data_3GFY # _model_server_result.job_id JwG3T6G9zUCw3sOUBwDtgw _model_server_result.datetime_utc '2025-03-04 17:13:47' _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 3gfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":504}' # _entry.id 3GFY # _exptl.entry_id 3GFY _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 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 90 _cell.entry_id 3GFY _cell.length_a 68.43 _cell.length_b 96.53 _cell.length_c 127.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GFY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 ? 3 D N N ? 3 F 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 159 n n N1 C10 FMN doub 160 n n C2 O2 FMN doub 161 n n C2 N3 FMN sing 162 n n N3 C4 FMN sing 163 n n N3 HN3 FMN sing 164 n n C4 O4 FMN doub 165 n n C4 C4A FMN sing 166 n n C4A N5 FMN doub 167 n n C4A C10 FMN sing 168 n n N5 C5A FMN sing 169 n n C5A C6 FMN doub 170 n y C5A C9A FMN sing 171 n y C6 C7 FMN sing 172 n y C6 H6 FMN sing 173 n n C7 C7M FMN sing 174 n n C7 C8 FMN doub 175 n y C7M HM71 FMN sing 176 n n C7M HM72 FMN sing 177 n n C7M HM73 FMN sing 178 n n C8 C8M FMN sing 179 n n C8 C9 FMN sing 180 n y C8M HM81 FMN sing 181 n n C8M HM82 FMN sing 182 n n C8M HM83 FMN sing 183 n n C9 C9A FMN doub 184 n y C9 H9 FMN sing 185 n n C9A N10 FMN sing 186 n n N10 C10 FMN sing 187 n n N10 C1' FMN sing 188 n n C1' C2' FMN sing 189 n n C1' "H1'1" FMN sing 190 n n C1' "H1'2" FMN sing 191 n n C2' O2' FMN sing 192 n n C2' C3' FMN sing 193 n n C2' H2' FMN sing 194 n n O2' HO2' FMN sing 195 n n C3' O3' FMN sing 196 n n C3' C4' FMN sing 197 n n C3' H3' FMN sing 198 n n O3' HO3' FMN sing 199 n n C4' O4' FMN sing 200 n n C4' C5' FMN sing 201 n n C4' H4' FMN sing 202 n n O4' HO4' FMN sing 203 n n C5' O5' FMN sing 204 n n C5' "H5'1" FMN sing 205 n n C5' "H5'2" FMN sing 206 n n O5' P FMN sing 207 n n P O1P FMN doub 208 n n P O2P FMN sing 209 n n P O3P FMN sing 210 n n O2P HOP2 FMN sing 211 n n O3P HOP3 FMN sing 212 n n # _atom_sites.entry_id 3GFY _atom_sites.fract_transf_matrix[1][1] 0.014613 _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] 0.010359 _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] 0.00787 _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 C2E A 1 501 501 C2E C2E . D 3 FMN A 1 504 504 FMN FMN . E 2 C2E B 1 501 501 C2E C2E . F 3 FMN B 1 504 504 FMN FMN . G 4 HOH A 1 406 7 HOH HOH . G 4 HOH A 2 407 15 HOH HOH . G 4 HOH A 3 408 22 HOH HOH . G 4 HOH A 4 409 23 HOH HOH . G 4 HOH A 5 410 26 HOH HOH . G 4 HOH A 6 411 32 HOH HOH . G 4 HOH A 7 412 34 HOH HOH . G 4 HOH A 8 413 35 HOH HOH . G 4 HOH A 9 414 40 HOH HOH . G 4 HOH A 10 415 47 HOH HOH . G 4 HOH A 11 416 49 HOH HOH . G 4 HOH A 12 417 51 HOH HOH . G 4 HOH A 13 418 56 HOH HOH . G 4 HOH A 14 419 57 HOH HOH . G 4 HOH A 15 420 58 HOH HOH . G 4 HOH A 16 421 65 HOH HOH . G 4 HOH A 17 422 71 HOH HOH . G 4 HOH A 18 423 72 HOH HOH . G 4 HOH A 19 424 73 HOH HOH . G 4 HOH A 20 425 75 HOH HOH . H 4 HOH B 1 406 1 HOH HOH . H 4 HOH B 2 407 6 HOH HOH . H 4 HOH B 3 408 12 HOH HOH . H 4 HOH B 4 409 18 HOH HOH . H 4 HOH B 5 410 24 HOH HOH . H 4 HOH B 6 411 25 HOH HOH . H 4 HOH B 7 412 27 HOH HOH . H 4 HOH B 8 413 28 HOH HOH . H 4 HOH B 9 414 29 HOH HOH . H 4 HOH B 10 415 30 HOH HOH . H 4 HOH B 11 416 31 HOH HOH . H 4 HOH B 12 417 36 HOH HOH . H 4 HOH B 13 418 37 HOH HOH . H 4 HOH B 14 419 38 HOH HOH . H 4 HOH B 15 420 42 HOH HOH . H 4 HOH B 16 421 43 HOH HOH . H 4 HOH B 17 422 44 HOH HOH . H 4 HOH B 18 423 45 HOH HOH . H 4 HOH B 19 424 46 HOH HOH . H 4 HOH B 20 425 50 HOH HOH . H 4 HOH B 21 426 53 HOH HOH . H 4 HOH B 22 427 55 HOH HOH . H 4 HOH B 23 428 61 HOH HOH . H 4 HOH B 24 429 62 HOH HOH . H 4 HOH B 25 430 63 HOH HOH . H 4 HOH B 26 431 64 HOH HOH . H 4 HOH B 27 432 66 HOH HOH . H 4 HOH B 28 433 67 HOH HOH . H 4 HOH B 29 434 70 HOH HOH . H 4 HOH B 30 435 74 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 . . . D 3 -37.746 20.954 -33.337 1 18.38 ? N1 FMN 504 A 1 HETATM 2 C C2 FMN . . . D 3 -37.73 22.29 -32.999 1 18.36 ? C2 FMN 504 A 1 HETATM 3 O O2 FMN . . . D 3 -38.79 22.9 -32.927 1 18.61 ? O2 FMN 504 A 1 HETATM 4 N N3 FMN . . . D 3 -36.538 22.931 -32.729 1 18.26 ? N3 FMN 504 A 1 HETATM 5 C C4 FMN . . . D 3 -35.354 22.228 -32.802 1 18.02 ? C4 FMN 504 A 1 HETATM 6 O O4 FMN . . . D 3 -34.312 22.771 -32.445 1 16.83 ? O4 FMN 504 A 1 HETATM 7 C C4A FMN . . . D 3 -35.368 20.879 -33.152 1 18.16 ? C4A FMN 504 A 1 HETATM 8 N N5 FMN . . . D 3 -34.189 20.172 -33.237 1 18.42 ? N5 FMN 504 A 1 HETATM 9 C C5A FMN . . . D 3 -34.191 18.835 -33.579 1 18.32 ? C5A FMN 504 A 1 HETATM 10 C C6 FMN . . . D 3 -32.983 18.15 -33.653 1 18.27 ? C6 FMN 504 A 1 HETATM 11 C C7 FMN . . . D 3 -32.956 16.802 -33.996 1 18.35 ? C7 FMN 504 A 1 HETATM 12 C C7M FMN . . . D 3 -31.636 16.166 -34.323 1 17.74 ? C7M FMN 504 A 1 HETATM 13 C C8 FMN . . . D 3 -34.155 16.137 -34.264 1 18.49 ? C8 FMN 504 A 1 HETATM 14 C C8M FMN . . . D 3 -34.135 14.741 -34.827 1 18.6 ? C8M FMN 504 A 1 HETATM 15 C C9 FMN . . . D 3 -35.368 16.828 -34.184 1 18.43 ? C9 FMN 504 A 1 HETATM 16 C C9A FMN . . . D 3 -35.396 18.182 -33.843 1 18.58 ? C9A FMN 504 A 1 HETATM 17 N N10 FMN . . . D 3 -36.594 18.89 -33.761 1 18.99 ? N10 FMN 504 A 1 HETATM 18 C C10 FMN . . . D 3 -36.573 20.235 -33.419 1 18.28 ? C10 FMN 504 A 1 HETATM 19 C C1' FMN . . . D 3 -37.898 18.228 -34.128 1 20.76 ? C1' FMN 504 A 1 HETATM 20 C C2' FMN . . . D 3 -38.721 17.885 -32.882 1 22.91 ? C2' FMN 504 A 1 HETATM 21 O O2' FMN . . . D 3 -38.269 16.675 -32.317 1 22.35 ? O2' FMN 504 A 1 HETATM 22 C C3' FMN . . . D 3 -40.215 17.76 -33.18 1 24.52 ? C3' FMN 504 A 1 HETATM 23 O O3' FMN . . . D 3 -40.41 16.786 -34.182 1 25.26 ? O3' FMN 504 A 1 HETATM 24 C C4' FMN . . . D 3 -40.858 19.078 -33.611 1 26.26 ? C4' FMN 504 A 1 HETATM 25 O O4' FMN . . . D 3 -40.406 20.14 -32.796 1 26.14 ? O4' FMN 504 A 1 HETATM 26 C C5' FMN . . . D 3 -42.38 18.983 -33.533 1 27.75 ? C5' FMN 504 A 1 HETATM 27 O O5' FMN . . . D 3 -42.943 20.265 -33.706 1 29.93 ? O5' FMN 504 A 1 HETATM 28 P P FMN . . . D 3 -43.884 20.594 -34.97 1 31.6 ? P FMN 504 A 1 HETATM 29 O O1P FMN . . . D 3 -45.047 19.625 -34.954 1 31.57 ? O1P FMN 504 A 1 HETATM 30 O O2P FMN . . . D 3 -44.382 22.017 -34.873 1 31.25 ? O2P FMN 504 A 1 HETATM 31 O O3P FMN . . . D 3 -43.099 20.417 -36.249 1 31.99 ? O3P FMN 504 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #