data_2D38 # _model_server_result.job_id ZymlSBJORQ00ZmciWncOAQ _model_server_result.datetime_utc '2025-03-06 09:07:47' _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 2d38 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 2D38 # _exptl.entry_id 2D38 _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 1 _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 2D38 _cell.length_a 86.617 _cell.length_b 86.617 _cell.length_c 49.122 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D38 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 32.748 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 2D38 _atom_sites.fract_transf_matrix[1][1] 0.011545 _atom_sites.fract_transf_matrix[1][2] 0.006666 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013331 _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] 0.020357 _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 B 2 FMN A 1 200 200 FMN FMN . C 3 NAP A 1 300 300 NAP NAP . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 55 HOH HOH . D 4 HOH A 56 356 56 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 . . . B 2 35.585 12.308 17.761 1 25.79 ? N1 FMN 200 A 1 HETATM 2 C C2 FMN . . . B 2 34.501 11.514 17.508 1 26.54 ? C2 FMN 200 A 1 HETATM 3 O O2 FMN . . . B 2 33.373 12.028 17.476 1 26.13 ? O2 FMN 200 A 1 HETATM 4 N N3 FMN . . . B 2 34.71 10.167 17.294 1 25.33 ? N3 FMN 200 A 1 HETATM 5 C C4 FMN . . . B 2 35.984 9.621 17.322 1 24.82 ? C4 FMN 200 A 1 HETATM 6 O O4 FMN . . . B 2 36.133 8.428 17.052 1 22.5 ? O4 FMN 200 A 1 HETATM 7 C C4A FMN . . . B 2 37.086 10.45 17.576 1 25.84 ? C4A FMN 200 A 1 HETATM 8 N N5 FMN . . . B 2 38.38 9.962 17.632 1 24.13 ? N5 FMN 200 A 1 HETATM 9 C C5A FMN . . . B 2 39.436 10.822 17.872 1 26.28 ? C5A FMN 200 A 1 HETATM 10 C C6 FMN . . . B 2 40.721 10.274 17.91 1 26.59 ? C6 FMN 200 A 1 HETATM 11 C C7 FMN . . . B 2 41.794 11.143 18.148 1 26.58 ? C7 FMN 200 A 1 HETATM 12 C C7M FMN . . . B 2 43.128 10.651 17.673 1 26.79 ? C7M FMN 200 A 1 HETATM 13 C C8 FMN . . . B 2 41.584 12.516 18.37 1 26.38 ? C8 FMN 200 A 1 HETATM 14 C C8M FMN . . . B 2 42.712 13.429 18.781 1 26.88 ? C8M FMN 200 A 1 HETATM 15 C C9 FMN . . . B 2 40.293 13.03 18.338 1 26.39 ? C9 FMN 200 A 1 HETATM 16 C C9A FMN . . . B 2 39.205 12.192 18.09 1 26.36 ? C9A FMN 200 A 1 HETATM 17 N N10 FMN . . . B 2 37.896 12.678 18.055 1 26.1 ? N10 FMN 200 A 1 HETATM 18 C C10 FMN . . . B 2 36.861 11.809 17.792 1 25.48 ? C10 FMN 200 A 1 HETATM 19 C C1' FMN . . . B 2 37.528 14.127 18.257 1 25.81 ? C1' FMN 200 A 1 HETATM 20 C C2' FMN . . . B 2 37.29 14.779 16.897 1 26.64 ? C2' FMN 200 A 1 HETATM 21 O O2' FMN . . . B 2 38.426 14.606 16.061 1 22.44 ? O2' FMN 200 A 1 HETATM 22 C C3' FMN . . . B 2 36.962 16.264 17.059 1 28.36 ? C3' FMN 200 A 1 HETATM 23 O O3' FMN . . . B 2 35.917 16.417 17.99 1 28.74 ? O3' FMN 200 A 1 HETATM 24 C C4' FMN . . . B 2 36.564 16.865 15.715 1 29.92 ? C4' FMN 200 A 1 HETATM 25 O O4' FMN . . . B 2 37.74 16.999 14.96 1 27.7 ? O4' FMN 200 A 1 HETATM 26 C C5' FMN . . . B 2 35.892 18.233 15.837 1 33.03 ? C5' FMN 200 A 1 HETATM 27 O O5' FMN . . . B 2 36.715 19.082 16.61 1 35.78 ? O5' FMN 200 A 1 HETATM 28 P P FMN . . . B 2 36.083 20.255 17.512 1 41.93 ? P FMN 200 A 1 HETATM 29 O O1P FMN . . . B 2 35.432 21.238 16.613 1 41.16 ? O1P FMN 200 A 1 HETATM 30 O O2P FMN . . . B 2 37.218 20.931 18.303 1 40.08 ? O2P FMN 200 A 1 HETATM 31 O O3P FMN . . . B 2 35.045 19.669 18.496 1 40.77 ? O3P FMN 200 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #