data_5DKL # _model_server_result.job_id 22Oz9fMj2tqcMe8HtKroTg _model_server_result.datetime_utc '2024-11-24 22:47:08' _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 5dkl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 5DKL # _exptl.entry_id 5DKL _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 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 120 _cell.entry_id 5DKL _cell.length_a 108.56 _cell.length_b 108.56 _cell.length_c 104.66 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DKL _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 ? 2 C N N ? 2 D N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 54 A CYS 287 1_555 C C4A FMN . A FMN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale2 B SG CYS 54 B CYS 287 1_555 D C4A FMN . B FMN 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? # _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 5DKL _atom_sites.fract_transf_matrix[1][1] 0.009211 _atom_sites.fract_transf_matrix[1][2] 0.005318 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010637 _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] 0.009555 _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 FMN A 1 500 500 FMN FMN . D 2 FMN B 1 500 500 FMN FMN . E 3 HOH A 1 601 2 HOH HOH . F 3 HOH B 1 601 1 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 2 46.153 -54.471 -11.841 1 75.64 ? N1 FMN 500 B 1 HETATM 2 C C2 FMN . . . D 2 45.821 -54.378 -13.151 1 71.77 ? C2 FMN 500 B 1 HETATM 3 O O2 FMN . . . D 2 45.756 -55.367 -13.872 1 67.18 ? O2 FMN 500 B 1 HETATM 4 N N3 FMN . . . D 2 45.405 -53.127 -13.676 1 71.28 ? N3 FMN 500 B 1 HETATM 5 C C4 FMN . . . D 2 45.221 -51.991 -12.942 1 73.96 ? C4 FMN 500 B 1 HETATM 6 O O4 FMN . . . D 2 45.039 -50.901 -13.467 1 74.58 ? O4 FMN 500 B 1 HETATM 7 C C4A FMN . . . D 2 45.283 -52.16 -11.39 1 75.76 ? C4A FMN 500 B 1 HETATM 8 N N5 FMN . . . D 2 46.181 -51.102 -11.002 1 73.85 ? N5 FMN 500 B 1 HETATM 9 C C5A FMN . . . D 2 46.493 -51.117 -9.622 1 76.34 ? C5A FMN 500 B 1 HETATM 10 C C6 FMN . . . D 2 46.533 -49.965 -8.866 1 69.9 ? C6 FMN 500 B 1 HETATM 11 C C7 FMN . . . D 2 46.89 -49.992 -7.522 1 68.18 ? C7 FMN 500 B 1 HETATM 12 C C7M FMN . . . D 2 46.945 -48.681 -6.772 1 66.2 ? C7M FMN 500 B 1 HETATM 13 C C8 FMN . . . D 2 47.086 -51.238 -6.9 1 71.01 ? C8 FMN 500 B 1 HETATM 14 C C8M FMN . . . D 2 47.302 -51.346 -5.4 1 70.58 ? C8M FMN 500 B 1 HETATM 15 C C9 FMN . . . D 2 47 -52.408 -7.655 1 68.83 ? C9 FMN 500 B 1 HETATM 16 C C9A FMN . . . D 2 46.812 -52.363 -9.022 1 74.28 ? C9A FMN 500 B 1 HETATM 17 N N10 FMN . . . D 2 46.555 -53.527 -9.787 1 74.68 ? N10 FMN 500 B 1 HETATM 18 C C10 FMN . . . D 2 46.082 -53.423 -11.048 1 72.91 ? C10 FMN 500 B 1 HETATM 19 C C1' FMN . . . D 2 47.06 -54.863 -9.321 1 73.52 ? C1' FMN 500 B 1 HETATM 20 C C2' FMN . . . D 2 45.886 -55.681 -8.801 1 75.4 ? C2' FMN 500 B 1 HETATM 21 O O2' FMN . . . D 2 44.953 -54.841 -8.149 1 75.74 ? O2' FMN 500 B 1 HETATM 22 C C3' FMN . . . D 2 46.356 -56.733 -7.813 1 78.48 ? C3' FMN 500 B 1 HETATM 23 O O3' FMN . . . D 2 46.731 -56.131 -6.589 1 80.8 ? O3' FMN 500 B 1 HETATM 24 C C4' FMN . . . D 2 47.543 -57.514 -8.335 1 74.71 ? C4' FMN 500 B 1 HETATM 25 O O4' FMN . . . D 2 47.073 -58.457 -9.265 1 72.27 ? O4' FMN 500 B 1 HETATM 26 C C5' FMN . . . D 2 48.189 -58.169 -7.116 1 78.88 ? C5' FMN 500 B 1 HETATM 27 O O5' FMN . . . D 2 48.26 -59.574 -7.213 1 83.34 ? O5' FMN 500 B 1 HETATM 28 P P FMN . . . D 2 47.002 -60.562 -7.011 1 83.37 ? P FMN 500 B 1 HETATM 29 O O1P FMN . . . D 2 47.516 -61.972 -7.226 1 87.47 ? O1P FMN 500 B 1 HETATM 30 O O2P FMN . . . D 2 45.951 -60.245 -8.056 1 78.14 ? O2P FMN 500 B 1 HETATM 31 O O3P FMN . . . D 2 46.415 -60.415 -5.625 1 76.41 ? O3P FMN 500 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #