data_5KRD # _model_server_result.job_id jZMh-ApYCj0hBJ0FjjhuTA _model_server_result.datetime_utc '2024-11-01 18:27:12' _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 5krd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5KRD # _exptl.entry_id 5KRD _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 5KRD _cell.length_a 155.049 _cell.length_b 155.049 _cell.length_c 89.005 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KRD _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 29.668333 3 'crystal symmetry operation' 11_455 -x+y-1,y,-z -1 0 0 0 1 0 0 0 -1 -155.049 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 96 n n N1 C10 FMN doub 97 n n C2 O2 FMN doub 98 n n C2 N3 FMN sing 99 n n N3 C4 FMN sing 100 n n N3 HN3 FMN sing 101 n n C4 O4 FMN doub 102 n n C4 C4A FMN sing 103 n n C4A N5 FMN doub 104 n n C4A C10 FMN sing 105 n n N5 C5A FMN sing 106 n n C5A C6 FMN doub 107 n y C5A C9A FMN sing 108 n y C6 C7 FMN sing 109 n y C6 H6 FMN sing 110 n n C7 C7M FMN sing 111 n n C7 C8 FMN doub 112 n y C7M HM71 FMN sing 113 n n C7M HM72 FMN sing 114 n n C7M HM73 FMN sing 115 n n C8 C8M FMN sing 116 n n C8 C9 FMN sing 117 n y C8M HM81 FMN sing 118 n n C8M HM82 FMN sing 119 n n C8M HM83 FMN sing 120 n n C9 C9A FMN doub 121 n y C9 H9 FMN sing 122 n n C9A N10 FMN sing 123 n n N10 C10 FMN sing 124 n n N10 C1' FMN sing 125 n n C1' C2' FMN sing 126 n n C1' "H1'1" FMN sing 127 n n C1' "H1'2" FMN sing 128 n n C2' O2' FMN sing 129 n n C2' C3' FMN sing 130 n n C2' H2' FMN sing 131 n n O2' HO2' FMN sing 132 n n C3' O3' FMN sing 133 n n C3' C4' FMN sing 134 n n C3' H3' FMN sing 135 n n O3' HO3' FMN sing 136 n n C4' O4' FMN sing 137 n n C4' C5' FMN sing 138 n n C4' H4' FMN sing 139 n n O4' HO4' FMN sing 140 n n C5' O5' FMN sing 141 n n C5' "H5'1" FMN sing 142 n n C5' "H5'2" FMN sing 143 n n O5' P FMN sing 144 n n P O1P FMN doub 145 n n P O2P FMN sing 146 n n P O3P FMN sing 147 n n O2P HOP2 FMN sing 148 n n O3P HOP3 FMN sing 149 n n # _atom_sites.entry_id 5KRD _atom_sites.fract_transf_matrix[1][1] 0.00645 _atom_sites.fract_transf_matrix[1][2] 0.003724 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007447 _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] 0.011235 _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 6X8 A 1 302 302 6X8 2IP . E 2 FMN B 1 301 302 FMN FMN . F 3 6X8 B 1 302 303 6X8 2IP . G 4 HOH A 1 401 92 HOH HOH . G 4 HOH A 2 402 106 HOH HOH . G 4 HOH A 3 403 64 HOH HOH . G 4 HOH A 4 404 77 HOH HOH . G 4 HOH A 5 405 104 HOH HOH . G 4 HOH A 6 406 48 HOH HOH . G 4 HOH A 7 407 30 HOH HOH . G 4 HOH A 8 408 10 HOH HOH . G 4 HOH A 9 409 122 HOH HOH . G 4 HOH A 10 410 112 HOH HOH . G 4 HOH A 11 411 115 HOH HOH . G 4 HOH A 12 412 36 HOH HOH . G 4 HOH A 13 413 27 HOH HOH . G 4 HOH A 14 414 73 HOH HOH . G 4 HOH A 15 415 6 HOH HOH . G 4 HOH A 16 416 4 HOH HOH . G 4 HOH A 17 417 2 HOH HOH . G 4 HOH A 18 418 127 HOH HOH . G 4 HOH A 19 419 1 HOH HOH . G 4 HOH A 20 420 19 HOH HOH . G 4 HOH A 21 421 31 HOH HOH . G 4 HOH A 22 422 25 HOH HOH . G 4 HOH A 23 423 15 HOH HOH . G 4 HOH A 24 424 3 HOH HOH . G 4 HOH A 25 425 126 HOH HOH . G 4 HOH A 26 426 32 HOH HOH . G 4 HOH A 27 427 93 HOH HOH . G 4 HOH A 28 428 9 HOH HOH . G 4 HOH A 29 429 67 HOH HOH . G 4 HOH A 30 430 29 HOH HOH . G 4 HOH A 31 431 16 HOH HOH . G 4 HOH A 32 432 128 HOH HOH . G 4 HOH A 33 433 33 HOH HOH . G 4 HOH A 34 434 23 HOH HOH . G 4 HOH A 35 435 41 HOH HOH . G 4 HOH A 36 436 98 HOH HOH . G 4 HOH A 37 437 17 HOH HOH . G 4 HOH A 38 438 129 HOH HOH . G 4 HOH A 39 439 69 HOH HOH . G 4 HOH A 40 440 56 HOH HOH . G 4 HOH A 41 441 80 HOH HOH . G 4 HOH A 42 442 21 HOH HOH . G 4 HOH A 43 443 65 HOH HOH . G 4 HOH A 44 444 20 HOH HOH . G 4 HOH A 45 445 82 HOH HOH . G 4 HOH A 46 446 99 HOH HOH . G 4 HOH A 47 447 94 HOH HOH . G 4 HOH A 48 448 81 HOH HOH . G 4 HOH A 49 449 68 HOH HOH . G 4 HOH A 50 450 72 HOH HOH . G 4 HOH A 51 451 14 HOH HOH . G 4 HOH A 52 452 42 HOH HOH . G 4 HOH A 53 453 114 HOH HOH . G 4 HOH A 54 454 116 HOH HOH . G 4 HOH A 55 455 46 HOH HOH . G 4 HOH A 56 456 125 HOH HOH . G 4 HOH A 57 457 90 HOH HOH . G 4 HOH A 58 458 43 HOH HOH . G 4 HOH A 59 459 124 HOH HOH . G 4 HOH A 60 460 44 HOH HOH . G 4 HOH A 61 461 113 HOH HOH . G 4 HOH A 62 462 105 HOH HOH . G 4 HOH A 63 463 55 HOH HOH . G 4 HOH A 64 464 7 HOH HOH . G 4 HOH A 65 465 87 HOH HOH . G 4 HOH A 66 466 11 HOH HOH . G 4 HOH A 67 467 118 HOH HOH . G 4 HOH A 68 468 100 HOH HOH . G 4 HOH A 69 469 76 HOH HOH . G 4 HOH A 70 470 74 HOH HOH . G 4 HOH A 71 471 78 HOH HOH . G 4 HOH A 72 472 120 HOH HOH . G 4 HOH A 73 473 70 HOH HOH . G 4 HOH A 74 474 59 HOH HOH . G 4 HOH A 75 475 50 HOH HOH . G 4 HOH A 76 476 75 HOH HOH . G 4 HOH A 77 477 123 HOH HOH . G 4 HOH A 78 478 54 HOH HOH . H 4 HOH B 1 401 13 HOH HOH . H 4 HOH B 2 402 57 HOH HOH . H 4 HOH B 3 403 52 HOH HOH . H 4 HOH B 4 404 45 HOH HOH . H 4 HOH B 5 405 28 HOH HOH . H 4 HOH B 6 406 66 HOH HOH . H 4 HOH B 7 407 86 HOH HOH . H 4 HOH B 8 408 5 HOH HOH . H 4 HOH B 9 409 63 HOH HOH . H 4 HOH B 10 410 95 HOH HOH . H 4 HOH B 11 411 12 HOH HOH . H 4 HOH B 12 412 37 HOH HOH . H 4 HOH B 13 413 22 HOH HOH . H 4 HOH B 14 414 18 HOH HOH . H 4 HOH B 15 415 96 HOH HOH . H 4 HOH B 16 416 35 HOH HOH . H 4 HOH B 17 417 62 HOH HOH . H 4 HOH B 18 418 34 HOH HOH . H 4 HOH B 19 419 110 HOH HOH . H 4 HOH B 20 420 101 HOH HOH . H 4 HOH B 21 421 91 HOH HOH . H 4 HOH B 22 422 47 HOH HOH . H 4 HOH B 23 423 8 HOH HOH . H 4 HOH B 24 424 79 HOH HOH . H 4 HOH B 25 425 53 HOH HOH . H 4 HOH B 26 426 26 HOH HOH . H 4 HOH B 27 427 40 HOH HOH . H 4 HOH B 28 428 85 HOH HOH . H 4 HOH B 29 429 84 HOH HOH . H 4 HOH B 30 430 24 HOH HOH . H 4 HOH B 31 431 102 HOH HOH . H 4 HOH B 32 432 39 HOH HOH . H 4 HOH B 33 433 71 HOH HOH . H 4 HOH B 34 434 49 HOH HOH . H 4 HOH B 35 435 97 HOH HOH . H 4 HOH B 36 436 89 HOH HOH . H 4 HOH B 37 437 61 HOH HOH . H 4 HOH B 38 438 38 HOH HOH . H 4 HOH B 39 439 119 HOH HOH . H 4 HOH B 40 440 51 HOH HOH . H 4 HOH B 41 441 108 HOH HOH . H 4 HOH B 42 442 121 HOH HOH . H 4 HOH B 43 443 58 HOH HOH . H 4 HOH B 44 444 103 HOH HOH . H 4 HOH B 45 445 60 HOH HOH . H 4 HOH B 46 446 111 HOH HOH . H 4 HOH B 47 447 109 HOH HOH . H 4 HOH B 48 448 117 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 -66.639 -22.165 11.468 1 43.62 ? N1 FMN 301 A 1 HETATM 2 C C2 FMN . . . C 2 -65.407 -21.602 11.774 1 44.06 ? C2 FMN 301 A 1 HETATM 3 O O2 FMN . . . C 2 -64.627 -22.108 12.594 1 44.1 ? O2 FMN 301 A 1 HETATM 4 N N3 FMN . . . C 2 -65.047 -20.453 11.139 1 45.41 ? N3 FMN 301 A 1 HETATM 5 C C4 FMN . . . C 2 -65.877 -19.861 10.21 1 46.04 ? C4 FMN 301 A 1 HETATM 6 O O4 FMN . . . C 2 -65.535 -18.828 9.631 1 44.95 ? O4 FMN 301 A 1 HETATM 7 C C4A FMN . . . C 2 -67.111 -20.407 9.91 1 42.9 ? C4A FMN 301 A 1 HETATM 8 N N5 FMN . . . C 2 -67.929 -19.775 8.979 1 44.13 ? N5 FMN 301 A 1 HETATM 9 C C5A FMN . . . C 2 -69.139 -20.352 8.637 1 42.37 ? C5A FMN 301 A 1 HETATM 10 C C6 FMN . . . C 2 -69.935 -19.726 7.685 1 43.28 ? C6 FMN 301 A 1 HETATM 11 C C7 FMN . . . C 2 -71.147 -20.269 7.325 1 40.83 ? C7 FMN 301 A 1 HETATM 12 C C7M FMN . . . C 2 -71.964 -19.535 6.284 1 40.48 ? C7M FMN 301 A 1 HETATM 13 C C8 FMN . . . C 2 -71.549 -21.466 7.922 1 39.54 ? C8 FMN 301 A 1 HETATM 14 C C8M FMN . . . C 2 -72.855 -22.08 7.523 1 39.15 ? C8M FMN 301 A 1 HETATM 15 C C9 FMN . . . C 2 -70.774 -22.068 8.892 1 39.43 ? C9 FMN 301 A 1 HETATM 16 C C9A FMN . . . C 2 -69.544 -21.531 9.257 1 41.2 ? C9A FMN 301 A 1 HETATM 17 N N10 FMN . . . C 2 -68.723 -22.128 10.228 1 41.22 ? N10 FMN 301 A 1 HETATM 18 C C10 FMN . . . C 2 -67.498 -21.559 10.549 1 41.3 ? C10 FMN 301 A 1 HETATM 19 C C1' FMN . . . C 2 -69.079 -23.419 10.932 1 38.85 ? C1' FMN 301 A 1 HETATM 20 C C2' FMN . . . C 2 -70.019 -23.22 12.123 1 40.71 ? C2' FMN 301 A 1 HETATM 21 O O2' FMN . . . C 2 -69.38 -22.724 13.255 1 41.61 ? O2' FMN 301 A 1 HETATM 22 C C3' FMN . . . C 2 -70.705 -24.554 12.449 1 41.3 ? C3' FMN 301 A 1 HETATM 23 O O3' FMN . . . C 2 -71.39 -24.927 11.286 1 41.02 ? O3' FMN 301 A 1 HETATM 24 C C4' FMN . . . C 2 -71.64 -24.509 13.652 1 42.34 ? C4' FMN 301 A 1 HETATM 25 O O4' FMN . . . C 2 -70.872 -24.315 14.825 1 42.07 ? O4' FMN 301 A 1 HETATM 26 C C5' FMN . . . C 2 -72.482 -25.785 13.789 1 44.16 ? C5' FMN 301 A 1 HETATM 27 O O5' FMN . . . C 2 -71.639 -26.916 13.846 1 43.3 ? O5' FMN 301 A 1 HETATM 28 P P FMN . . . C 2 -71.973 -28.166 12.894 1 41.9 ? P FMN 301 A 1 HETATM 29 O O1P FMN . . . C 2 -71.809 -27.753 11.478 1 39.6 ? O1P FMN 301 A 1 HETATM 30 O O2P FMN . . . C 2 -73.423 -28.501 13.166 1 41.92 -1 O2P FMN 301 A 1 HETATM 31 O O3P FMN . . . C 2 -71.03 -29.285 13.284 1 40.65 ? O3P FMN 301 A 1 HETATM 32 H HN3 FMN . . . C 2 -64.13 -20.014 11.357 1 58.58 ? HN3 FMN 301 A 1 HETATM 33 H H6 FMN . . . C 2 -69.597 -18.799 7.22 1 54.97 ? H6 FMN 301 A 1 HETATM 34 H HM71 FMN . . . C 2 -72.886 -20.085 6.092 1 46.08 ? HM71 FMN 301 A 1 HETATM 35 H HM72 FMN . . . C 2 -71.39 -19.455 5.362 1 46.08 ? HM72 FMN 301 A 1 HETATM 36 H HM73 FMN . . . C 2 -72.207 -18.537 6.65 1 46.08 ? HM73 FMN 301 A 1 HETATM 37 H HM81 FMN . . . C 2 -73.021 -22.989 8.101 1 41.05 ? HM81 FMN 301 A 1 HETATM 38 H HM82 FMN . . . C 2 -72.832 -22.324 6.461 1 41.05 ? HM82 FMN 301 A 1 HETATM 39 H HM83 FMN . . . C 2 -73.663 -21.374 7.716 1 41.05 ? HM83 FMN 301 A 1 HETATM 40 H H9 FMN . . . C 2 -71.13 -22.977 9.378 1 40.31 ? H9 FMN 301 A 1 HETATM 41 H "H1'1" FMN . . . C 2 -68.163 -23.897 11.279 1 35.82 ? "H1'1" FMN 301 A 1 HETATM 42 H "H1'2" FMN . . . C 2 -69.55 -24.094 10.218 1 35.82 ? "H1'2" FMN 301 A 1 HETATM 43 H H2' FMN . . . C 2 -70.793 -22.515 11.82 1 41.85 ? H2' FMN 301 A 1 HETATM 44 H HO2' FMN . . . C 2 -69.515 -23.342 14.004 1 43.98 ? HO2' FMN 301 A 1 HETATM 45 H H3' FMN . . . C 2 -69.928 -25.289 12.656 1 43.5 ? H3' FMN 301 A 1 HETATM 46 H HO3' FMN . . . C 2 -72.334 -25.081 11.498 1 43.58 ? HO3' FMN 301 A 1 HETATM 47 H H4' FMN . . . C 2 -72.319 -23.666 13.523 1 46.01 ? H4' FMN 301 A 1 HETATM 48 H HO4' FMN . . . C 2 -71.054 -25.041 15.458 1 43.65 ? HO4' FMN 301 A 1 HETATM 49 H "H5'1" FMN . . . C 2 -73.157 -25.873 12.938 1 52.12 ? "H5'1" FMN 301 A 1 HETATM 50 H "H5'2" FMN . . . C 2 -73.085 -25.731 14.696 1 52.12 ? "H5'2" FMN 301 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 50 #