data_5JFE # _model_server_result.job_id LfKjkCIoZYIJ3KtutoPKFw _model_server_result.datetime_utc '2024-11-24 05:03:48' _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 5jfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5JFE # _exptl.entry_id 5JFE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.198 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-5'-uridylic acid" _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 5JFE _cell.length_a 110.322 _cell.length_b 110.322 _cell.length_c 120.765 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JFE _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 7_454 y-1/2,x+1/2,-z-1/2 0 1 0 1 0 0 0 0 -1 -55.161 55.161 -60.3825 3 'crystal symmetry operation' 10_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 110.322 0 4 'crystal symmetry operation' 16_554 -y+1/2,-x+1/2,-z-1/2 0 -1 0 -1 0 0 0 0 -1 55.161 55.161 -60.3825 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H15 N2 O8 P' _chem_comp.formula_weight 310.198 _chem_comp.id UMC _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-5'-uridylic acid" _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 O5' P UMC sing 458 n n O2P P UMC doub 459 n n P O1P UMC sing 460 n n P O3P UMC sing 461 n n C2 N1 UMC sing 462 n n C1' N1 UMC sing 463 n n N1 C6 UMC sing 464 n n O2 C2 UMC doub 465 n n C2 N3 UMC sing 466 n n HN3 N3 UMC sing 467 n n N3 C4 UMC sing 468 n n O4 C4 UMC doub 469 n n C4 C5 UMC sing 470 n n H5A C5 UMC sing 471 n n C5 C6 UMC sing 472 n n C5 H5 UMC sing 473 n n C6 H6 UMC sing 474 n n C6 H6A UMC sing 475 n n H1' C1' UMC sing 476 n n C1' C2' UMC sing 477 n n C1' O4' UMC sing 478 n n O1P HO1P UMC sing 479 n n "H2'A" C2' UMC sing 480 n n C2' C3' UMC sing 481 n n C2' H2' UMC sing 482 n n O3' C3' UMC sing 483 n n C3' H3' UMC sing 484 n n C3' C4' UMC sing 485 n n HO3' O3' UMC sing 486 n n O3P HO3P UMC sing 487 n n O4' C4' UMC sing 488 n n H4' C4' UMC sing 489 n n C4' C5' UMC sing 490 n n C5' H5' UMC sing 491 n n C5' "H5'A" UMC sing 492 n n C5' O5' UMC sing 493 n n # _atom_sites.entry_id 5JFE _atom_sites.fract_transf_matrix[1][1] 0.009064 _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] 0.009064 _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] 0.008281 _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 FAD A 1 301 1 FAD FAD . C 3 UMC A 1 302 1 UMC LIG . D 4 EDO A 1 303 1 EDO EDO . E 4 EDO A 1 304 2 EDO EDO . F 4 EDO A 1 305 3 EDO EDO . G 4 EDO A 1 306 4 EDO EDO . H 4 EDO A 1 307 5 EDO EDO . I 5 HOH A 1 401 42 HOH HOH . I 5 HOH A 2 402 93 HOH HOH . I 5 HOH A 3 403 106 HOH HOH . I 5 HOH A 4 404 47 HOH HOH . I 5 HOH A 5 405 14 HOH HOH . I 5 HOH A 6 406 39 HOH HOH . I 5 HOH A 7 407 20 HOH HOH . I 5 HOH A 8 408 57 HOH HOH . I 5 HOH A 9 409 87 HOH HOH . I 5 HOH A 10 410 21 HOH HOH . I 5 HOH A 11 411 34 HOH HOH . I 5 HOH A 12 412 84 HOH HOH . I 5 HOH A 13 413 25 HOH HOH . I 5 HOH A 14 414 58 HOH HOH . I 5 HOH A 15 415 100 HOH HOH . I 5 HOH A 16 416 99 HOH HOH . I 5 HOH A 17 417 91 HOH HOH . I 5 HOH A 18 418 43 HOH HOH . I 5 HOH A 19 419 81 HOH HOH . I 5 HOH A 20 420 74 HOH HOH . I 5 HOH A 21 421 2 HOH HOH . I 5 HOH A 22 422 71 HOH HOH . I 5 HOH A 23 423 54 HOH HOH . I 5 HOH A 24 424 95 HOH HOH . I 5 HOH A 25 425 88 HOH HOH . I 5 HOH A 26 426 68 HOH HOH . I 5 HOH A 27 427 24 HOH HOH . I 5 HOH A 28 428 63 HOH HOH . I 5 HOH A 29 429 70 HOH HOH . I 5 HOH A 30 430 109 HOH HOH . I 5 HOH A 31 431 73 HOH HOH . I 5 HOH A 32 432 22 HOH HOH . I 5 HOH A 33 433 78 HOH HOH . I 5 HOH A 34 434 5 HOH HOH . I 5 HOH A 35 435 67 HOH HOH . I 5 HOH A 36 436 51 HOH HOH . I 5 HOH A 37 437 30 HOH HOH . I 5 HOH A 38 438 86 HOH HOH . I 5 HOH A 39 439 8 HOH HOH . I 5 HOH A 40 440 44 HOH HOH . I 5 HOH A 41 441 3 HOH HOH . I 5 HOH A 42 442 90 HOH HOH . I 5 HOH A 43 443 110 HOH HOH . I 5 HOH A 44 444 62 HOH HOH . I 5 HOH A 45 445 77 HOH HOH . I 5 HOH A 46 446 13 HOH HOH . I 5 HOH A 47 447 31 HOH HOH . I 5 HOH A 48 448 107 HOH HOH . I 5 HOH A 49 449 79 HOH HOH . I 5 HOH A 50 450 105 HOH HOH . I 5 HOH A 51 451 36 HOH HOH . I 5 HOH A 52 452 102 HOH HOH . I 5 HOH A 53 453 50 HOH HOH . I 5 HOH A 54 454 49 HOH HOH . I 5 HOH A 55 455 52 HOH HOH . I 5 HOH A 56 456 9 HOH HOH . I 5 HOH A 57 457 17 HOH HOH . I 5 HOH A 58 458 76 HOH HOH . I 5 HOH A 59 459 35 HOH HOH . I 5 HOH A 60 460 69 HOH HOH . I 5 HOH A 61 461 6 HOH HOH . I 5 HOH A 62 462 66 HOH HOH . I 5 HOH A 63 463 29 HOH HOH . I 5 HOH A 64 464 72 HOH HOH . I 5 HOH A 65 465 11 HOH HOH . I 5 HOH A 66 466 108 HOH HOH . I 5 HOH A 67 467 92 HOH HOH . I 5 HOH A 68 468 83 HOH HOH . I 5 HOH A 69 469 41 HOH HOH . I 5 HOH A 70 470 7 HOH HOH . I 5 HOH A 71 471 16 HOH HOH . I 5 HOH A 72 472 97 HOH HOH . I 5 HOH A 73 473 10 HOH HOH . I 5 HOH A 74 474 61 HOH HOH . I 5 HOH A 75 475 101 HOH HOH . I 5 HOH A 76 476 45 HOH HOH . I 5 HOH A 77 477 65 HOH HOH . I 5 HOH A 78 478 40 HOH HOH . I 5 HOH A 79 479 85 HOH HOH . I 5 HOH A 80 480 53 HOH HOH . I 5 HOH A 81 481 89 HOH HOH . I 5 HOH A 82 482 94 HOH HOH . I 5 HOH A 83 483 38 HOH HOH . I 5 HOH A 84 484 75 HOH HOH . I 5 HOH A 85 485 23 HOH HOH . I 5 HOH A 86 486 59 HOH HOH . I 5 HOH A 87 487 60 HOH HOH . I 5 HOH A 88 488 48 HOH HOH . I 5 HOH A 89 489 28 HOH HOH . I 5 HOH A 90 490 19 HOH HOH . I 5 HOH A 91 491 37 HOH HOH . I 5 HOH A 92 492 80 HOH HOH . I 5 HOH A 93 493 46 HOH HOH . I 5 HOH A 94 494 64 HOH HOH . I 5 HOH A 95 495 98 HOH HOH . I 5 HOH A 96 496 12 HOH HOH . I 5 HOH A 97 497 82 HOH HOH . I 5 HOH A 98 498 1 HOH HOH . I 5 HOH A 99 499 104 HOH HOH . I 5 HOH A 100 500 15 HOH HOH . I 5 HOH A 101 501 4 HOH HOH . I 5 HOH A 102 502 18 HOH HOH . I 5 HOH A 103 503 32 HOH HOH . I 5 HOH A 104 504 56 HOH HOH . I 5 HOH A 105 505 33 HOH HOH . I 5 HOH A 106 506 96 HOH HOH . I 5 HOH A 107 507 27 HOH HOH . I 5 HOH A 108 508 55 HOH HOH . I 5 HOH A 109 509 26 HOH HOH . I 5 HOH A 110 510 103 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 P P UMC . . . C 3 8.949 34.33 -33.433 1 18.31 ? P UMC 302 A 1 HETATM 2 N N1 UMC . . . C 3 5.543 37.074 -32.809 1 15.57 ? N1 UMC 302 A 1 HETATM 3 C C2 UMC . . . C 3 4.869 37.276 -31.649 1 17.39 ? C2 UMC 302 A 1 HETATM 4 O O2 UMC . . . C 3 4.805 38.369 -31.111 1 14.53 ? O2 UMC 302 A 1 HETATM 5 N N3 UMC . . . C 3 4.218 36.186 -31.115 1 17.63 ? N3 UMC 302 A 1 HETATM 6 C C4 UMC . . . C 3 4.2 34.911 -31.624 1 17.49 ? C4 UMC 302 A 1 HETATM 7 O O4 UMC . . . C 3 3.601 34.011 -31.045 1 18.75 ? O4 UMC 302 A 1 HETATM 8 C C5 UMC . . . C 3 4.935 34.666 -32.899 1 14.96 ? C5 UMC 302 A 1 HETATM 9 C C6 UMC . . . C 3 5.564 35.849 -33.613 1 14.21 ? C6 UMC 302 A 1 HETATM 10 C C1' UMC . . . C 3 6.402 38.225 -33.333 1 15.18 ? C1' UMC 302 A 1 HETATM 11 O O1P UMC . . . C 3 10.29 34.001 -34.026 1 17.4 -1 O1P UMC 302 A 1 HETATM 12 C C2' UMC . . . C 3 7.674 38.464 -32.518 1 14.97 ? C2' UMC 302 A 1 HETATM 13 O O2P UMC . . . C 3 7.835 33.64 -34.118 1 17.98 ? O2P UMC 302 A 1 HETATM 14 C C3' UMC . . . C 3 8.729 38.785 -33.574 1 15.52 ? C3' UMC 302 A 1 HETATM 15 O O3' UMC . . . C 3 8.661 40.173 -33.909 1 16.66 ? O3' UMC 302 A 1 HETATM 16 O O3P UMC . . . C 3 8.927 34.133 -31.891 1 17.51 ? O3P UMC 302 A 1 HETATM 17 C C4' UMC . . . C 3 8.257 37.968 -34.776 1 15.89 ? C4' UMC 302 A 1 HETATM 18 O O4' UMC . . . C 3 6.815 37.939 -34.671 1 16.58 ? O4' UMC 302 A 1 HETATM 19 C C5' UMC . . . C 3 8.809 36.555 -34.89 1 14.92 ? C5' UMC 302 A 1 HETATM 20 O O5' UMC . . . C 3 8.667 35.892 -33.609 1 15.91 ? O5' UMC 302 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #