data_5YJY
#
_model_server_result.job_id            Bo5_AwWVEpB1TDOciUnyKw 
_model_server_result.datetime_utc      '2024-11-18 04:19:07' 
_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          5yjy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":601}' 
#
_entry.id    5YJY 
#
_exptl.entry_id    5YJY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              785.55 
_entity.id                          3 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5YJY 
_cell.length_a            69.854 
_cell.length_b            115.795 
_cell.length_c            166.499 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YJY 
_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,I,J,K,L,M,N,O,P 
_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 C N N 
? 3 J 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
metalc ? metalc1 A O LEU 61 A LEU 89 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc2 A O ALA 147 A ALA 175 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc3 A O ILE 353 A ILE 381 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? 
metalc ? metalc4 C O2P FAD . A FAD 601 1_555 D MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc5 C O1P FAD . A FAD 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc6 C O2A FAD . A FAD 601 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? 
metalc ? metalc7 C O3P FAD . A FAD 601 1_555 G MG MG . A MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc8 B O ALA 148 B ALA 175 1_555 L MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc9 J O2P FAD . B FAD 601 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc10 J O3P FAD . B FAD 601 1_555 K MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc11 J O5B FAD . B FAD 601 1_555 L MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? 
metalc ? metalc12 J O1P FAD . B FAD 601 1_555 L MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc13 J O1A FAD . B FAD 601 1_555 M MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc14 J O2A FAD . B FAD 601 1_555 N MG MG . B MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc15 J O3P FAD . B FAD 601 1_555 N MG MG . B MG 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? 
#
_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 126 n n 
PA O2A FAD sing 127 n n 
PA O5B FAD sing 128 n n 
PA O3P FAD sing 129 n n 
O2A HOA2 FAD sing 130 n n 
O5B C5B FAD sing 131 n n 
C5B C4B FAD sing 132 n n 
C5B H51A FAD sing 133 n n 
C5B H52A FAD sing 134 n n 
C4B O4B FAD sing 135 n n 
C4B C3B FAD sing 136 n n 
C4B H4B FAD sing 137 n n 
O4B C1B FAD sing 138 n n 
C3B O3B FAD sing 139 n n 
C3B C2B FAD sing 140 n n 
C3B H3B FAD sing 141 n n 
O3B HO3A FAD sing 142 n n 
C2B O2B FAD sing 143 n n 
C2B C1B FAD sing 144 n n 
C2B H2B FAD sing 145 n n 
O2B HO2A FAD sing 146 n n 
C1B N9A FAD sing 147 n n 
C1B H1B FAD sing 148 n n 
N9A C8A FAD sing 149 n y 
N9A C4A FAD sing 150 n y 
C8A N7A FAD doub 151 n y 
C8A H8A FAD sing 152 n n 
N7A C5A FAD sing 153 n y 
C5A C6A FAD sing 154 n y 
C5A C4A FAD doub 155 n y 
C6A N6A FAD sing 156 n n 
C6A N1A FAD doub 157 n y 
N6A H61A FAD sing 158 n n 
N6A H62A FAD sing 159 n n 
N1A C2A FAD sing 160 n y 
C2A N3A FAD doub 161 n y 
C2A H2A FAD sing 162 n n 
N3A C4A FAD sing 163 n y 
N1 C2 FAD sing 164 n n 
N1 C10 FAD doub 165 n n 
C2 O2 FAD doub 166 n n 
C2 N3 FAD sing 167 n n 
N3 C4 FAD sing 168 n n 
N3 HN3 FAD sing 169 n n 
C4 O4 FAD doub 170 n n 
C4 C4X FAD sing 171 n n 
C4X N5 FAD doub 172 n n 
C4X C10 FAD sing 173 n n 
N5 C5X FAD sing 174 n n 
C5X C6 FAD doub 175 n y 
C5X C9A FAD sing 176 n y 
C6 C7 FAD sing 177 n y 
C6 H6 FAD sing 178 n n 
C7 C7M FAD sing 179 n n 
C7 C8 FAD doub 180 n y 
C7M HM71 FAD sing 181 n n 
C7M HM72 FAD sing 182 n n 
C7M HM73 FAD sing 183 n n 
C8 C8M FAD sing 184 n n 
C8 C9 FAD sing 185 n y 
C8M HM81 FAD sing 186 n n 
C8M HM82 FAD sing 187 n n 
C8M HM83 FAD sing 188 n n 
C9 C9A FAD doub 189 n y 
C9 H9 FAD sing 190 n n 
C9A N10 FAD sing 191 n n 
N10 C10 FAD sing 192 n n 
N10 C1' FAD sing 193 n n 
C1' C2' FAD sing 194 n n 
C1' "H1'1" FAD sing 195 n n 
C1' "H1'2" FAD sing 196 n n 
C2' O2' FAD sing 197 n n 
C2' C3' FAD sing 198 n n 
C2' H2' FAD sing 199 n n 
O2' HO2' FAD sing 200 n n 
C3' O3' FAD sing 201 n n 
C3' C4' FAD sing 202 n n 
C3' H3' FAD sing 203 n n 
O3' HO3' FAD sing 204 n n 
C4' O4' FAD sing 205 n n 
C4' C5' FAD sing 206 n n 
C4' H4' FAD sing 207 n n 
O4' HO4' FAD sing 208 n n 
C5' O5' FAD sing 209 n n 
C5' "H5'1" FAD sing 210 n n 
C5' "H5'2" FAD sing 211 n n 
O5' P FAD sing 212 n n 
P O1P FAD doub 213 n n 
P O2P FAD sing 214 n n 
P O3P FAD sing 215 n n 
O2P HOP2 FAD sing 216 n n 
#
_atom_sites.entry_id                     5YJY 
_atom_sites.fract_transf_matrix[1][1]    0.014316 
_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]    0.008636 
_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]    0.006006 
_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 3 FAD A 1 601 601 FAD FAD . 
D 4 MG A 1 602 602 MG MG . 
E 4 MG A 1 603 603 MG MG . 
F 4 MG A 1 604 604 MG MG . 
G 4 MG A 1 605 605 MG MG . 
H 5 8WF A 1 606 701 8WF DRG . 
I 6 MES A 1 607 802 MES MES . 
J 3 FAD B 1 601 601 FAD FAD . 
K 4 MG B 1 602 602 MG MG . 
L 4 MG B 1 603 603 MG MG . 
M 4 MG B 1 604 604 MG MG . 
N 4 MG B 1 605 605 MG MG . 
O 5 8WF B 1 606 701 8WF DRG . 
P 6 MES B 1 607 801 MES MES . 
#
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 . . . J 3 19.143 16.273 18.662 1 26.65 ? PA FAD 601 B 1 
HETATM 2 O O1A FAD . . . J 3 17.638 16.352 18.939 1 25.06 ? O1A FAD 601 B 1 
HETATM 3 O O2A FAD . . . J 3 20.181 17.122 19.377 1 25.95 ? O2A FAD 601 B 1 
HETATM 4 O O5B FAD . . . J 3 19.651 14.791 18.865 1 25.85 ? O5B FAD 601 B 1 
HETATM 5 C C5B FAD . . . J 3 21.024 14.557 18.868 1 26.24 ? C5B FAD 601 B 1 
HETATM 6 C C4B FAD . . . J 3 21.121 13.331 19.709 1 27.82 ? C4B FAD 601 B 1 
HETATM 7 O O4B FAD . . . J 3 22.369 12.683 19.574 1 29.54 ? O4B FAD 601 B 1 
HETATM 8 C C3B FAD . . . J 3 21.004 13.724 21.152 1 28.91 ? C3B FAD 601 B 1 
HETATM 9 O O3B FAD . . . J 3 20.311 12.687 21.845 1 28.4 ? O3B FAD 601 B 1 
HETATM 10 C C2B FAD . . . J 3 22.438 13.801 21.604 1 29.96 ? C2B FAD 601 B 1 
HETATM 11 O O2B FAD . . . J 3 22.502 13.637 23.017 1 29.89 ? O2B FAD 601 B 1 
HETATM 12 C C1B FAD . . . J 3 23.051 12.651 20.833 1 31.33 ? C1B FAD 601 B 1 
HETATM 13 N N9A FAD . . . J 3 24.482 12.712 20.459 1 34.34 ? N9A FAD 601 B 1 
HETATM 14 C C8A FAD . . . J 3 25.288 13.789 20.315 1 34.86 ? C8A FAD 601 B 1 
HETATM 15 N N7A FAD . . . J 3 26.529 13.415 19.897 1 34.88 ? N7A FAD 601 B 1 
HETATM 16 C C5A FAD . . . J 3 26.514 12.081 19.76 1 36.63 ? C5A FAD 601 B 1 
HETATM 17 C C6A FAD . . . J 3 27.48 11.04 19.362 1 38.33 ? C6A FAD 601 B 1 
HETATM 18 N N6A FAD . . . J 3 28.732 11.368 19.018 1 38.51 ? N6A FAD 601 B 1 
HETATM 19 N N1A FAD . . . J 3 27.074 9.751 19.359 1 41.28 ? N1A FAD 601 B 1 
HETATM 20 C C2A FAD . . . J 3 25.816 9.395 19.702 1 40.72 ? C2A FAD 601 B 1 
HETATM 21 N N3A FAD . . . J 3 24.867 10.289 20.072 1 38.99 ? N3A FAD 601 B 1 
HETATM 22 C C4A FAD . . . J 3 25.162 11.62 20.12 1 36.87 ? C4A FAD 601 B 1 
HETATM 23 N N1 FAD . . . J 3 12.899 23.287 17.172 1 52.25 ? N1 FAD 601 B 1 
HETATM 24 C C2 FAD . . . J 3 11.596 23.44 16.803 1 55.66 ? C2 FAD 601 B 1 
HETATM 25 O O2 FAD . . . J 3 11.222 23.038 15.663 1 51.36 ? O2 FAD 601 B 1 
HETATM 26 N N3 FAD . . . J 3 10.697 24.02 17.637 1 57.47 ? N3 FAD 601 B 1 
HETATM 27 C C4 FAD . . . J 3 10.998 24.491 18.86 1 51.43 ? C4 FAD 601 B 1 
HETATM 28 O O4 FAD . . . J 3 10.157 25.026 19.609 1 50.45 ? O4 FAD 601 B 1 
HETATM 29 C C4X FAD . . . J 3 12.385 24.375 19.305 1 47.92 ? C4X FAD 601 B 1 
HETATM 30 N N5 FAD . . . J 3 12.723 24.826 20.514 1 46.55 ? N5 FAD 601 B 1 
HETATM 31 C C5X FAD . . . J 3 13.999 24.685 20.922 1 46.8 ? C5X FAD 601 B 1 
HETATM 32 C C6 FAD . . . J 3 14.345 25.141 22.186 1 44.96 ? C6 FAD 601 B 1 
HETATM 33 C C7 FAD . . . J 3 15.662 25.012 22.622 1 45.39 ? C7 FAD 601 B 1 
HETATM 34 C C7M FAD . . . J 3 16.01 25.543 23.979 1 46.62 ? C7M FAD 601 B 1 
HETATM 35 C C8 FAD . . . J 3 16.71 24.375 21.764 1 44.68 ? C8 FAD 601 B 1 
HETATM 36 C C8M FAD . . . J 3 18.147 24.219 22.205 1 43.47 ? C8M FAD 601 B 1 
HETATM 37 C C9 FAD . . . J 3 16.362 23.921 20.503 1 46.65 ? C9 FAD 601 B 1 
HETATM 38 C C9A FAD . . . J 3 15.048 24.052 20.032 1 46.82 ? C9A FAD 601 B 1 
HETATM 39 N N10 FAD . . . J 3 14.698 23.585 18.74 1 42.97 ? N10 FAD 601 B 1 
HETATM 40 C C10 FAD . . . J 3 13.35 23.733 18.368 1 47.37 ? C10 FAD 601 B 1 
HETATM 41 C C1' FAD . . . J 3 15.678 22.972 17.831 1 37.79 ? C1' FAD 601 B 1 
HETATM 42 C C2' FAD . . . J 3 15.686 21.467 17.918 1 36.1 ? C2' FAD 601 B 1 
HETATM 43 O O2' FAD . . . J 3 15.8 21.037 19.275 1 34.98 ? O2' FAD 601 B 1 
HETATM 44 C C3' FAD . . . J 3 16.815 20.832 17.115 1 34.05 ? C3' FAD 601 B 1 
HETATM 45 O O3' FAD . . . J 3 16.767 21.264 15.744 1 31.43 ? O3' FAD 601 B 1 
HETATM 46 C C4' FAD . . . J 3 16.597 19.323 17.246 1 32.61 ? C4' FAD 601 B 1 
HETATM 47 O O4' FAD . . . J 3 17.005 18.833 18.538 1 31.9 ? O4' FAD 601 B 1 
HETATM 48 C C5' FAD . . . J 3 17.299 18.509 16.188 1 30.89 ? C5' FAD 601 B 1 
HETATM 49 O O5' FAD . . . J 3 16.995 17.155 16.454 1 28.64 ? O5' FAD 601 B 1 
HETATM 50 P P FAD . . . J 3 18.132 16.13 16.047 1 27.11 ? P FAD 601 B 1 
HETATM 51 O O1P FAD . . . J 3 17.605 14.736 16.293 1 26.63 ? O1P FAD 601 B 1 
HETATM 52 O O2P FAD . . . J 3 18.627 16.621 14.712 1 26.5 ? O2P FAD 601 B 1 
HETATM 53 O O3P FAD . . . J 3 19.341 16.425 17.075 1 27.25 ? O3P FAD 601 B 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           53 
#