data_9DLY # _model_server_result.job_id hFMXUkr6GbRzIzdGcnNhiQ _model_server_result.datetime_utc '2025-01-08 10:09:48' _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 9dly # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1002}' # _entry.id 9DLY # _exptl.entry_id 9DLY _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 9DLY _cell.length_a 85.977 _cell.length_b 85.977 _cell.length_c 139.849 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DLY _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 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 9DLY _atom_sites.fract_transf_matrix[1][1] 0.011631 _atom_sites.fract_transf_matrix[1][2] 0.006715 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01343 _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] 0.007151 _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 A1A6E A 1 1001 1001 A1A6E 211 . 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 -3.037 -21.453 15.591 1 23.24 ? N1 FMN 1002 A 1 HETATM 2 C C2 FMN . . . C 3 -2.532 -20.466 14.775 1 23.72 ? C2 FMN 1002 A 1 HETATM 3 O O2 FMN . . . C 3 -2.812 -20.467 13.578 1 27.46 ? O2 FMN 1002 A 1 HETATM 4 N N3 FMN . . . C 3 -1.714 -19.484 15.296 1 20 ? N3 FMN 1002 A 1 HETATM 5 C C4 FMN . . . C 3 -1.4 -19.486 16.638 1 23.11 ? C4 FMN 1002 A 1 HETATM 6 O O4 FMN . . . C 3 -0.671 -18.612 17.105 1 27.93 ? O4 FMN 1002 A 1 HETATM 7 C C4A FMN . . . C 3 -1.912 -20.48 17.459 1 27.69 ? C4A FMN 1002 A 1 HETATM 8 N N5 FMN . . . C 3 -1.608 -20.478 18.799 1 27.63 ? N5 FMN 1002 A 1 HETATM 9 C C5A FMN . . . C 3 -2.105 -21.465 19.618 1 21.43 ? C5A FMN 1002 A 1 HETATM 10 C C6 FMN . . . C 3 -1.777 -21.45 20.965 1 21.33 ? C6 FMN 1002 A 1 HETATM 11 C C7 FMN . . . C 3 -2.268 -22.429 21.814 1 27.47 ? C7 FMN 1002 A 1 HETATM 12 C C7M FMN . . . C 3 -1.892 -22.372 23.266 1 27.13 ? C7M FMN 1002 A 1 HETATM 13 C C8 FMN . . . C 3 -3.099 -23.427 21.303 1 33.02 ? C8 FMN 1002 A 1 HETATM 14 C C8M FMN . . . C 3 -3.653 -24.508 22.182 1 35.68 ? C8M FMN 1002 A 1 HETATM 15 C C9 FMN . . . C 3 -3.422 -23.441 19.951 1 22.05 ? C9 FMN 1002 A 1 HETATM 16 C C9A FMN . . . C 3 -2.929 -22.458 19.102 1 20.77 ? C9A FMN 1002 A 1 HETATM 17 N N10 FMN . . . C 3 -3.245 -22.456 17.755 1 20.88 ? N10 FMN 1002 A 1 HETATM 18 C C10 FMN . . . C 3 -2.734 -21.468 16.935 1 24.32 ? C10 FMN 1002 A 1 HETATM 19 C C1' FMN . . . C 3 -4.132 -23.517 17.169 1 30.41 ? C1' FMN 1002 A 1 HETATM 20 C C2' FMN . . . C 3 -3.284 -24.737 16.837 1 37.25 ? C2' FMN 1002 A 1 HETATM 21 O O2' FMN . . . C 3 -2.303 -24.344 15.901 1 44.61 ? O2' FMN 1002 A 1 HETATM 22 C C3' FMN . . . C 3 -4.112 -25.878 16.26 1 24.54 ? C3' FMN 1002 A 1 HETATM 23 O O3' FMN . . . C 3 -4.791 -25.411 15.118 1 32.69 ? O3' FMN 1002 A 1 HETATM 24 C C4' FMN . . . C 3 -5.118 -26.412 17.27 1 27 ? C4' FMN 1002 A 1 HETATM 25 O O4' FMN . . . C 3 -4.517 -26.479 18.546 1 25.63 ? O4' FMN 1002 A 1 HETATM 26 C C5' FMN . . . C 3 -5.626 -27.804 16.909 1 35.55 ? C5' FMN 1002 A 1 HETATM 27 O O5' FMN . . . C 3 -4.583 -28.742 17.069 1 31.72 ? O5' FMN 1002 A 1 HETATM 28 P P FMN . . . C 3 -4.757 -30.016 18.04 1 29.8 ? P FMN 1002 A 1 HETATM 29 O O1P FMN . . . C 3 -4.336 -29.603 19.429 1 27.35 ? O1P FMN 1002 A 1 HETATM 30 O O2P FMN . . . C 3 -3.895 -31.165 17.567 1 39.21 ? O2P FMN 1002 A 1 HETATM 31 O O3P FMN . . . C 3 -6.205 -30.436 18.076 1 48.31 ? O3P FMN 1002 A 1 HETATM 32 H HN3 FMN . . . C 3 -1.333 -18.742 14.675 1 23.96 ? HN3 FMN 1002 A 1 HETATM 33 H H6 FMN . . . C 3 -1.129 -20.666 21.358 1 25.56 ? H6 FMN 1002 A 1 HETATM 34 H HM71 FMN . . . C 3 -2.575 -22.995 23.843 1 32.52 ? HM71 FMN 1002 A 1 HETATM 35 H HM72 FMN . . . C 3 -1.954 -21.342 23.617 1 32.52 ? HM72 FMN 1002 A 1 HETATM 36 H HM73 FMN . . . C 3 -0.873 -22.738 23.392 1 32.52 ? HM73 FMN 1002 A 1 HETATM 37 H HM81 FMN . . . C 3 -4.172 -25.245 21.569 1 42.78 ? HM81 FMN 1002 A 1 HETATM 38 H HM82 FMN . . . C 3 -4.353 -24.072 22.896 1 42.78 ? HM82 FMN 1002 A 1 HETATM 39 H HM83 FMN . . . C 3 -2.838 -24.991 22.721 1 42.78 ? HM83 FMN 1002 A 1 HETATM 40 H H9 FMN . . . C 3 -4.065 -24.227 19.555 1 26.42 ? H9 FMN 1002 A 1 HETATM 41 H "H1'1" FMN . . . C 3 -4.617 -23.142 16.268 1 36.45 ? "H1'1" FMN 1002 A 1 HETATM 42 H "H1'2" FMN . . . C 3 -4.912 -23.787 17.882 1 36.45 ? "H1'2" FMN 1002 A 1 HETATM 43 H H2' FMN . . . C 3 -2.826 -25.105 17.755 1 44.67 ? H2' FMN 1002 A 1 HETATM 44 H HO2' FMN . . . C 3 -2.436 -24.834 15.063 1 53.5 ? HO2' FMN 1002 A 1 HETATM 45 H H3' FMN . . . C 3 -3.442 -26.696 15.997 1 29.41 ? H3' FMN 1002 A 1 HETATM 46 H HO3' FMN . . . C 3 -5.754 -25.554 15.229 1 39.2 ? HO3' FMN 1002 A 1 HETATM 47 H H4' FMN . . . C 3 -5.964 -25.726 17.271 1 32.36 ? H4' FMN 1002 A 1 HETATM 48 H HO4' FMN . . . C 3 -4.601 -27.389 18.899 1 30.72 ? HO4' FMN 1002 A 1 HETATM 49 H "H5'1" FMN . . . C 3 -5.978 -27.814 15.878 1 42.62 ? "H5'1" FMN 1002 A 1 HETATM 50 H "H5'2" FMN . . . C 3 -6.465 -28.07 17.552 1 42.62 ? "H5'2" FMN 1002 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 50 #