4' UMP 302 A 1 HETATM 15 C C5' UMP . . . F 3 -1.019 9.382 7.377 1 26.7 ? C5' UMP 302 A 1 HETATM 16 O O5' UMP . . . F 3 -1.239 7.978 7.59 1 28.3 ? O5' UMP 302 A 1 HETATM 17 P P UMP . . . F 3 -2.057 7.019 6.575 1 31.66 ? P UMP 302 A 1 HETATM 18 O OP1 UMP . . . F 3 -1.28 7.092 5.303 1 32.12 ? OP1 UMP 302 A 1 HETATM 19 O OP2 UMP . . . F 3 -3.441 7.602 6.458 1 30 ? OP2 UMP 302 A 1 HETATM 20 O OP3 UMP . . . F 3 -1.95 5.628 7.133 1 30.6 ? OP3 UMP 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 530 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #