data_3ZOD # _model_server_result.job_id xzZrsWRxQI9sGecXn3OAQQ _model_server_result.datetime_utc '2025-01-10 09:24:51' _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 3zod # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":173}' # _entry.id 3ZOD # _exptl.entry_id 3ZOD _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 3ZOD _cell.length_a 46.395 _cell.length_b 46.395 _cell.length_c 269.637 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZOD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -23.1975 -40.179249 -44.9395 # _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 3ZOD _atom_sites.fract_transf_matrix[1][1] 0.021554 _atom_sites.fract_transf_matrix[1][2] 0.012444 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024888 _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] 0.003709 _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 1 173 173 FMN FMN . C 3 HQE A 1 1173 1173 HQE HQE . D 4 HOH A 1 2001 2001 HOH HOH . D 4 HOH A 2 2002 2002 HOH HOH . D 4 HOH A 3 2003 2003 HOH HOH . D 4 HOH A 4 2004 2004 HOH HOH . D 4 HOH A 5 2005 2005 HOH HOH . D 4 HOH A 6 2006 2006 HOH HOH . D 4 HOH A 7 2007 2007 HOH HOH . D 4 HOH A 8 2008 2008 HOH HOH . D 4 HOH A 9 2009 2009 HOH HOH . D 4 HOH A 10 2010 2010 HOH HOH . D 4 HOH A 11 2011 2011 HOH HOH . D 4 HOH A 12 2012 2012 HOH HOH . D 4 HOH A 13 2013 2013 HOH HOH . D 4 HOH A 14 2014 2014 HOH HOH . D 4 HOH A 15 2015 2015 HOH HOH . D 4 HOH A 16 2016 2016 HOH HOH . D 4 HOH A 17 2017 2017 HOH HOH . D 4 HOH A 18 2018 2018 HOH HOH . D 4 HOH A 19 2019 2019 HOH HOH . D 4 HOH A 20 2020 2020 HOH HOH . D 4 HOH A 21 2021 2021 HOH HOH . D 4 HOH A 22 2022 2022 HOH HOH . D 4 HOH A 23 2023 2023 HOH HOH . D 4 HOH A 24 2024 2024 HOH HOH . D 4 HOH A 25 2025 2025 HOH HOH . D 4 HOH A 26 2026 2026 HOH HOH . D 4 HOH A 27 2027 2027 HOH HOH . D 4 HOH A 28 2028 2028 HOH HOH . D 4 HOH A 29 2029 2029 HOH HOH . D 4 HOH A 30 2030 2030 HOH HOH . D 4 HOH A 31 2031 2031 HOH HOH . D 4 HOH A 32 2032 2032 HOH HOH . D 4 HOH A 33 2033 2033 HOH HOH . D 4 HOH A 34 2034 2034 HOH HOH . D 4 HOH A 35 2035 2035 HOH HOH . D 4 HOH A 36 2036 2036 HOH HOH . D 4 HOH A 37 2037 2037 HOH HOH . D 4 HOH A 38 2038 2038 HOH HOH . D 4 HOH A 39 2039 2039 HOH HOH . D 4 HOH A 40 2040 2040 HOH HOH . D 4 HOH A 41 2041 2041 HOH HOH . D 4 HOH A 42 2042 2042 HOH HOH . D 4 HOH A 43 2043 2043 HOH HOH . D 4 HOH A 44 2044 2044 HOH HOH . D 4 HOH A 45 2045 2045 HOH HOH . D 4 HOH A 46 2046 2046 HOH HOH . D 4 HOH A 47 2047 2047 HOH HOH . D 4 HOH A 48 2048 2048 HOH HOH . D 4 HOH A 49 2049 2049 HOH HOH . D 4 HOH A 50 2050 2050 HOH HOH . D 4 HOH A 51 2051 2051 HOH HOH . D 4 HOH A 52 2052 2052 HOH HOH . D 4 HOH A 53 2053 2053 HOH HOH . D 4 HOH A 54 2054 2054 HOH HOH . D 4 HOH A 55 2055 2055 HOH HOH . D 4 HOH A 56 2056 2056 HOH HOH . D 4 HOH A 57 2057 2057 HOH HOH . D 4 HOH A 58 2058 2058 HOH HOH . D 4 HOH A 59 2059 2059 HOH HOH . D 4 HOH A 60 2060 2060 HOH HOH . D 4 HOH A 61 2061 2061 HOH HOH . D 4 HOH A 62 2062 2062 HOH HOH . D 4 HOH A 63 2063 2063 HOH HOH . D 4 HOH A 64 2064 2064 HOH HOH . D 4 HOH A 65 2065 2065 HOH HOH . D 4 HOH A 66 2066 2066 HOH HOH . D 4 HOH A 67 2067 2067 HOH HOH . D 4 HOH A 68 2068 2068 HOH HOH . D 4 HOH A 69 2069 2069 HOH HOH . D 4 HOH A 70 2070 2070 HOH HOH . D 4 HOH A 71 2071 2071 HOH HOH . D 4 HOH A 72 2072 2072 HOH HOH . D 4 HOH A 73 2073 2073 HOH HOH . D 4 HOH A 74 2074 2074 HOH HOH . D 4 HOH A 75 2075 2075 HOH HOH . D 4 HOH A 76 2076 2076 HOH HOH . D 4 HOH A 77 2077 2077 HOH HOH . D 4 HOH A 78 2078 2078 HOH HOH . D 4 HOH A 79 2079 2079 HOH HOH . D 4 HOH A 80 2080 2080 HOH HOH . D 4 HOH A 81 2081 2081 HOH HOH . D 4 HOH A 82 2082 2082 HOH HOH . D 4 HOH A 83 2083 2083 HOH HOH . D 4 HOH A 84 2084 2084 HOH HOH . D 4 HOH A 85 2085 2085 HOH HOH . D 4 HOH A 86 2086 2086 HOH HOH . D 4 HOH A 87 2087 2087 HOH HOH . D 4 HOH A 88 2088 2088 HOH HOH . D 4 HOH A 89 2089 2089 HOH HOH . D 4 HOH A 90 2090 2090 HOH HOH . D 4 HOH A 91 2091 2091 HOH HOH . D 4 HOH A 92 2092 2092 HOH HOH . D 4 HOH A 93 2093 2093 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 -19.899 -21.508 -10.453 1 12.16 ? N1 FMN 173 A 1 HETATM 2 C C2 FMN . . . B 2 -20.543 -20.694 -11.302 1 13.14 ? C2 FMN 173 A 1 HETATM 3 O O2 FMN . . . B 2 -21.657 -20.219 -10.972 1 13.48 ? O2 FMN 173 A 1 HETATM 4 N N3 FMN . . . B 2 -19.98 -20.309 -12.463 1 13.02 ? N3 FMN 173 A 1 HETATM 5 C C4 FMN . . . B 2 -18.802 -20.762 -12.877 1 12.68 ? C4 FMN 173 A 1 HETATM 6 O O4 FMN . . . B 2 -18.338 -20.39 -13.988 1 12.82 ? O4 FMN 173 A 1 HETATM 7 C C4A FMN . . . B 2 -18.062 -21.672 -12.002 1 12.01 ? C4A FMN 173 A 1 HETATM 8 N N5 FMN . . . B 2 -16.859 -22.149 -12.365 1 12.55 ? N5 FMN 173 A 1 HETATM 9 C C5A FMN . . . B 2 -16.17 -22.942 -11.524 1 12.14 ? C5A FMN 173 A 1 HETATM 10 C C6 FMN . . . B 2 -14.922 -23.429 -11.901 1 12.73 ? C6 FMN 173 A 1 HETATM 11 C C7 FMN . . . B 2 -14.206 -24.287 -11.059 1 12.02 ? C7 FMN 173 A 1 HETATM 12 C C7M FMN . . . B 2 -12.829 -24.757 -11.47 1 11.94 ? C7M FMN 173 A 1 HETATM 13 C C8 FMN . . . B 2 -14.802 -24.694 -9.779 1 12.24 ? C8 FMN 173 A 1 HETATM 14 C C8M FMN . . . B 2 -14.002 -25.601 -8.895 1 12.39 ? C8M FMN 173 A 1 HETATM 15 C C9 FMN . . . B 2 -16.051 -24.22 -9.382 1 12.26 ? C9 FMN 173 A 1 HETATM 16 C C9A FMN . . . B 2 -16.755 -23.354 -10.214 1 12.43 ? C9A FMN 173 A 1 HETATM 17 N N10 FMN . . . B 2 -18.053 -22.89 -9.878 1 12.66 ? N10 FMN 173 A 1 HETATM 18 C C10 FMN . . . B 2 -18.683 -22.022 -10.728 1 12.58 ? C10 FMN 173 A 1 HETATM 19 C C1' FMN . . . B 2 -18.676 -23.227 -8.594 1 13.47 ? C1' FMN 173 A 1 HETATM 20 C C2' FMN . . . B 2 -18.372 -22.186 -7.565 1 13.38 ? C2' FMN 173 A 1 HETATM 21 O O2' FMN . . . B 2 -17.002 -21.723 -7.613 1 12.23 ? O2' FMN 173 A 1 HETATM 22 C C3' FMN . . . B 2 -18.628 -22.854 -6.21 1 14.25 ? C3' FMN 173 A 1 HETATM 23 O O3' FMN . . . B 2 -20.035 -23.138 -6.145 1 14.96 ? O3' FMN 173 A 1 HETATM 24 C C4' FMN . . . B 2 -18.2 -21.984 -5.036 1 15.52 ? C4' FMN 173 A 1 HETATM 25 O O4' FMN . . . B 2 -18.212 -22.817 -3.857 1 17.03 ? O4' FMN 173 A 1 HETATM 26 C C5' FMN . . . B 2 -19.177 -20.823 -4.809 1 15.68 ? C5' FMN 173 A 1 HETATM 27 O O5' FMN . . . B 2 -18.824 -20.027 -3.687 1 16.33 ? O5' FMN 173 A 1 HETATM 28 P P FMN . . . B 2 -19.731 -18.815 -3.132 1 17.28 ? P FMN 173 A 1 HETATM 29 O O1P FMN . . . B 2 -21.019 -19.457 -2.602 1 18.01 ? O1P FMN 173 A 1 HETATM 30 O O2P FMN . . . B 2 -19.954 -17.79 -4.212 1 17.74 ? O2P FMN 173 A 1 HETATM 31 O O3P FMN . . . B 2 -18.863 -18.234 -2.028 1 17.85 ? O3P FMN 173 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 31 #