data_5KO8 # _model_server_result.job_id LW6KBid7EwLxBlK1eR9oxw _model_server_result.datetime_utc '2024-11-01 16:25:33' _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 5ko8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5KO8 # _exptl.entry_id 5KO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.344 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN MONONUCLEOTIDE' _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 5KO8 _cell.length_a 152.718 _cell.length_b 152.718 _cell.length_c 87.286 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 64 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,G 1 1,3 B,E,F,H 2 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' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 29.095333 3 'crystal symmetry operation' 11_455 -x+y-1,y,-z -1 0 0 0 1 0 0 0 -1 -152.718 0 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 E N N # _chem_comp.formula 'C17 H21 N4 O9 P' _chem_comp.formula_weight 456.344 _chem_comp.id FMN _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN MONONUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVIN MONOPHOSPHATE' # 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 FMN sing 83 n n N1 C10 FMN doub 84 n n C2 O2 FMN doub 85 n n C2 N3 FMN sing 86 n n N3 C4 FMN sing 87 n n N3 HN3 FMN sing 88 n n C4 O4 FMN doub 89 n n C4 C4A FMN sing 90 n n C4A N5 FMN doub 91 n n C4A C10 FMN sing 92 n n N5 C5A FMN sing 93 n n C5A C6 FMN doub 94 n y C5A C9A FMN sing 95 n y C6 C7 FMN sing 96 n y C6 H6 FMN sing 97 n n C7 C7M FMN sing 98 n n C7 C8 FMN doub 99 n y C7M HM71 FMN sing 100 n n C7M HM72 FMN sing 101 n n C7M HM73 FMN sing 102 n n C8 C8M FMN sing 103 n n C8 C9 FMN sing 104 n y C8M HM81 FMN sing 105 n n C8M HM82 FMN sing 106 n n C8M HM83 FMN sing 107 n n C9 C9A FMN doub 108 n y C9 H9 FMN sing 109 n n C9A N10 FMN sing 110 n n N10 C10 FMN sing 111 n n N10 C1' FMN sing 112 n n C1' C2' FMN sing 113 n n C1' "H1'1" FMN sing 114 n n C1' "H1'2" FMN sing 115 n n C2' O2' FMN sing 116 n n C2' C3' FMN sing 117 n n C2' H2' FMN sing 118 n n O2' HO2' FMN sing 119 n n C3' O3' FMN sing 120 n n C3' C4' FMN sing 121 n n C3' H3' FMN sing 122 n n O3' HO3' FMN sing 123 n n C4' O4' FMN sing 124 n n C4' C5' FMN sing 125 n n C4' H4' FMN sing 126 n n O4' HO4' FMN sing 127 n n C5' O5' FMN sing 128 n n C5' "H5'1" FMN sing 129 n n C5' "H5'2" FMN sing 130 n n O5' P FMN sing 131 n n P O1P FMN doub 132 n n P O2P FMN sing 133 n n P O3P FMN sing 134 n n O2P HOP2 FMN sing 135 n n O3P HOP3 FMN sing 136 n n # _atom_sites.entry_id 5KO8 _atom_sites.fract_transf_matrix[1][1] 0.006548 _atom_sites.fract_transf_matrix[1][2] 0.00378 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007561 _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] 0.011457 _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 FMN A 1 301 301 FMN FMN . D 3 IYR A 1 302 302 IYR IYR . E 2 FMN B 1 301 301 FMN FMN . F 3 IYR B 1 302 302 IYR IYR . G 4 HOH A 1 401 2 HOH HOH . G 4 HOH A 2 402 455 HOH HOH . G 4 HOH A 3 403 405 HOH HOH . G 4 HOH A 4 404 404 HOH HOH . G 4 HOH A 5 405 402 HOH HOH . G 4 HOH A 6 406 410 HOH HOH . G 4 HOH A 7 407 423 HOH HOH . G 4 HOH A 8 408 403 HOH HOH . G 4 HOH A 9 409 408 HOH HOH . G 4 HOH A 10 410 415 HOH HOH . G 4 HOH A 11 411 412 HOH HOH . G 4 HOH A 12 412 411 HOH HOH . G 4 HOH A 13 413 409 HOH HOH . G 4 HOH A 14 414 414 HOH HOH . G 4 HOH A 15 415 406 HOH HOH . G 4 HOH A 16 416 418 HOH HOH . G 4 HOH A 17 417 424 HOH HOH . G 4 HOH A 18 418 407 HOH HOH . G 4 HOH A 19 419 416 HOH HOH . G 4 HOH A 20 420 441 HOH HOH . G 4 HOH A 21 421 420 HOH HOH . G 4 HOH A 22 422 413 HOH HOH . G 4 HOH A 23 423 428 HOH HOH . G 4 HOH A 24 424 436 HOH HOH . G 4 HOH A 25 425 426 HOH HOH . G 4 HOH A 26 426 422 HOH HOH . G 4 HOH A 27 427 427 HOH HOH . G 4 HOH A 28 428 439 HOH HOH . G 4 HOH A 29 429 432 HOH HOH . G 4 HOH A 30 430 431 HOH HOH . G 4 HOH A 31 431 434 HOH HOH . G 4 HOH A 32 432 419 HOH HOH . G 4 HOH A 33 433 440 HOH HOH . G 4 HOH A 34 434 430 HOH HOH . G 4 HOH A 35 435 443 HOH HOH . G 4 HOH A 36 436 417 HOH HOH . G 4 HOH A 37 437 438 HOH HOH . G 4 HOH A 38 438 433 HOH HOH . G 4 HOH A 39 439 445 HOH HOH . G 4 HOH A 40 440 446 HOH HOH . G 4 HOH A 41 441 437 HOH HOH . G 4 HOH A 42 442 429 HOH HOH . G 4 HOH A 43 443 421 HOH HOH . G 4 HOH A 44 444 435 HOH HOH . G 4 HOH A 45 445 425 HOH HOH . G 4 HOH A 46 446 451 HOH HOH . G 4 HOH A 47 447 442 HOH HOH . G 4 HOH A 48 448 447 HOH HOH . G 4 HOH A 49 449 452 HOH HOH . G 4 HOH A 50 450 444 HOH HOH . G 4 HOH A 51 451 449 HOH HOH . G 4 HOH A 52 452 453 HOH HOH . G 4 HOH A 53 453 450 HOH HOH . G 4 HOH A 54 454 468 HOH HOH . G 4 HOH A 55 455 457 HOH HOH . G 4 HOH A 56 456 456 HOH HOH . G 4 HOH A 57 457 459 HOH HOH . G 4 HOH A 58 458 458 HOH HOH . G 4 HOH A 59 459 437 HOH HOH . G 4 HOH A 60 460 460 HOH HOH . G 4 HOH A 61 461 461 HOH HOH . G 4 HOH A 62 462 454 HOH HOH . G 4 HOH A 63 463 471 HOH HOH . G 4 HOH A 64 464 469 HOH HOH . G 4 HOH A 65 465 463 HOH HOH . G 4 HOH A 66 466 466 HOH HOH . G 4 HOH A 67 467 467 HOH HOH . G 4 HOH A 68 468 465 HOH HOH . G 4 HOH A 69 469 448 HOH HOH . G 4 HOH A 70 470 472 HOH HOH . G 4 HOH A 71 471 464 HOH HOH . G 4 HOH A 72 472 470 HOH HOH . G 4 HOH A 73 473 462 HOH HOH . G 4 HOH A 74 474 474 HOH HOH . G 4 HOH A 75 475 475 HOH HOH . G 4 HOH A 76 476 476 HOH HOH . G 4 HOH A 77 477 477 HOH HOH . G 4 HOH A 78 478 480 HOH HOH . G 4 HOH A 79 479 473 HOH HOH . G 4 HOH A 80 480 478 HOH HOH . G 4 HOH A 81 481 479 HOH HOH . G 4 HOH A 82 482 481 HOH HOH . G 4 HOH A 83 483 482 HOH HOH . G 4 HOH A 84 484 483 HOH HOH . H 4 HOH B 1 401 401 HOH HOH . H 4 HOH B 2 402 402 HOH HOH . H 4 HOH B 3 403 411 HOH HOH . H 4 HOH B 4 404 403 HOH HOH . H 4 HOH B 5 405 404 HOH HOH . H 4 HOH B 6 406 406 HOH HOH . H 4 HOH B 7 407 405 HOH HOH . H 4 HOH B 8 408 409 HOH HOH . H 4 HOH B 9 409 410 HOH HOH . H 4 HOH B 10 410 412 HOH HOH . H 4 HOH B 11 411 430 HOH HOH . H 4 HOH B 12 412 408 HOH HOH . H 4 HOH B 13 413 407 HOH HOH . H 4 HOH B 14 414 417 HOH HOH . H 4 HOH B 15 415 419 HOH HOH . H 4 HOH B 16 416 413 HOH HOH . H 4 HOH B 17 417 423 HOH HOH . H 4 HOH B 18 418 416 HOH HOH . H 4 HOH B 19 419 426 HOH HOH . H 4 HOH B 20 420 427 HOH HOH . H 4 HOH B 21 421 418 HOH HOH . H 4 HOH B 22 422 429 HOH HOH . H 4 HOH B 23 423 421 HOH HOH . H 4 HOH B 24 424 425 HOH HOH . H 4 HOH B 25 425 432 HOH HOH . H 4 HOH B 26 426 424 HOH HOH . H 4 HOH B 27 427 414 HOH HOH . H 4 HOH B 28 428 415 HOH HOH . H 4 HOH B 29 429 420 HOH HOH . H 4 HOH B 30 430 431 HOH HOH . H 4 HOH B 31 431 422 HOH HOH . H 4 HOH B 32 432 438 HOH HOH . H 4 HOH B 33 433 433 HOH HOH . H 4 HOH B 34 434 428 HOH HOH . H 4 HOH B 35 435 435 HOH HOH . H 4 HOH B 36 436 1 HOH HOH . H 4 HOH B 37 437 434 HOH HOH . H 4 HOH B 38 438 436 HOH HOH . H 4 HOH B 39 439 444 HOH HOH . H 4 HOH B 40 440 441 HOH HOH . H 4 HOH B 41 441 442 HOH HOH . H 4 HOH B 42 442 443 HOH HOH . H 4 HOH B 43 443 440 HOH HOH . H 4 HOH B 44 444 445 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 FMN . . . C 2 -65.537 -21.279 11.618 1 38.95 ? N1 FMN 301 A 1 HETATM 2 C C2 FMN . . . C 2 -64.335 -20.705 11.98 1 49.42 ? C2 FMN 301 A 1 HETATM 3 O O2 FMN . . . C 2 -63.618 -21.253 12.815 1 42.39 ? O2 FMN 301 A 1 HETATM 4 N N3 FMN . . . C 2 -63.94 -19.514 11.407 1 48.06 ? N3 FMN 301 A 1 HETATM 5 C C4 FMN . . . C 2 -64.739 -18.898 10.467 1 52.53 ? C4 FMN 301 A 1 HETATM 6 O O4 FMN . . . C 2 -64.374 -17.839 9.957 1 48.01 ? O4 FMN 301 A 1 HETATM 7 C C4A FMN . . . C 2 -65.951 -19.476 10.099 1 45.1 ? C4A FMN 301 A 1 HETATM 8 N N5 FMN . . . C 2 -66.757 -18.86 9.157 1 45.23 ? N5 FMN 301 A 1 HETATM 9 C C5A FMN . . . C 2 -67.955 -19.432 8.786 1 42.24 ? C5A FMN 301 A 1 HETATM 10 C C6 FMN . . . C 2 -68.752 -18.804 7.834 1 49.05 ? C6 FMN 301 A 1 HETATM 11 C C7 FMN . . . C 2 -69.965 -19.361 7.444 1 40.77 ? C7 FMN 301 A 1 HETATM 12 C C7M FMN . . . C 2 -70.798 -18.649 6.409 1 35.22 ? C7M FMN 301 A 1 HETATM 13 C C8 FMN . . . C 2 -70.366 -20.558 8.021 1 38.8 ? C8 FMN 301 A 1 HETATM 14 C C8M FMN . . . C 2 -71.656 -21.198 7.621 1 43.29 ? C8M FMN 301 A 1 HETATM 15 C C9 FMN . . . C 2 -69.569 -21.188 8.969 1 41.39 ? C9 FMN 301 A 1 HETATM 16 C C9A FMN . . . C 2 -68.36 -20.633 9.366 1 45.45 ? C9A FMN 301 A 1 HETATM 17 N N10 FMN . . . C 2 -67.561 -21.256 10.32 1 38.03 ? N10 FMN 301 A 1 HETATM 18 C C10 FMN . . . C 2 -66.351 -20.676 10.679 1 41.87 ? C10 FMN 301 A 1 HETATM 19 C C1' FMN . . . C 2 -67.975 -22.563 10.951 1 39.72 ? C1' FMN 301 A 1 HETATM 20 C C2' FMN . . . C 2 -69.049 -22.366 12.023 1 42.28 ? C2' FMN 301 A 1 HETATM 21 O O2' FMN . . . C 2 -68.491 -21.744 13.158 1 39.55 ? O2' FMN 301 A 1 HETATM 22 C C3' FMN . . . C 2 -69.675 -23.714 12.389 1 39.42 ? C3' FMN 301 A 1 HETATM 23 O O3' FMN . . . C 2 -70.371 -24.161 11.247 1 34.43 ? O3' FMN 301 A 1 HETATM 24 C C4' FMN . . . C 2 -70.601 -23.619 13.601 1 36.97 ? C4' FMN 301 A 1 HETATM 25 O O4' FMN . . . C 2 -69.826 -23.365 14.755 1 40.07 ? O4' FMN 301 A 1 HETATM 26 C C5' FMN . . . C 2 -71.428 -24.881 13.824 1 33.7 ? C5' FMN 301 A 1 HETATM 27 O O5' FMN . . . C 2 -70.624 -26.035 13.883 1 37.99 ? O5' FMN 301 A 1 HETATM 28 P P FMN . . . C 2 -71.007 -27.296 12.961 1 34.24 ? P FMN 301 A 1 HETATM 29 O O1P FMN . . . C 2 -70.062 -28.426 13.301 1 32.67 ? O1P FMN 301 A 1 HETATM 30 O O2P FMN . . . C 2 -70.841 -26.898 11.52 1 31.83 -1 O2P FMN 301 A 1 HETATM 31 O O3P FMN . . . C 2 -72.44 -27.706 13.197 1 35.33 ? O3P FMN 301 A 1 HETATM 32 H HN3 FMN . . . C 2 -63.037 -19.079 11.684 1 57.67 ? HN3 FMN 301 A 1 HETATM 33 H H6 FMN . . . C 2 -68.422 -17.865 7.389 1 58.86 ? H6 FMN 301 A 1 HETATM 34 H HM71 FMN . . . C 2 -71.707 -19.219 6.22 1 42.26 ? HM71 FMN 301 A 1 HETATM 35 H HM72 FMN . . . C 2 -70.228 -18.557 5.484 1 42.26 ? HM72 FMN 301 A 1 HETATM 36 H HM73 FMN . . . C 2 -71.061 -17.656 6.774 1 42.26 ? HM73 FMN 301 A 1 HETATM 37 H HM81 FMN . . . C 2 -71.786 -22.129 8.173 1 51.95 ? HM81 FMN 301 A 1 HETATM 38 H HM82 FMN . . . C 2 -71.641 -21.409 6.552 1 51.95 ? HM82 FMN 301 A 1 HETATM 39 H HM83 FMN . . . C 2 -72.482 -20.523 7.847 1 51.95 ? HM83 FMN 301 A 1 HETATM 40 H H9 FMN . . . C 2 -69.898 -22.131 9.408 1 49.67 ? H9 FMN 301 A 1 HETATM 41 H "H1'1" FMN . . . C 2 -67.102 -23.038 11.4 1 47.66 ? "H1'1" FMN 301 A 1 HETATM 42 H "H1'2" FMN . . . C 2 -68.356 -23.231 10.179 1 47.66 ? "H1'2" FMN 301 A 1 HETATM 43 H H2' FMN . . . C 2 -69.83 -21.729 11.609 1 50.74 ? H2' FMN 301 A 1 HETATM 44 H HO2' FMN . . . C 2 -68.628 -22.315 13.943 1 47.46 ? HO2' FMN 301 A 1 HETATM 45 H H3' FMN . . . C 2 -68.873 -24.414 12.623 1 47.3 ? H3' FMN 301 A 1 HETATM 46 H HO3' FMN . . . C 2 -71.311 -24.318 11.478 1 41.31 ? HO3' FMN 301 A 1 HETATM 47 H H4' FMN . . . C 2 -71.287 -22.789 13.439 1 44.36 ? H4' FMN 301 A 1 HETATM 48 H HO4' FMN . . . C 2 -70.002 -24.057 15.426 1 48.09 ? HO4' FMN 301 A 1 HETATM 49 H "H5'1" FMN . . . C 2 -72.149 -24.985 13.013 1 40.44 ? "H5'1" FMN 301 A 1 HETATM 50 H "H5'2" FMN . . . C 2 -71.987 -24.784 14.754 1 40.44 ? "H5'2" FMN 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 50 #