data_5ZYR # _model_server_result.job_id RY5hH3RrkEZYtD0i4uodTA _model_server_result.datetime_utc '2024-10-10 07:28:17' _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 5zyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5ZYR # _exptl.entry_id 5ZYR _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 90 _cell.entry_id 5ZYR _cell.length_a 47.992 _cell.length_b 59.9 _cell.length_c 212.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 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 89 n n N1 C10 FMN doub 90 n n C2 O2 FMN doub 91 n n C2 N3 FMN sing 92 n n N3 C4 FMN sing 93 n n N3 HN3 FMN sing 94 n n C4 O4 FMN doub 95 n n C4 C4A FMN sing 96 n n C4A N5 FMN doub 97 n n C4A C10 FMN sing 98 n n N5 C5A FMN sing 99 n n C5A C6 FMN doub 100 n y C5A C9A FMN sing 101 n y C6 C7 FMN sing 102 n y C6 H6 FMN sing 103 n n C7 C7M FMN sing 104 n n C7 C8 FMN doub 105 n y C7M HM71 FMN sing 106 n n C7M HM72 FMN sing 107 n n C7M HM73 FMN sing 108 n n C8 C8M FMN sing 109 n n C8 C9 FMN sing 110 n y C8M HM81 FMN sing 111 n n C8M HM82 FMN sing 112 n n C8M HM83 FMN sing 113 n n C9 C9A FMN doub 114 n y C9 H9 FMN sing 115 n n C9A N10 FMN sing 116 n n N10 C10 FMN sing 117 n n N10 C1' FMN sing 118 n n C1' C2' FMN sing 119 n n C1' "H1'1" FMN sing 120 n n C1' "H1'2" FMN sing 121 n n C2' O2' FMN sing 122 n n C2' C3' FMN sing 123 n n C2' H2' FMN sing 124 n n O2' HO2' FMN sing 125 n n C3' O3' FMN sing 126 n n C3' C4' FMN sing 127 n n C3' H3' FMN sing 128 n n O3' HO3' FMN sing 129 n n C4' O4' FMN sing 130 n n C4' C5' FMN sing 131 n n C4' H4' FMN sing 132 n n O4' HO4' FMN sing 133 n n C5' O5' FMN sing 134 n n C5' "H5'1" FMN sing 135 n n C5' "H5'2" FMN sing 136 n n O5' P FMN sing 137 n n P O1P FMN doub 138 n n P O2P FMN sing 139 n n P O3P FMN sing 140 n n O2P HOP2 FMN sing 141 n n O3P HOP3 FMN sing 142 n n # _atom_sites.entry_id 5ZYR _atom_sites.fract_transf_matrix[1][1] 0.020837 _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] 0.016694 _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] 0.00471 _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 1 401 1 FMN FMN . D 3 ACT A 1 402 2 ACT ACT . E 2 FMN B 1 401 2 FMN FMN . F 3 ACT B 1 402 1 ACT ACT . G 4 HOH A 1 501 103 HOH HOH . G 4 HOH A 2 502 12 HOH HOH . G 4 HOH A 3 503 3 HOH HOH . G 4 HOH A 4 504 14 HOH HOH . G 4 HOH A 5 505 39 HOH HOH . G 4 HOH A 6 506 125 HOH HOH . G 4 HOH A 7 507 10 HOH HOH . G 4 HOH A 8 508 67 HOH HOH . G 4 HOH A 9 509 6 HOH HOH . G 4 HOH A 10 510 102 HOH HOH . G 4 HOH A 11 511 21 HOH HOH . G 4 HOH A 12 512 18 HOH HOH . G 4 HOH A 13 513 28 HOH HOH . G 4 HOH A 14 514 105 HOH HOH . G 4 HOH A 15 515 26 HOH HOH . G 4 HOH A 16 516 2 HOH HOH . G 4 HOH A 17 517 17 HOH HOH . G 4 HOH A 18 518 35 HOH HOH . G 4 HOH A 19 519 5 HOH HOH . G 4 HOH A 20 520 104 HOH HOH . G 4 HOH A 21 521 62 HOH HOH . G 4 HOH A 22 522 54 HOH HOH . G 4 HOH A 23 523 69 HOH HOH . G 4 HOH A 24 524 16 HOH HOH . G 4 HOH A 25 525 60 HOH HOH . G 4 HOH A 26 526 63 HOH HOH . G 4 HOH A 27 527 20 HOH HOH . G 4 HOH A 28 528 46 HOH HOH . G 4 HOH A 29 529 77 HOH HOH . G 4 HOH A 30 530 29 HOH HOH . G 4 HOH A 31 531 8 HOH HOH . G 4 HOH A 32 532 126 HOH HOH . G 4 HOH A 33 533 118 HOH HOH . G 4 HOH A 34 534 30 HOH HOH . G 4 HOH A 35 535 47 HOH HOH . G 4 HOH A 36 536 4 HOH HOH . G 4 HOH A 37 537 59 HOH HOH . G 4 HOH A 38 538 52 HOH HOH . G 4 HOH A 39 539 74 HOH HOH . G 4 HOH A 40 540 40 HOH HOH . G 4 HOH A 41 541 45 HOH HOH . G 4 HOH A 42 542 84 HOH HOH . G 4 HOH A 43 543 61 HOH HOH . G 4 HOH A 44 544 55 HOH HOH . G 4 HOH A 45 545 27 HOH HOH . G 4 HOH A 46 546 38 HOH HOH . G 4 HOH A 47 547 112 HOH HOH . G 4 HOH A 48 548 88 HOH HOH . G 4 HOH A 49 549 42 HOH HOH . G 4 HOH A 50 550 111 HOH HOH . G 4 HOH A 51 551 41 HOH HOH . G 4 HOH A 52 552 87 HOH HOH . G 4 HOH A 53 553 86 HOH HOH . G 4 HOH A 54 554 90 HOH HOH . G 4 HOH A 55 555 75 HOH HOH . G 4 HOH A 56 556 33 HOH HOH . G 4 HOH A 57 557 68 HOH HOH . G 4 HOH A 58 558 114 HOH HOH . G 4 HOH A 59 559 72 HOH HOH . G 4 HOH A 60 560 89 HOH HOH . G 4 HOH A 61 561 66 HOH HOH . G 4 HOH A 62 562 73 HOH HOH . G 4 HOH A 63 563 113 HOH HOH . H 4 HOH B 1 501 108 HOH HOH . H 4 HOH B 2 502 115 HOH HOH . H 4 HOH B 3 503 106 HOH HOH . H 4 HOH B 4 504 119 HOH HOH . H 4 HOH B 5 505 101 HOH HOH . H 4 HOH B 6 506 70 HOH HOH . H 4 HOH B 7 507 127 HOH HOH . H 4 HOH B 8 508 98 HOH HOH . H 4 HOH B 9 509 96 HOH HOH . H 4 HOH B 10 510 85 HOH HOH . H 4 HOH B 11 511 15 HOH HOH . H 4 HOH B 12 512 82 HOH HOH . H 4 HOH B 13 513 36 HOH HOH . H 4 HOH B 14 514 97 HOH HOH . H 4 HOH B 15 515 92 HOH HOH . H 4 HOH B 16 516 13 HOH HOH . H 4 HOH B 17 517 94 HOH HOH . H 4 HOH B 18 518 53 HOH HOH . H 4 HOH B 19 519 76 HOH HOH . H 4 HOH B 20 520 50 HOH HOH . H 4 HOH B 21 521 31 HOH HOH . H 4 HOH B 22 522 25 HOH HOH . H 4 HOH B 23 523 7 HOH HOH . H 4 HOH B 24 524 58 HOH HOH . H 4 HOH B 25 525 19 HOH HOH . H 4 HOH B 26 526 65 HOH HOH . H 4 HOH B 27 527 83 HOH HOH . H 4 HOH B 28 528 49 HOH HOH . H 4 HOH B 29 529 48 HOH HOH . H 4 HOH B 30 530 1 HOH HOH . H 4 HOH B 31 531 43 HOH HOH . H 4 HOH B 32 532 32 HOH HOH . H 4 HOH B 33 533 9 HOH HOH . H 4 HOH B 34 534 64 HOH HOH . H 4 HOH B 35 535 122 HOH HOH . H 4 HOH B 36 536 93 HOH HOH . H 4 HOH B 37 537 56 HOH HOH . H 4 HOH B 38 538 11 HOH HOH . H 4 HOH B 39 539 51 HOH HOH . H 4 HOH B 40 540 37 HOH HOH . H 4 HOH B 41 541 71 HOH HOH . H 4 HOH B 42 542 34 HOH HOH . H 4 HOH B 43 543 57 HOH HOH . H 4 HOH B 44 544 110 HOH HOH . H 4 HOH B 45 545 81 HOH HOH . H 4 HOH B 46 546 116 HOH HOH . H 4 HOH B 47 547 23 HOH HOH . H 4 HOH B 48 548 120 HOH HOH . H 4 HOH B 49 549 22 HOH HOH . H 4 HOH B 50 550 107 HOH HOH . H 4 HOH B 51 551 99 HOH HOH . H 4 HOH B 52 552 91 HOH HOH . H 4 HOH B 53 553 95 HOH HOH . H 4 HOH B 54 554 109 HOH HOH . H 4 HOH B 55 555 44 HOH HOH . H 4 HOH B 56 556 79 HOH HOH . H 4 HOH B 57 557 24 HOH HOH . H 4 HOH B 58 558 80 HOH HOH . H 4 HOH B 59 559 100 HOH HOH . H 4 HOH B 60 560 128 HOH HOH . H 4 HOH B 61 561 124 HOH HOH . H 4 HOH B 62 562 78 HOH HOH . H 4 HOH B 63 563 123 HOH HOH . H 4 HOH B 64 564 121 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 21.172 7.216 41.796 1 42.46 ? N1 FMN 401 A 1 HETATM 2 C C2 FMN . . . C 2 20.844 6.197 42.637 1 42.86 ? C2 FMN 401 A 1 HETATM 3 O O2 FMN . . . C 2 20.933 6.392 43.88 1 46.79 ? O2 FMN 401 A 1 HETATM 4 N N3 FMN . . . C 2 20.435 4.992 42.184 1 38.77 ? N3 FMN 401 A 1 HETATM 5 C C4 FMN . . . C 2 20.315 4.741 40.86 1 39.12 ? C4 FMN 401 A 1 HETATM 6 O O4 FMN . . . C 2 19.917 3.634 40.421 1 42.33 ? O4 FMN 401 A 1 HETATM 7 C C4A FMN . . . C 2 20.673 5.799 39.895 1 34.94 ? C4A FMN 401 A 1 HETATM 8 N N5 FMN . . . C 2 20.581 5.603 38.566 1 37.59 ? N5 FMN 401 A 1 HETATM 9 C C5A FMN . . . C 2 20.878 6.585 37.688 1 39.47 ? C5A FMN 401 A 1 HETATM 10 C C6 FMN . . . C 2 20.769 6.352 36.32 1 38.94 ? C6 FMN 401 A 1 HETATM 11 C C7 FMN . . . C 2 21.066 7.36 35.415 1 40.38 ? C7 FMN 401 A 1 HETATM 12 C C7M FMN . . . C 2 20.933 7.121 33.926 1 42.6 ? C7M FMN 401 A 1 HETATM 13 C C8 FMN . . . C 2 21.519 8.682 35.91 1 38.81 ? C8 FMN 401 A 1 HETATM 14 C C8M FMN . . . C 2 21.847 9.77 34.916 1 41.36 ? C8M FMN 401 A 1 HETATM 15 C C9 FMN . . . C 2 21.624 8.928 37.277 1 39.83 ? C9 FMN 401 A 1 HETATM 16 C C9A FMN . . . C 2 21.313 7.916 38.182 1 42.38 ? C9A FMN 401 A 1 HETATM 17 N N10 FMN . . . C 2 21.44 8.136 39.566 1 42.12 ? N10 FMN 401 A 1 HETATM 18 C C10 FMN . . . C 2 21.114 7.091 40.453 1 41.36 ? C10 FMN 401 A 1 HETATM 19 C C1' FMN . . . C 2 21.904 9.439 40.039 1 43.75 ? C1' FMN 401 A 1 HETATM 20 C C2' FMN . . . C 2 20.805 10.266 40.665 1 44.74 ? C2' FMN 401 A 1 HETATM 21 O O2' FMN . . . C 2 19.771 10.56 39.718 1 39.82 ? O2' FMN 401 A 1 HETATM 22 C C3' FMN . . . C 2 21.426 11.546 41.191 1 49.15 ? C3' FMN 401 A 1 HETATM 23 O O3' FMN . . . C 2 22.495 11.189 42.073 1 48.93 ? O3' FMN 401 A 1 HETATM 24 C C4' FMN . . . C 2 20.366 12.283 41.996 1 53.69 ? C4' FMN 401 A 1 HETATM 25 O O4' FMN . . . C 2 19.31 12.771 41.131 1 52.06 ? O4' FMN 401 A 1 HETATM 26 C C5' FMN . . . C 2 21.026 13.402 42.802 1 57.65 ? C5' FMN 401 A 1 HETATM 27 O O5' FMN . . . C 2 20.013 14.056 43.557 1 66.28 ? O5' FMN 401 A 1 HETATM 28 P P FMN . . . C 2 19.821 13.779 45.136 1 72.58 ? P FMN 401 A 1 HETATM 29 O O1P FMN . . . C 2 18.864 14.887 45.507 1 75.58 ? O1P FMN 401 A 1 HETATM 30 O O2P FMN . . . C 2 21.213 13.879 45.736 1 79.2 ? O2P FMN 401 A 1 HETATM 31 O O3P FMN . . . C 2 19.259 12.381 45.242 1 66.12 ? O3P FMN 401 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #