data_3D8X # _model_server_result.job_id SIP5wXJP3xyg7FP3m_zmvQ _model_server_result.datetime_utc '2025-01-11 01:59:57' _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 3d8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 3D8X # _exptl.entry_id 3D8X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 785.55 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN-ADENINE DINUCLEOTIDE' _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 114.16 _cell.angle_gamma 90 _cell.entry_id 3D8X _cell.length_a 54.229 _cell.length_b 125.004 _cell.length_c 60.967 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 E 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 disulf ? disulf1 A SG CYS 149 A CYS 142 1_555 A SG CYS 152 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 149 B CYS 142 1_555 B SG CYS 152 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C27 H33 N9 O15 P2' _chem_comp.formula_weight 785.55 _chem_comp.id FAD _chem_comp.mon_nstd_flag . _chem_comp.name 'FLAVIN-ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PA O1A FAD doub 83 n n PA O2A FAD sing 84 n n PA O5B FAD sing 85 n n PA O3P FAD sing 86 n n O2A HOA2 FAD sing 87 n n O5B C5B FAD sing 88 n n C5B C4B FAD sing 89 n n C5B H51A FAD sing 90 n n C5B H52A FAD sing 91 n n C4B O4B FAD sing 92 n n C4B C3B FAD sing 93 n n C4B H4B FAD sing 94 n n O4B C1B FAD sing 95 n n C3B O3B FAD sing 96 n n C3B C2B FAD sing 97 n n C3B H3B FAD sing 98 n n O3B HO3A FAD sing 99 n n C2B O2B FAD sing 100 n n C2B C1B FAD sing 101 n n C2B H2B FAD sing 102 n n O2B HO2A FAD sing 103 n n C1B N9A FAD sing 104 n n C1B H1B FAD sing 105 n n N9A C8A FAD sing 106 n y N9A C4A FAD sing 107 n y C8A N7A FAD doub 108 n y C8A H8A FAD sing 109 n n N7A C5A FAD sing 110 n y C5A C6A FAD sing 111 n y C5A C4A FAD doub 112 n y C6A N6A FAD sing 113 n n C6A N1A FAD doub 114 n y N6A H61A FAD sing 115 n n N6A H62A FAD sing 116 n n N1A C2A FAD sing 117 n y C2A N3A FAD doub 118 n y C2A H2A FAD sing 119 n n N3A C4A FAD sing 120 n y N1 C2 FAD sing 121 n n N1 C10 FAD doub 122 n n C2 O2 FAD doub 123 n n C2 N3 FAD sing 124 n n N3 C4 FAD sing 125 n n N3 HN3 FAD sing 126 n n C4 O4 FAD doub 127 n n C4 C4X FAD sing 128 n n C4X N5 FAD doub 129 n n C4X C10 FAD sing 130 n n N5 C5X FAD sing 131 n n C5X C6 FAD doub 132 n y C5X C9A FAD sing 133 n y C6 C7 FAD sing 134 n y C6 H6 FAD sing 135 n n C7 C7M FAD sing 136 n n C7 C8 FAD doub 137 n y C7M HM71 FAD sing 138 n n C7M HM72 FAD sing 139 n n C7M HM73 FAD sing 140 n n C8 C8M FAD sing 141 n n C8 C9 FAD sing 142 n y C8M HM81 FAD sing 143 n n C8M HM82 FAD sing 144 n n C8M HM83 FAD sing 145 n n C9 C9A FAD doub 146 n y C9 H9 FAD sing 147 n n C9A N10 FAD sing 148 n n N10 C10 FAD sing 149 n n N10 C1' FAD sing 150 n n C1' C2' FAD sing 151 n n C1' "H1'1" FAD sing 152 n n C1' "H1'2" FAD sing 153 n n C2' O2' FAD sing 154 n n C2' C3' FAD sing 155 n n C2' H2' FAD sing 156 n n O2' HO2' FAD sing 157 n n C3' O3' FAD sing 158 n n C3' C4' FAD sing 159 n n C3' H3' FAD sing 160 n n O3' HO3' FAD sing 161 n n C4' O4' FAD sing 162 n n C4' C5' FAD sing 163 n n C4' H4' FAD sing 164 n n O4' HO4' FAD sing 165 n n C5' O5' FAD sing 166 n n C5' "H5'1" FAD sing 167 n n C5' "H5'2" FAD sing 168 n n O5' P FAD sing 169 n n P O1P FAD doub 170 n n P O2P FAD sing 171 n n P O3P FAD sing 172 n n O2P HOP2 FAD sing 173 n n # _atom_sites.entry_id 3D8X _atom_sites.fract_transf_matrix[1][1] 0.01844 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00827 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008 _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] 0.017976 _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 FAD A 1 1001 1001 FAD FAD . D 3 NDP A 1 481 481 NDP NDP . E 2 FAD B 1 1001 1001 FAD FAD . F 4 HOH A 1 1002 1 HOH HOH . F 4 HOH A 2 1003 2 HOH HOH . F 4 HOH A 3 1004 4 HOH HOH . F 4 HOH A 4 1005 5 HOH HOH . F 4 HOH A 5 1006 6 HOH HOH . F 4 HOH A 6 1007 10 HOH HOH . F 4 HOH A 7 1008 13 HOH HOH . F 4 HOH A 8 1009 14 HOH HOH . F 4 HOH A 9 1010 18 HOH HOH . F 4 HOH A 10 1011 19 HOH HOH . F 4 HOH A 11 1012 20 HOH HOH . F 4 HOH A 12 1013 26 HOH HOH . F 4 HOH A 13 1014 27 HOH HOH . F 4 HOH A 14 1015 28 HOH HOH . F 4 HOH A 15 1016 30 HOH HOH . F 4 HOH A 16 1017 31 HOH HOH . F 4 HOH A 17 1018 39 HOH HOH . F 4 HOH A 18 1019 41 HOH HOH . F 4 HOH A 19 1020 45 HOH HOH . F 4 HOH A 20 1021 47 HOH HOH . F 4 HOH A 21 1022 49 HOH HOH . F 4 HOH A 22 1023 50 HOH HOH . F 4 HOH A 23 1024 53 HOH HOH . F 4 HOH A 24 1025 56 HOH HOH . F 4 HOH A 25 1026 58 HOH HOH . F 4 HOH A 26 1027 61 HOH HOH . F 4 HOH A 27 1028 62 HOH HOH . F 4 HOH A 28 1029 63 HOH HOH . F 4 HOH A 29 1030 66 HOH HOH . F 4 HOH A 30 1031 68 HOH HOH . F 4 HOH A 31 1032 71 HOH HOH . F 4 HOH A 32 1033 72 HOH HOH . F 4 HOH A 33 1034 73 HOH HOH . F 4 HOH A 34 1035 74 HOH HOH . F 4 HOH A 35 1036 75 HOH HOH . F 4 HOH A 36 1037 80 HOH HOH . F 4 HOH A 37 1038 81 HOH HOH . F 4 HOH A 38 1039 82 HOH HOH . F 4 HOH A 39 1040 83 HOH HOH . F 4 HOH A 40 1041 84 HOH HOH . F 4 HOH A 41 1042 88 HOH HOH . F 4 HOH A 42 1043 89 HOH HOH . F 4 HOH A 43 1044 90 HOH HOH . F 4 HOH A 44 1045 91 HOH HOH . F 4 HOH A 45 1046 92 HOH HOH . F 4 HOH A 46 1047 94 HOH HOH . F 4 HOH A 47 1048 97 HOH HOH . G 4 HOH B 1 1049 99 HOH HOH . G 4 HOH B 2 1050 3 HOH HOH . G 4 HOH B 3 1051 7 HOH HOH . G 4 HOH B 4 1052 8 HOH HOH . G 4 HOH B 5 1053 9 HOH HOH . G 4 HOH B 6 1054 11 HOH HOH . G 4 HOH B 7 1055 12 HOH HOH . G 4 HOH B 8 1056 15 HOH HOH . G 4 HOH B 9 1057 16 HOH HOH . G 4 HOH B 10 1058 17 HOH HOH . G 4 HOH B 11 1059 21 HOH HOH . G 4 HOH B 12 1060 22 HOH HOH . G 4 HOH B 13 1061 23 HOH HOH . G 4 HOH B 14 1062 24 HOH HOH . G 4 HOH B 15 1063 25 HOH HOH . G 4 HOH B 16 1064 29 HOH HOH . G 4 HOH B 17 1065 32 HOH HOH . G 4 HOH B 18 1066 33 HOH HOH . G 4 HOH B 19 1067 34 HOH HOH . G 4 HOH B 20 1068 35 HOH HOH . G 4 HOH B 21 1069 36 HOH HOH . G 4 HOH B 22 1070 37 HOH HOH . G 4 HOH B 23 1071 38 HOH HOH . G 4 HOH B 24 1072 40 HOH HOH . G 4 HOH B 25 1073 42 HOH HOH . G 4 HOH B 26 1074 43 HOH HOH . G 4 HOH B 27 1075 44 HOH HOH . G 4 HOH B 28 1076 46 HOH HOH . G 4 HOH B 29 1077 48 HOH HOH . G 4 HOH B 30 1078 51 HOH HOH . G 4 HOH B 31 1079 52 HOH HOH . G 4 HOH B 32 1080 54 HOH HOH . G 4 HOH B 33 1081 55 HOH HOH . G 4 HOH B 34 1082 57 HOH HOH . G 4 HOH B 35 1083 59 HOH HOH . G 4 HOH B 36 1084 60 HOH HOH . G 4 HOH B 37 1085 64 HOH HOH . G 4 HOH B 38 1086 65 HOH HOH . G 4 HOH B 39 1087 67 HOH HOH . G 4 HOH B 40 1088 69 HOH HOH . G 4 HOH B 41 1089 70 HOH HOH . G 4 HOH B 42 1090 76 HOH HOH . G 4 HOH B 43 1091 77 HOH HOH . G 4 HOH B 44 1092 78 HOH HOH . G 4 HOH B 45 1093 79 HOH HOH . G 4 HOH B 46 1094 85 HOH HOH . G 4 HOH B 47 1095 86 HOH HOH . G 4 HOH B 48 1096 87 HOH HOH . G 4 HOH B 49 1097 93 HOH HOH . G 4 HOH B 50 1098 95 HOH HOH . G 4 HOH B 51 1099 96 HOH HOH . G 4 HOH B 52 1100 98 HOH HOH . G 4 HOH B 53 1101 100 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 P PA FAD . . . E 2 3.917 -7.912 3.946 1 19.62 ? PA FAD 1001 B 1 HETATM 2 O O1A FAD . . . E 2 5.417 -7.966 4.055 1 19.13 ? O1A FAD 1001 B 1 HETATM 3 O O2A FAD . . . E 2 3.204 -9.166 4.387 1 18.12 ? O2A FAD 1001 B 1 HETATM 4 O O5B FAD . . . E 2 3.497 -7.605 2.415 1 20.95 ? O5B FAD 1001 B 1 HETATM 5 C C5B FAD . . . E 2 3.871 -6.411 1.746 1 21.48 ? C5B FAD 1001 B 1 HETATM 6 C C4B FAD . . . E 2 3.527 -6.538 0.267 1 21.65 ? C4B FAD 1001 B 1 HETATM 7 O O4B FAD . . . E 2 3.337 -5.289 -0.383 1 22.86 ? O4B FAD 1001 B 1 HETATM 8 C C3B FAD . . . E 2 4.62 -7.214 -0.54 1 20.98 ? C3B FAD 1001 B 1 HETATM 9 O O3B FAD . . . E 2 4.568 -8.609 -0.398 1 20.09 ? O3B FAD 1001 B 1 HETATM 10 C C2B FAD . . . E 2 4.291 -6.774 -1.953 1 21.07 ? C2B FAD 1001 B 1 HETATM 11 O O2B FAD . . . E 2 3.332 -7.615 -2.549 1 20.5 ? O2B FAD 1001 B 1 HETATM 12 C C1B FAD . . . E 2 3.665 -5.404 -1.762 1 21.41 ? C1B FAD 1001 B 1 HETATM 13 N N9A FAD . . . E 2 4.644 -4.402 -2.227 1 21.39 ? N9A FAD 1001 B 1 HETATM 14 C C8A FAD . . . E 2 5.986 -4.351 -1.946 1 21.82 ? C8A FAD 1001 B 1 HETATM 15 N N7A FAD . . . E 2 6.539 -3.292 -2.589 1 21.5 ? N7A FAD 1001 B 1 HETATM 16 C C5A FAD . . . E 2 5.577 -2.668 -3.294 1 21.07 ? C5A FAD 1001 B 1 HETATM 17 C C6A FAD . . . E 2 5.593 -1.54 -4.12 1 20.79 ? C6A FAD 1001 B 1 HETATM 18 N N6A FAD . . . E 2 6.599 -0.667 -4.101 1 19.97 ? N6A FAD 1001 B 1 HETATM 19 N N1A FAD . . . E 2 4.411 -1.141 -4.696 1 21.23 ? N1A FAD 1001 B 1 HETATM 20 C C2A FAD . . . E 2 3.24 -1.843 -4.466 1 21.72 ? C2A FAD 1001 B 1 HETATM 21 N N3A FAD . . . E 2 3.229 -2.953 -3.646 1 21.33 ? N3A FAD 1001 B 1 HETATM 22 C C4A FAD . . . E 2 4.381 -3.359 -3.068 1 21.33 ? C4A FAD 1001 B 1 HETATM 23 N N1 FAD . . . E 2 3.77 -14.056 10.804 1 17.35 ? N1 FAD 1001 B 1 HETATM 24 C C2 FAD . . . E 2 2.787 -14.435 11.694 1 18.11 ? C2 FAD 1001 B 1 HETATM 25 O O2 FAD . . . E 2 2.375 -13.588 12.499 1 18.22 ? O2 FAD 1001 B 1 HETATM 26 N N3 FAD . . . E 2 2.289 -15.746 11.66 1 18.02 ? N3 FAD 1001 B 1 HETATM 27 C C4 FAD . . . E 2 2.789 -16.658 10.721 1 17.65 ? C4 FAD 1001 B 1 HETATM 28 O O4 FAD . . . E 2 2.364 -17.821 10.682 1 17.13 ? O4 FAD 1001 B 1 HETATM 29 C C4X FAD . . . E 2 3.775 -16.245 9.821 1 16.59 ? C4X FAD 1001 B 1 HETATM 30 N N5 FAD . . . E 2 4.287 -17.118 8.883 1 17 ? N5 FAD 1001 B 1 HETATM 31 C C5X FAD . . . E 2 5.276 -16.711 8 1 17.29 ? C5X FAD 1001 B 1 HETATM 32 C C6 FAD . . . E 2 5.792 -17.592 7.059 1 17.42 ? C6 FAD 1001 B 1 HETATM 33 C C7 FAD . . . E 2 6.781 -17.169 6.169 1 17.97 ? C7 FAD 1001 B 1 HETATM 34 C C7M FAD . . . E 2 7.046 -18.006 4.951 1 18.23 ? C7M FAD 1001 B 1 HETATM 35 C C8 FAD . . . E 2 7.299 -15.867 6.229 1 17.91 ? C8 FAD 1001 B 1 HETATM 36 C C8M FAD . . . E 2 8.791 -15.743 6.077 1 16.82 ? C8M FAD 1001 B 1 HETATM 37 C C9 FAD . . . E 2 6.756 -14.989 7.164 1 17.38 ? C9 FAD 1001 B 1 HETATM 38 C C9A FAD . . . E 2 5.766 -15.405 8.054 1 17.59 ? C9A FAD 1001 B 1 HETATM 39 N N10 FAD . . . E 2 5.245 -14.522 8.988 1 17.82 ? N10 FAD 1001 B 1 HETATM 40 C C10 FAD . . . E 2 4.262 -14.942 9.871 1 16.81 ? C10 FAD 1001 B 1 HETATM 41 C C1' FAD . . . E 2 5.693 -13.082 8.977 1 17.61 ? C1' FAD 1001 B 1 HETATM 42 C C2' FAD . . . E 2 4.68 -12.207 8.263 1 17.03 ? C2' FAD 1001 B 1 HETATM 43 O O2' FAD . . . E 2 4.5 -12.679 6.95 1 16.94 ? O2' FAD 1001 B 1 HETATM 44 C C3' FAD . . . E 2 5.139 -10.755 8.197 1 17.91 ? C3' FAD 1001 B 1 HETATM 45 O O3' FAD . . . E 2 5.757 -10.371 9.409 1 17.33 ? O3' FAD 1001 B 1 HETATM 46 C C4' FAD . . . E 2 3.951 -9.837 7.899 1 18.12 ? C4' FAD 1001 B 1 HETATM 47 O O4' FAD . . . E 2 3.146 -10.397 6.879 1 18.74 ? O4' FAD 1001 B 1 HETATM 48 C C5' FAD . . . E 2 4.408 -8.465 7.446 1 16.82 ? C5' FAD 1001 B 1 HETATM 49 O O5' FAD . . . E 2 3.243 -7.81 7.036 1 16.77 ? O5' FAD 1001 B 1 HETATM 50 P P FAD . . . E 2 3.327 -6.37 6.34 1 18.07 ? P FAD 1001 B 1 HETATM 51 O O1P FAD . . . E 2 2.04 -5.618 6.565 1 15.91 ? O1P FAD 1001 B 1 HETATM 52 O O2P FAD . . . E 2 4.503 -5.591 6.885 1 17.89 ? O2P FAD 1001 B 1 HETATM 53 O O3P FAD . . . E 2 3.441 -6.593 4.746 1 18.97 ? O3P FAD 1001 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 53 #