data_1YRX # _model_server_result.job_id Vedy_Oh7fEKGDELE-9HZFA _model_server_result.datetime_utc '2025-04-04 05:10:01' _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 1yrx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":203}' # _entry.id 1YRX # _exptl.entry_id 1YRX _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 3 _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 1YRX _cell.length_a 98.671 _cell.length_b 98.671 _cell.length_c 127.453 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YRX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 PQS hexameric 6 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,F,G,H,M,N 1 1 C,I,J,K,L,O 2 1,2 C,I,J,K,L,O 3 3,4 A,B,D,E,F,G,H,M,N 3 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 4 1,5 # 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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 63.7265 3 'crystal symmetry operation' 2_554 -x,-y,z-1/2 -1 0 0 0 -1 0 0 0 1 0 0 -63.7265 4 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 5 'crystal symmetry operation' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -63.7265 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 H N N ? 2 I 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 134 n n N1 C10 FMN doub 135 n n C2 O2 FMN doub 136 n n C2 N3 FMN sing 137 n n N3 C4 FMN sing 138 n n N3 HN3 FMN sing 139 n n C4 O4 FMN doub 140 n n C4 C4A FMN sing 141 n n C4A N5 FMN doub 142 n n C4A C10 FMN sing 143 n n N5 C5A FMN sing 144 n n C5A C6 FMN doub 145 n y C5A C9A FMN sing 146 n y C6 C7 FMN sing 147 n y C6 H6 FMN sing 148 n n C7 C7M FMN sing 149 n n C7 C8 FMN doub 150 n y C7M HM71 FMN sing 151 n n C7M HM72 FMN sing 152 n n C7M HM73 FMN sing 153 n n C8 C8M FMN sing 154 n n C8 C9 FMN sing 155 n y C8M HM81 FMN sing 156 n n C8M HM82 FMN sing 157 n n C8M HM83 FMN sing 158 n n C9 C9A FMN doub 159 n y C9 H9 FMN sing 160 n n C9A N10 FMN sing 161 n n N10 C10 FMN sing 162 n n N10 C1' FMN sing 163 n n C1' C2' FMN sing 164 n n C1' "H1'1" FMN sing 165 n n C1' "H1'2" FMN sing 166 n n C2' O2' FMN sing 167 n n C2' C3' FMN sing 168 n n C2' H2' FMN sing 169 n n O2' HO2' FMN sing 170 n n C3' O3' FMN sing 171 n n C3' C4' FMN sing 172 n n C3' H3' FMN sing 173 n n O3' HO3' FMN sing 174 n n C4' O4' FMN sing 175 n n C4' C5' FMN sing 176 n n C4' H4' FMN sing 177 n n O4' HO4' FMN sing 178 n n C5' O5' FMN sing 179 n n C5' "H5'1" FMN sing 180 n n C5' "H5'2" FMN sing 181 n n O5' P FMN sing 182 n n P O1P FMN doub 183 n n P O2P FMN sing 184 n n P O3P FMN sing 185 n n O2P HOP2 FMN sing 186 n n O3P HOP3 FMN sing 187 n n # _atom_sites.entry_id 1YRX _atom_sites.fract_transf_matrix[1][1] 0.010135 _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] 0.010135 _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] 0.007846 _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 D 2 FMN A 1 201 201 FMN FMN . E 3 D9G A 1 302 302 D9G DMG . F 3 D9G A 1 303 303 D9G DMG . G 3 D9G A 1 306 306 D9G DMG . H 2 FMN B 1 202 201 FMN FMN . I 2 FMN C 1 203 201 FMN FMN . J 3 D9G C 1 301 301 D9G DMG . K 3 D9G C 1 304 304 D9G DMG . L 3 D9G C 1 305 305 D9G DMG . M 4 HOH A 1 307 1 HOH HOH . M 4 HOH A 2 308 3 HOH HOH . M 4 HOH A 3 309 4 HOH HOH . M 4 HOH A 4 310 6 HOH HOH . M 4 HOH A 5 311 7 HOH HOH . M 4 HOH A 6 312 8 HOH HOH . M 4 HOH A 7 313 9 HOH HOH . M 4 HOH A 8 314 10 HOH HOH . M 4 HOH A 9 315 11 HOH HOH . M 4 HOH A 10 316 12 HOH HOH . M 4 HOH A 11 317 14 HOH HOH . M 4 HOH A 12 318 18 HOH HOH . M 4 HOH A 13 319 20 HOH HOH . M 4 HOH A 14 320 30 HOH HOH . M 4 HOH A 15 321 31 HOH HOH . M 4 HOH A 16 322 33 HOH HOH . M 4 HOH A 17 323 35 HOH HOH . M 4 HOH A 18 324 36 HOH HOH . M 4 HOH A 19 325 37 HOH HOH . M 4 HOH A 20 326 38 HOH HOH . M 4 HOH A 21 327 45 HOH HOH . M 4 HOH A 22 328 47 HOH HOH . M 4 HOH A 23 329 48 HOH HOH . M 4 HOH A 24 330 49 HOH HOH . M 4 HOH A 25 331 51 HOH HOH . M 4 HOH A 26 332 53 HOH HOH . M 4 HOH A 27 333 54 HOH HOH . M 4 HOH A 28 334 55 HOH HOH . M 4 HOH A 29 335 57 HOH HOH . M 4 HOH A 30 336 59 HOH HOH . M 4 HOH A 31 337 62 HOH HOH . M 4 HOH A 32 338 68 HOH HOH . M 4 HOH A 33 339 69 HOH HOH . M 4 HOH A 34 340 71 HOH HOH . M 4 HOH A 35 341 73 HOH HOH . M 4 HOH A 36 342 74 HOH HOH . M 4 HOH A 37 343 75 HOH HOH . M 4 HOH A 38 344 78 HOH HOH . M 4 HOH A 39 345 79 HOH HOH . M 4 HOH A 40 346 84 HOH HOH . M 4 HOH A 41 347 85 HOH HOH . M 4 HOH A 42 348 88 HOH HOH . M 4 HOH A 43 349 91 HOH HOH . M 4 HOH A 44 350 93 HOH HOH . M 4 HOH A 45 351 96 HOH HOH . M 4 HOH A 46 352 97 HOH HOH . N 4 HOH B 1 203 2 HOH HOH . N 4 HOH B 2 204 5 HOH HOH . N 4 HOH B 3 205 15 HOH HOH . N 4 HOH B 4 206 16 HOH HOH . N 4 HOH B 5 207 17 HOH HOH . N 4 HOH B 6 208 19 HOH HOH . N 4 HOH B 7 209 21 HOH HOH . N 4 HOH B 8 210 23 HOH HOH . N 4 HOH B 9 211 25 HOH HOH . N 4 HOH B 10 212 28 HOH HOH . N 4 HOH B 11 213 29 HOH HOH . N 4 HOH B 12 214 32 HOH HOH . N 4 HOH B 13 215 34 HOH HOH . N 4 HOH B 14 216 39 HOH HOH . N 4 HOH B 15 217 41 HOH HOH . N 4 HOH B 16 218 43 HOH HOH . N 4 HOH B 17 219 50 HOH HOH . N 4 HOH B 18 220 60 HOH HOH . N 4 HOH B 19 221 61 HOH HOH . N 4 HOH B 20 222 63 HOH HOH . N 4 HOH B 21 223 65 HOH HOH . N 4 HOH B 22 224 72 HOH HOH . N 4 HOH B 23 225 76 HOH HOH . N 4 HOH B 24 226 77 HOH HOH . N 4 HOH B 25 227 81 HOH HOH . N 4 HOH B 26 228 82 HOH HOH . N 4 HOH B 27 229 83 HOH HOH . N 4 HOH B 28 230 89 HOH HOH . N 4 HOH B 29 231 94 HOH HOH . N 4 HOH B 30 232 95 HOH HOH . O 4 HOH C 1 306 13 HOH HOH . O 4 HOH C 2 307 22 HOH HOH . O 4 HOH C 3 308 24 HOH HOH . O 4 HOH C 4 309 26 HOH HOH . O 4 HOH C 5 310 27 HOH HOH . O 4 HOH C 6 311 40 HOH HOH . O 4 HOH C 7 312 42 HOH HOH . O 4 HOH C 8 313 44 HOH HOH . O 4 HOH C 9 314 46 HOH HOH . O 4 HOH C 10 315 52 HOH HOH . O 4 HOH C 11 316 56 HOH HOH . O 4 HOH C 12 317 58 HOH HOH . O 4 HOH C 13 318 64 HOH HOH . O 4 HOH C 14 319 66 HOH HOH . O 4 HOH C 15 320 67 HOH HOH . O 4 HOH C 16 321 70 HOH HOH . O 4 HOH C 17 322 80 HOH HOH . O 4 HOH C 18 323 86 HOH HOH . O 4 HOH C 19 324 87 HOH HOH . O 4 HOH C 20 325 90 HOH HOH . O 4 HOH C 21 326 92 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 . . . I 2 -1.123 25.564 24.615 1 61.71 ? N1 FMN 203 C 1 HETATM 2 C C2 FMN . . . I 2 -0.7 25.977 25.845 1 62.7 ? C2 FMN 203 C 1 HETATM 3 O O2 FMN . . . I 2 0.079 26.933 25.931 1 63.75 ? O2 FMN 203 C 1 HETATM 4 N N3 FMN . . . I 2 -1.158 25.335 26.977 1 63.42 ? N3 FMN 203 C 1 HETATM 5 C C4 FMN . . . I 2 -2.024 24.263 26.864 1 62.86 ? C4 FMN 203 C 1 HETATM 6 O O4 FMN . . . I 2 -2.325 23.662 27.9 1 66.12 ? O4 FMN 203 C 1 HETATM 7 C C4A FMN . . . I 2 -2.466 23.846 25.605 1 62.6 ? C4A FMN 203 C 1 HETATM 8 N N5 FMN . . . I 2 -3.341 22.779 25.428 1 62.69 ? N5 FMN 203 C 1 HETATM 9 C C5A FMN . . . I 2 -3.738 22.386 24.145 1 62.15 ? C5A FMN 203 C 1 HETATM 10 C C6 FMN . . . I 2 -4.622 21.309 23.969 1 61.51 ? C6 FMN 203 C 1 HETATM 11 C C7 FMN . . . I 2 -5.021 20.923 22.683 1 62.43 ? C7 FMN 203 C 1 HETATM 12 C C7M FMN . . . I 2 -5.948 19.74 22.522 1 61.68 ? C7M FMN 203 C 1 HETATM 13 C C8 FMN . . . I 2 -4.535 21.621 21.561 1 61.97 ? C8 FMN 203 C 1 HETATM 14 C C8M FMN . . . I 2 -4.82 21.153 20.163 1 59.45 ? C8M FMN 203 C 1 HETATM 15 C C9 FMN . . . I 2 -3.666 22.695 21.74 1 61.46 ? C9 FMN 203 C 1 HETATM 16 C C9A FMN . . . I 2 -3.268 23.077 23.026 1 61.75 ? C9A FMN 203 C 1 HETATM 17 N N10 FMN . . . I 2 -2.387 24.127 23.207 1 63.66 ? N10 FMN 203 C 1 HETATM 18 C C10 FMN . . . I 2 -2.001 24.519 24.479 1 62.93 ? C10 FMN 203 C 1 HETATM 19 C C1' FMN . . . I 2 -1.709 24.772 22.03 1 67.69 ? C1' FMN 203 C 1 HETATM 20 C C2' FMN . . . I 2 -2.418 26.122 21.766 1 70.74 ? C2' FMN 203 C 1 HETATM 21 O O2' FMN . . . I 2 -3.658 25.869 21.15 1 66.88 ? O2' FMN 203 C 1 HETATM 22 C C3' FMN . . . I 2 -1.623 27.069 20.858 1 71.1 ? C3' FMN 203 C 1 HETATM 23 O O3' FMN . . . I 2 -1.26 26.391 19.662 1 74.72 ? O3' FMN 203 C 1 HETATM 24 C C4' FMN . . . I 2 -0.38 27.645 21.515 1 72.15 ? C4' FMN 203 C 1 HETATM 25 O O4' FMN . . . I 2 -0.702 28.332 22.708 1 74.46 ? O4' FMN 203 C 1 HETATM 26 C C5' FMN . . . I 2 0.396 28.564 20.569 1 72.84 ? C5' FMN 203 C 1 HETATM 27 O O5' FMN . . . I 2 -0.474 29.435 19.878 0.5 71.53 ? O5' FMN 203 C 1 HETATM 28 P P FMN . . . I 2 -0.49 29.505 18.277 0.5 70.91 ? P FMN 203 C 1 HETATM 29 O O1P FMN . . . I 2 -1.52 28.536 17.77 0.5 72.46 ? O1P FMN 203 C 1 HETATM 30 O O2P FMN . . . I 2 0.849 29.127 17.685 0.5 71.55 ? O2P FMN 203 C 1 HETATM 31 O O3P FMN . . . I 2 -0.915 30.892 17.862 0.5 71.66 ? O3P FMN 203 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 1728 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 31 #