data_6YMH # _model_server_result.job_id jfl87hLpmeZepB5mwlT5yA _model_server_result.datetime_utc '2024-12-23 09:41:05' _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 6ymh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6YMH # _exptl.entry_id 6YMH _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 6YMH _cell.length_a 54.164 _cell.length_b 54.164 _cell.length_c 271.968 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMH _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 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 6YMH _atom_sites.fract_transf_matrix[1][1] 0.018462 _atom_sites.fract_transf_matrix[1][2] 0.010659 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021319 _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] 0.003677 _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 AAA 1 301 250 FMN FMN . D 3 SO4 AAA 1 302 1 SO4 SO4 . E 2 FMN BBB 1 301 250 FMN FMN . F 4 PLP BBB 1 302 1 PLP PLP . G 5 HOH AAA 1 401 4 HOH HOH . G 5 HOH AAA 2 402 68 HOH HOH . G 5 HOH AAA 3 403 31 HOH HOH . G 5 HOH AAA 4 404 123 HOH HOH . G 5 HOH AAA 5 405 79 HOH HOH . G 5 HOH AAA 6 406 162 HOH HOH . G 5 HOH AAA 7 407 35 HOH HOH . G 5 HOH AAA 8 408 5 HOH HOH . G 5 HOH AAA 9 409 122 HOH HOH . G 5 HOH AAA 10 410 149 HOH HOH . G 5 HOH AAA 11 411 86 HOH HOH . G 5 HOH AAA 12 412 98 HOH HOH . G 5 HOH AAA 13 413 147 HOH HOH . G 5 HOH AAA 14 414 71 HOH HOH . G 5 HOH AAA 15 415 56 HOH HOH . H 5 HOH BBB 1 401 24 HOH HOH . H 5 HOH BBB 2 402 66 HOH HOH . H 5 HOH BBB 3 403 20 HOH HOH . H 5 HOH BBB 4 404 6 HOH HOH . H 5 HOH BBB 5 405 176 HOH HOH . H 5 HOH BBB 6 406 52 HOH HOH . H 5 HOH BBB 7 407 27 HOH HOH . H 5 HOH BBB 8 408 43 HOH HOH . H 5 HOH BBB 9 409 21 HOH HOH . H 5 HOH BBB 10 410 115 HOH HOH . H 5 HOH BBB 11 411 39 HOH HOH . H 5 HOH BBB 12 412 29 HOH HOH . H 5 HOH BBB 13 413 23 HOH HOH . H 5 HOH BBB 14 414 22 HOH HOH . H 5 HOH BBB 15 415 3 HOH HOH . H 5 HOH BBB 16 416 34 HOH HOH . H 5 HOH BBB 17 417 107 HOH HOH . H 5 HOH BBB 18 418 41 HOH HOH . H 5 HOH BBB 19 419 55 HOH HOH . H 5 HOH BBB 20 420 177 HOH HOH . H 5 HOH BBB 21 421 37 HOH HOH . H 5 HOH BBB 22 422 92 HOH HOH . H 5 HOH BBB 23 423 28 HOH HOH . H 5 HOH BBB 24 424 80 HOH HOH . H 5 HOH BBB 25 425 125 HOH HOH . H 5 HOH BBB 26 426 57 HOH HOH . H 5 HOH BBB 27 427 128 HOH HOH . H 5 HOH BBB 28 428 53 HOH HOH . H 5 HOH BBB 29 429 126 HOH HOH . H 5 HOH BBB 30 430 87 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 -30.491 22.277 -12.292 1 59.91 ? N1 FMN 301 AAA 1 HETATM 2 C C2 FMN . . . C 2 -29.677 21.768 -13.255 1 61.4 ? C2 FMN 301 AAA 1 HETATM 3 O O2 FMN . . . C 2 -28.98 22.554 -13.928 1 58.84 ? O2 FMN 301 AAA 1 HETATM 4 N N3 FMN . . . C 2 -29.589 20.435 -13.492 1 64.21 ? N3 FMN 301 AAA 1 HETATM 5 C C4 FMN . . . C 2 -30.314 19.532 -12.791 1 60.66 ? C4 FMN 301 AAA 1 HETATM 6 O O4 FMN . . . C 2 -30.226 18.305 -13.005 1 59.06 ? O4 FMN 301 AAA 1 HETATM 7 C C4A FMN . . . C 2 -31.238 20.018 -11.742 1 59.26 ? C4A FMN 301 AAA 1 HETATM 8 N N5 FMN . . . C 2 -31.988 19.165 -11.016 1 61.55 ? N5 FMN 301 AAA 1 HETATM 9 C C5A FMN . . . C 2 -32.818 19.601 -10.047 1 59.72 ? C5A FMN 301 AAA 1 HETATM 10 C C6 FMN . . . C 2 -33.551 18.658 -9.336 1 56.32 ? C6 FMN 301 AAA 1 HETATM 11 C C7 FMN . . . C 2 -34.428 19.043 -8.332 1 56.55 ? C7 FMN 301 AAA 1 HETATM 12 C C7M FMN . . . C 2 -35.207 17.985 -7.582 1 56.84 ? C7M FMN 301 AAA 1 HETATM 13 C C8 FMN . . . C 2 -34.554 20.491 -8.009 1 59.17 ? C8 FMN 301 AAA 1 HETATM 14 C C8M FMN . . . C 2 -35.487 20.955 -6.918 1 62.34 ? C8M FMN 301 AAA 1 HETATM 15 C C9 FMN . . . C 2 -33.82 21.444 -8.72 1 58.91 ? C9 FMN 301 AAA 1 HETATM 16 C C9A FMN . . . C 2 -32.945 21.069 -9.752 1 60.62 ? C9A FMN 301 AAA 1 HETATM 17 N N10 FMN . . . C 2 -32.155 21.994 -10.517 1 61.34 ? N10 FMN 301 AAA 1 HETATM 18 C C10 FMN . . . C 2 -31.286 21.48 -11.517 1 60.37 ? C10 FMN 301 AAA 1 HETATM 19 C C1' FMN . . . C 2 -32.167 23.457 -10.328 1 61.3 ? C1' FMN 301 AAA 1 HETATM 20 C C2' FMN . . . C 2 -30.907 23.855 -9.567 1 65.21 ? C2' FMN 301 AAA 1 HETATM 21 O O2' FMN . . . C 2 -31.127 23.528 -8.193 1 61.12 ? O2' FMN 301 AAA 1 HETATM 22 C C3' FMN . . . C 2 -30.534 25.33 -9.778 1 67.63 ? C3' FMN 301 AAA 1 HETATM 23 O O3' FMN . . . C 2 -31.67 26.161 -9.516 1 73.47 ? O3' FMN 301 AAA 1 HETATM 24 C C4' FMN . . . C 2 -30.013 25.62 -11.194 1 65.9 ? C4' FMN 301 AAA 1 HETATM 25 O O4' FMN . . . C 2 -29.155 24.562 -11.63 1 66.92 ? O4' FMN 301 AAA 1 HETATM 26 C C5' FMN . . . C 2 -29.239 26.929 -11.295 1 62.62 ? C5' FMN 301 AAA 1 HETATM 27 O O5' FMN . . . C 2 -28.095 26.877 -10.445 1 61.89 ? O5' FMN 301 AAA 1 HETATM 28 P P FMN . . . C 2 -26.887 27.945 -10.533 1 63.45 ? P FMN 301 AAA 1 HETATM 29 O O1P FMN . . . C 2 -26.255 27.913 -9.166 1 60.07 ? O1P FMN 301 AAA 1 HETATM 30 O O2P FMN . . . C 2 -25.988 27.39 -11.61 1 58.77 ? O2P FMN 301 AAA 1 HETATM 31 O O3P FMN . . . C 2 -27.539 29.277 -10.865 1 59.57 ? O3P FMN 301 AAA 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #