data_9DKY # _model_server_result.job_id '_HV2w5FEck1Rbvm2lcruPw' _model_server_result.datetime_utc '2025-01-08 10:06:29' _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 9dky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1002}' # _entry.id 9DKY # _exptl.entry_id 9DKY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 456.344 _entity.id 3 _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 9DKY _cell.length_a 85.303 _cell.length_b 85.303 _cell.length_c 140.703 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DKY _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall 'P 64' _symmetry.space_group_name_H-M 'P 64' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 143 n n N1 C10 FMN doub 144 n n C2 O2 FMN doub 145 n n C2 N3 FMN sing 146 n n N3 C4 FMN sing 147 n n N3 HN3 FMN sing 148 n n C4 O4 FMN doub 149 n n C4 C4A FMN sing 150 n n C4A N5 FMN doub 151 n n C4A C10 FMN sing 152 n n N5 C5A FMN sing 153 n n C5A C6 FMN doub 154 n y C5A C9A FMN sing 155 n y C6 C7 FMN sing 156 n y C6 H6 FMN sing 157 n n C7 C7M FMN sing 158 n n C7 C8 FMN doub 159 n y C7M HM71 FMN sing 160 n n C7M HM72 FMN sing 161 n n C7M HM73 FMN sing 162 n n C8 C8M FMN sing 163 n n C8 C9 FMN sing 164 n y C8M HM81 FMN sing 165 n n C8M HM82 FMN sing 166 n n C8M HM83 FMN sing 167 n n C9 C9A FMN doub 168 n y C9 H9 FMN sing 169 n n C9A N10 FMN sing 170 n n N10 C10 FMN sing 171 n n N10 C1' FMN sing 172 n n C1' C2' FMN sing 173 n n C1' "H1'1" FMN sing 174 n n C1' "H1'2" FMN sing 175 n n C2' O2' FMN sing 176 n n C2' C3' FMN sing 177 n n C2' H2' FMN sing 178 n n O2' HO2' FMN sing 179 n n C3' O3' FMN sing 180 n n C3' C4' FMN sing 181 n n C3' H3' FMN sing 182 n n O3' HO3' FMN sing 183 n n C4' O4' FMN sing 184 n n C4' C5' FMN sing 185 n n C4' H4' FMN sing 186 n n O4' HO4' FMN sing 187 n n C5' O5' FMN sing 188 n n C5' "H5'1" FMN sing 189 n n C5' "H5'2" FMN sing 190 n n O5' P FMN sing 191 n n P O1P FMN doub 192 n n P O2P FMN sing 193 n n P O3P FMN sing 194 n n O2P HOP2 FMN sing 195 n n O3P HOP3 FMN sing 196 n n # _atom_sites.entry_id 9DKY _atom_sites.fract_transf_matrix[1][1] 0.011723 _atom_sites.fract_transf_matrix[1][2] 0.006768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013536 _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] 0.007107 _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 A1A59 A 1 1001 1001 A1A59 174 . C 3 FMN A 1 1002 1002 FMN FMN . D 4 OG6 A 1 1003 1003 OG6 ORO . # 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 3 16.754 -13.355 4.269 1 31.36 ? N1 FMN 1002 A 1 HETATM 2 C C2 FMN . . . C 3 16.169 -12.38 3.486 1 29.7 ? C2 FMN 1002 A 1 HETATM 3 O O2 FMN . . . C 3 16.032 -12.566 2.281 1 33.75 ? O2 FMN 1002 A 1 HETATM 4 N N3 FMN . . . C 3 15.743 -11.199 4.053 1 34.36 ? N3 FMN 1002 A 1 HETATM 5 C C4 FMN . . . C 3 15.898 -10.992 5.405 1 30.27 ? C4 FMN 1002 A 1 HETATM 6 O O4 FMN . . . C 3 15.521 -9.943 5.919 1 30.11 ? O4 FMN 1002 A 1 HETATM 7 C C4A FMN . . . C 3 16.483 -11.972 6.193 1 27.44 ? C4A FMN 1002 A 1 HETATM 8 N N5 FMN . . . C 3 16.628 -11.753 7.541 1 26.09 ? N5 FMN 1002 A 1 HETATM 9 C C5A FMN . . . C 3 17.211 -12.714 8.331 1 26.84 ? C5A FMN 1002 A 1 HETATM 10 C C6 FMN . . . C 3 17.349 -12.466 9.689 1 36.67 ? C6 FMN 1002 A 1 HETATM 11 C C7 FMN . . . C 3 17.926 -13.41 10.521 1 42.94 ? C7 FMN 1002 A 1 HETATM 12 C C7M FMN . . . C 3 18.054 -13.093 11.982 1 32.43 ? C7M FMN 1002 A 1 HETATM 13 C C8 FMN . . . C 3 18.371 -14.618 9.976 1 51.63 ? C8 FMN 1002 A 1 HETATM 14 C C8M FMN . . . C 3 19.005 -15.682 10.825 1 60.31 ? C8M FMN 1002 A 1 HETATM 15 C C9 FMN . . . C 3 18.23 -14.86 8.611 1 40.3 ? C9 FMN 1002 A 1 HETATM 16 C C9A FMN . . . C 3 17.648 -13.911 7.777 1 30.71 ? C9A FMN 1002 A 1 HETATM 17 N N10 FMN . . . C 3 17.501 -14.134 6.415 1 31.43 ? N10 FMN 1002 A 1 HETATM 18 C C10 FMN . . . C 3 16.915 -13.162 5.626 1 30.55 ? C10 FMN 1002 A 1 HETATM 19 C C1' FMN . . . C 3 17.954 -15.421 5.786 1 34.84 ? C1' FMN 1002 A 1 HETATM 20 C C2' FMN . . . C 3 19.434 -15.362 5.437 1 47.67 ? C2' FMN 1002 A 1 HETATM 21 O O2' FMN . . . C 3 19.621 -14.295 4.528 1 50.11 ? O2' FMN 1002 A 1 HETATM 22 C C3' FMN . . . C 3 19.939 -16.655 4.816 1 57.51 ? C3' FMN 1002 A 1 HETATM 23 O O3' FMN . . . C 3 19.245 -16.887 3.61 1 38.17 ? O3' FMN 1002 A 1 HETATM 24 C C4' FMN . . . C 3 19.755 -17.847 5.746 1 52.17 ? C4' FMN 1002 A 1 HETATM 25 O O4' FMN . . . C 3 19.816 -17.414 7.09 1 51.34 ? O4' FMN 1002 A 1 HETATM 26 C C5' FMN . . . C 3 20.82 -18.92 5.532 1 44.24 ? C5' FMN 1002 A 1 HETATM 27 O O5' FMN . . . C 3 22.092 -18.387 5.833 1 56.68 ? O5' FMN 1002 A 1 HETATM 28 P P FMN . . . C 3 23.135 -19.193 6.759 1 50.96 ? P FMN 1002 A 1 HETATM 29 O O1P FMN . . . C 3 22.987 -18.683 8.173 1 45.92 ? O1P FMN 1002 A 1 HETATM 30 O O2P FMN . . . C 3 24.549 -18.958 6.282 1 46.22 ? O2P FMN 1002 A 1 HETATM 31 O O3P FMN . . . C 3 22.822 -20.669 6.721 1 46.79 ? O3P FMN 1002 A 1 HETATM 32 H HN3 FMN . . . C 3 15.304 -10.466 3.461 1 41.23 ? HN3 FMN 1002 A 1 HETATM 33 H H6 FMN . . . C 3 17.001 -11.52 10.104 1 44.01 ? H6 FMN 1002 A 1 HETATM 34 H HM71 FMN . . . C 3 18.635 -13.873 12.473 1 38.92 ? HM71 FMN 1002 A 1 HETATM 35 H HM72 FMN . . . C 3 17.062 -13.041 12.43 1 38.92 ? HM72 FMN 1002 A 1 HETATM 36 H HM73 FMN . . . C 3 18.558 -12.134 12.102 1 38.92 ? HM73 FMN 1002 A 1 HETATM 37 H HM81 FMN . . . C 3 19.377 -16.483 10.186 1 72.37 ? HM81 FMN 1002 A 1 HETATM 38 H HM82 FMN . . . C 3 18.265 -16.084 11.517 1 72.37 ? HM82 FMN 1002 A 1 HETATM 39 H HM83 FMN . . . C 3 19.833 -15.252 11.388 1 72.37 ? HM83 FMN 1002 A 1 HETATM 40 H H9 FMN . . . C 3 18.58 -15.803 8.192 1 48.36 ? H9 FMN 1002 A 1 HETATM 41 H "H1'1" FMN . . . C 3 17.776 -16.246 6.477 1 41.81 ? "H1'1" FMN 1002 A 1 HETATM 42 H "H1'2" FMN . . . C 3 17.374 -15.609 4.883 1 41.81 ? "H1'2" FMN 1002 A 1 HETATM 43 H H2' FMN . . . C 3 20.004 -15.206 6.353 1 57.2 ? H2' FMN 1002 A 1 HETATM 44 H HO2' FMN . . . C 3 19.943 -14.648 3.673 1 60.14 ? HO2' FMN 1002 A 1 HETATM 45 H H3' FMN . . . C 3 21.007 -16.547 4.626 1 69.01 ? H3' FMN 1002 A 1 HETATM 46 H H4' FMN . . . C 3 18.78 -18.282 5.524 1 62.6 ? H4' FMN 1002 A 1 HETATM 47 H HO4' FMN . . . C 3 20.601 -17.808 7.525 1 61.61 ? HO4' FMN 1002 A 1 HETATM 48 H "H5'1" FMN . . . C 3 20.797 -19.264 4.498 1 53.09 ? "H5'1" FMN 1002 A 1 HETATM 49 H "H5'2" FMN . . . C 3 20.616 -19.777 6.174 1 53.09 ? "H5'2" FMN 1002 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 49 #