data_4YXD # _model_server_result.job_id FX5sxPSpJn6Zqh_-eRkeQg _model_server_result.datetime_utc '2024-11-06 03:08:36' _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 4yxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 4YXD # _exptl.entry_id 4YXD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 785.55 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FLAVIN-ADENINE DINUCLEOTIDE' _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 90 _cell.entry_id 4YXD _cell.length_a 70.366 _cell.length_b 83.746 _cell.length_c 292.625 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXD _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 B SG CYS 93 B CYS 65 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 B SG CYS 98 B CYS 70 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc3 B SG CYS 101 B CYS 73 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 B SG CYS 113 B CYS 85 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc5 B SG CYS 186 B CYS 158 1_555 G FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc6 B SG CYS 189 B CYS 161 1_555 G FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 B SG CYS 192 B CYS 164 1_555 G FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.806 ? metalc ? metalc8 B SG CYS 196 B CYS 168 1_555 H FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc9 B SG CYS 243 B CYS 215 1_555 H FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc10 B SG CYS 249 B CYS 221 1_555 H FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc11 B SG CYS 253 B CYS 225 1_555 G FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc12 C NE2 HIS 127 C HIS 101 1_555 I FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc13 I FE HEM . C HEM 301 1_555 D NE2 HIS 102 D HIS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? # _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 92 n n PA O2A FAD sing 93 n n PA O5B FAD sing 94 n n PA O3P FAD sing 95 n n O2A HOA2 FAD sing 96 n n O5B C5B FAD sing 97 n n C5B C4B FAD sing 98 n n C5B H51A FAD sing 99 n n C5B H52A FAD sing 100 n n C4B O4B FAD sing 101 n n C4B C3B FAD sing 102 n n C4B H4B FAD sing 103 n n O4B C1B FAD sing 104 n n C3B O3B FAD sing 105 n n C3B C2B FAD sing 106 n n C3B H3B FAD sing 107 n n O3B HO3A FAD sing 108 n n C2B O2B FAD sing 109 n n C2B C1B FAD sing 110 n n C2B H2B FAD sing 111 n n O2B HO2A FAD sing 112 n n C1B N9A FAD sing 113 n n C1B H1B FAD sing 114 n n N9A C8A FAD sing 115 n y N9A C4A FAD sing 116 n y C8A N7A FAD doub 117 n y C8A H8A FAD sing 118 n n N7A C5A FAD sing 119 n y C5A C6A FAD sing 120 n y C5A C4A FAD doub 121 n y C6A N6A FAD sing 122 n n C6A N1A FAD doub 123 n y N6A H61A FAD sing 124 n n N6A H62A FAD sing 125 n n N1A C2A FAD sing 126 n y C2A N3A FAD doub 127 n y C2A H2A FAD sing 128 n n N3A C4A FAD sing 129 n y N1 C2 FAD sing 130 n n N1 C10 FAD doub 131 n n C2 O2 FAD doub 132 n n C2 N3 FAD sing 133 n n N3 C4 FAD sing 134 n n N3 HN3 FAD sing 135 n n C4 O4 FAD doub 136 n n C4 C4X FAD sing 137 n n C4X N5 FAD doub 138 n n C4X C10 FAD sing 139 n n N5 C5X FAD sing 140 n n C5X C6 FAD doub 141 n y C5X C9A FAD sing 142 n y C6 C7 FAD sing 143 n y C6 H6 FAD sing 144 n n C7 C7M FAD sing 145 n n C7 C8 FAD doub 146 n y C7M HM71 FAD sing 147 n n C7M HM72 FAD sing 148 n n C7M HM73 FAD sing 149 n n C8 C8M FAD sing 150 n n C8 C9 FAD sing 151 n y C8M HM81 FAD sing 152 n n C8M HM82 FAD sing 153 n n C8M HM83 FAD sing 154 n n C9 C9A FAD doub 155 n y C9 H9 FAD sing 156 n n C9A N10 FAD sing 157 n n N10 C10 FAD sing 158 n n N10 C1' FAD sing 159 n n C1' C2' FAD sing 160 n n C1' "H1'1" FAD sing 161 n n C1' "H1'2" FAD sing 162 n n C2' O2' FAD sing 163 n n C2' C3' FAD sing 164 n n C2' H2' FAD sing 165 n n O2' HO2' FAD sing 166 n n C3' O3' FAD sing 167 n n C3' C4' FAD sing 168 n n C3' H3' FAD sing 169 n n O3' HO3' FAD sing 170 n n C4' O4' FAD sing 171 n n C4' C5' FAD sing 172 n n C4' H4' FAD sing 173 n n O4' HO4' FAD sing 174 n n C5' O5' FAD sing 175 n n C5' "H5'1" FAD sing 176 n n C5' "H5'2" FAD sing 177 n n O5' P FAD sing 178 n n P O1P FAD doub 179 n n P O2P FAD sing 180 n n P O3P FAD sing 181 n n O2P HOP2 FAD sing 182 n n # _atom_sites.entry_id 4YXD _atom_sites.fract_transf_matrix[1][1] 0.014211 _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] 0.011941 _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] 0.003417 _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 E 5 FAD A 1 700 700 FAD FAD . F 6 FES B 1 301 302 FES FES . G 7 SF4 B 1 302 303 SF4 SF4 . H 8 F3S B 1 303 304 F3S F3S . I 9 HEM C 1 301 301 HEM HEM . J 10 FTN C 1 302 302 FTN FTN . # 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 5 -11.124 -15.67 22.688 1 68.25 ? PA FAD 700 A 1 HETATM 2 O O1A FAD . . . E 5 -12.517 -15.413 23.186 1 69.04 ? O1A FAD 700 A 1 HETATM 3 O O2A FAD . . . E 5 -10.009 -14.775 23.155 1 73.35 ? O2A FAD 700 A 1 HETATM 4 O O5B FAD . . . E 5 -10.761 -17.171 23.115 1 70.09 ? O5B FAD 700 A 1 HETATM 5 C C5B FAD . . . E 5 -9.407 -17.588 23.076 1 71.17 ? C5B FAD 700 A 1 HETATM 6 C C4B FAD . . . E 5 -9.324 -19.069 23.38 1 69.95 ? C4B FAD 700 A 1 HETATM 7 O O4B FAD . . . E 5 -8.074 -19.587 22.927 1 69.79 ? O4B FAD 700 A 1 HETATM 8 C C3B FAD . . . E 5 -9.371 -19.315 24.867 1 69.84 ? C3B FAD 700 A 1 HETATM 9 O O3B FAD . . . E 5 -10.111 -20.512 25.102 1 72.73 ? O3B FAD 700 A 1 HETATM 10 C C2B FAD . . . E 5 -7.935 -19.527 25.257 1 70.08 ? C2B FAD 700 A 1 HETATM 11 O O2B FAD . . . E 5 -7.859 -20.369 26.406 1 73.99 ? O2B FAD 700 A 1 HETATM 12 C C1B FAD . . . E 5 -7.387 -20.192 24.015 1 68.96 ? C1B FAD 700 A 1 HETATM 13 N N9A FAD . . . E 5 -5.916 -20.084 23.883 1 70.46 ? N9A FAD 700 A 1 HETATM 14 C C8A FAD . . . E 5 -5.147 -18.991 23.673 1 70.56 ? C8A FAD 700 A 1 HETATM 15 N N7A FAD . . . E 5 -3.829 -19.342 23.605 1 67.07 ? N7A FAD 700 A 1 HETATM 16 C C5A FAD . . . E 5 -3.762 -20.673 23.774 1 65.74 ? C5A FAD 700 A 1 HETATM 17 C C6A FAD . . . E 5 -2.717 -21.709 23.833 1 63 ? C6A FAD 700 A 1 HETATM 18 N N6A FAD . . . E 5 -1.427 -21.39 23.693 1 64.04 ? N6A FAD 700 A 1 HETATM 19 N N1A FAD . . . E 5 -3.082 -22.994 24.027 1 63.78 ? N1A FAD 700 A 1 HETATM 20 C C2A FAD . . . E 5 -4.372 -23.361 24.174 1 65.57 ? C2A FAD 700 A 1 HETATM 21 N N3A FAD . . . E 5 -5.382 -22.476 24.138 1 65.04 ? N3A FAD 700 A 1 HETATM 22 C C4A FAD . . . E 5 -5.139 -21.154 23.95 1 69.08 ? C4A FAD 700 A 1 HETATM 23 N N1 FAD . . . E 5 -17.25 -8.41 19.686 1 89.03 ? N1 FAD 700 A 1 HETATM 24 C C2 FAD . . . E 5 -18.574 -8.301 19.357 1 90.43 ? C2 FAD 700 A 1 HETATM 25 O O2 FAD . . . E 5 -18.989 -8.81 18.28 1 90.46 ? O2 FAD 700 A 1 HETATM 26 N N3 FAD . . . E 5 -19.451 -7.665 20.157 1 86.14 ? N3 FAD 700 A 1 HETATM 27 C C4 FAD . . . E 5 -19.072 -7.105 21.312 1 83.45 ? C4 FAD 700 A 1 HETATM 28 O O4 FAD . . . E 5 -19.885 -6.514 22.05 1 89.16 ? O4 FAD 700 A 1 HETATM 29 C C4X FAD . . . E 5 -17.659 -7.186 21.72 1 77.97 ? C4X FAD 700 A 1 HETATM 30 N N5 FAD . . . E 5 -17.244 -6.644 22.867 1 74.05 ? N5 FAD 700 A 1 HETATM 31 C C5X FAD . . . E 5 -15.955 -6.725 23.238 1 71.05 ? C5X FAD 700 A 1 HETATM 32 C C6 FAD . . . E 5 -15.621 -6.132 24.444 1 72.7 ? C6 FAD 700 A 1 HETATM 33 C C7 FAD . . . E 5 -14.315 -6.173 24.895 1 73.84 ? C7 FAD 700 A 1 HETATM 34 C C7M FAD . . . E 5 -13.932 -5.539 26.208 1 75.86 ? C7M FAD 700 A 1 HETATM 35 C C8 FAD . . . E 5 -13.282 -6.864 24.088 1 70.67 ? C8 FAD 700 A 1 HETATM 36 C C8M FAD . . . E 5 -11.889 -6.822 24.639 1 67.1 ? C8M FAD 700 A 1 HETATM 37 C C9 FAD . . . E 5 -13.609 -7.471 22.869 1 67.77 ? C9 FAD 700 A 1 HETATM 38 C C9A FAD . . . E 5 -14.929 -7.424 22.402 1 67.25 ? C9A FAD 700 A 1 HETATM 39 N N10 FAD . . . E 5 -15.358 -7.996 21.178 1 69.06 ? N10 FAD 700 A 1 HETATM 40 C C10 FAD . . . E 5 -16.727 -7.889 20.825 1 76.78 ? C10 FAD 700 A 1 HETATM 41 C C1' FAD . . . E 5 -14.465 -8.732 20.277 1 68.02 ? C1' FAD 700 A 1 HETATM 42 C C2' FAD . . . E 5 -14.768 -10.232 20.432 1 66.7 ? C2' FAD 700 A 1 HETATM 43 O O2' FAD . . . E 5 -15.378 -10.534 21.691 1 67.82 ? O2' FAD 700 A 1 HETATM 44 C C3' FAD . . . E 5 -13.529 -11.106 20.366 1 66.28 ? C3' FAD 700 A 1 HETATM 45 O O3' FAD . . . E 5 -12.85 -10.845 19.142 1 68.93 ? O3' FAD 700 A 1 HETATM 46 C C4' FAD . . . E 5 -13.954 -12.57 20.487 1 63.71 ? C4' FAD 700 A 1 HETATM 47 O O4' FAD . . . E 5 -14.387 -12.689 21.837 1 63.12 ? O4' FAD 700 A 1 HETATM 48 C C5' FAD . . . E 5 -12.859 -13.598 20.16 1 60.03 ? C5' FAD 700 A 1 HETATM 49 O O5' FAD . . . E 5 -13.308 -14.949 20.257 1 57.15 ? O5' FAD 700 A 1 HETATM 50 P P FAD . . . E 5 -12.241 -16.147 20.074 1 70.4 ? P FAD 700 A 1 HETATM 51 O O1P FAD . . . E 5 -12.799 -17.514 20.467 1 64.06 ? O1P FAD 700 A 1 HETATM 52 O O2P FAD . . . E 5 -11.579 -16.039 18.709 1 70.87 ? O2P FAD 700 A 1 HETATM 53 O O3P FAD . . . E 5 -11.06 -15.697 21.081 1 67.34 ? O3P FAD 700 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 429 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 53 #