data_4YXD
#
_model_server_result.job_id            FQsRmpCjOOnQRXhvRhPxfg 
_model_server_result.datetime_utc      '2024-11-24 09:51:12' 
_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              13 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           1069 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           53 
#