data_5EBK
#
_model_server_result.job_id            TNgbh7bBz2jjrwlbriqOqQ 
_model_server_result.datetime_utc      '2024-12-15 03:50:06' 
_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          5ebk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":502}' 
#
_entry.id    5EBK 
#
_exptl.entry_id    5EBK 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            5EBK 
_cell.length_a            102.5 
_cell.length_b            102.5 
_cell.length_c            192 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5EBK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        76 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
_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 I 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 72 A CYS 52 1_555 A SG CYS 77 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 109 A CYS 89 1_555 A SG CYS 233 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 B SG CYS 72 B CYS 52 1_555 B SG CYS 77 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf4 B SG CYS 109 B CYS 89 1_555 B SG CYS 233 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
#
_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                     5EBK 
_atom_sites.fract_transf_matrix[1][1]    0.009756 
_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]    0.009756 
_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]    0.005208 
_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 1 501 1486 FAD FAD . 
D 3 RDS A 1 502 2001 RDS RDS . 
E 3 RDS A 1 503 2002 RDS RDS . 
F 3 RDS A 1 504 2003 RDS RDS . 
G 4 SO4 A 1 505 3 SO4 SO4 . 
H 3 RDS B 1 501 2004 RDS RDS . 
I 2 FAD B 1 502 1486 FAD FAD . 
J 3 RDS B 1 503 2001 RDS RDS . 
K 3 RDS B 1 504 2002 RDS RDS . 
L 3 RDS B 1 505 2003 RDS RDS . 
#
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 . . . I 2 30.913 56.435 -7.91 1 111.02 ? PA FAD 502 B 1 
HETATM 2 O O1A FAD . . . I 2 31.724 55.952 -6.73 1 116.64 ? O1A FAD 502 B 1 
HETATM 3 O O2A FAD . . . I 2 29.965 55.477 -8.588 1 112.98 ? O2A FAD 502 B 1 
HETATM 4 O O5B FAD . . . I 2 31.869 57.057 -9.05 1 105.25 ? O5B FAD 502 B 1 
HETATM 5 C C5B FAD . . . I 2 33.275 57.085 -8.867 1 101.54 ? C5B FAD 502 B 1 
HETATM 6 C C4B FAD . . . I 2 33.99 57.271 -10.201 1 101.18 ? C4B FAD 502 B 1 
HETATM 7 O O4B FAD . . . I 2 34.43 58.625 -10.377 1 102.31 ? O4B FAD 502 B 1 
HETATM 8 C C3B FAD . . . I 2 35.234 56.398 -10.254 1 101.8 ? C3B FAD 502 B 1 
HETATM 9 O O3B FAD . . . I 2 35.181 55.483 -11.352 1 108.62 ? O3B FAD 502 B 1 
HETATM 10 C C2B FAD . . . I 2 36.412 57.345 -10.342 1 101.12 ? C2B FAD 502 B 1 
HETATM 11 O O2B FAD . . . I 2 37.468 56.869 -11.178 1 100.51 ? O2B FAD 502 B 1 
HETATM 12 C C1B FAD . . . I 2 35.778 58.623 -10.875 1 102.59 ? C1B FAD 502 B 1 
HETATM 13 N N9A FAD . . . I 2 36.58 59.824 -10.521 1 104.9 ? N9A FAD 502 B 1 
HETATM 14 C C8A FAD . . . I 2 37.147 60.11 -9.333 1 111.12 ? C8A FAD 502 B 1 
HETATM 15 N N7A FAD . . . I 2 37.821 61.285 -9.392 1 115.87 ? N7A FAD 502 B 1 
HETATM 16 C C5A FAD . . . I 2 37.699 61.773 -10.635 1 106.67 ? C5A FAD 502 B 1 
HETATM 17 C C6A FAD . . . I 2 38.164 62.976 -11.367 1 105.27 ? C6A FAD 502 B 1 
HETATM 18 N N6A FAD . . . I 2 38.92 63.925 -10.771 1 107.39 ? N6A FAD 502 B 1 
HETATM 19 N N1A FAD . . . I 2 37.804 63.102 -12.66 1 103.92 ? N1A FAD 502 B 1 
HETATM 20 C C2A FAD . . . I 2 37.051 62.174 -13.279 1 102.94 ? C2A FAD 502 B 1 
HETATM 21 N N3A FAD . . . I 2 36.606 61.062 -12.667 1 100.06 ? N3A FAD 502 B 1 
HETATM 22 C C4A FAD . . . I 2 36.882 60.804 -11.372 1 102.65 ? C4A FAD 502 B 1 
HETATM 23 N N1 FAD . . . I 2 26.463 50.714 -2.281 1 99.82 ? N1 FAD 502 B 1 
HETATM 24 C C2 FAD . . . I 2 25.342 49.933 -2.242 1 98.02 ? C2 FAD 502 B 1 
HETATM 25 O O2 FAD . . . I 2 24.235 50.442 -2.525 1 92.14 ? O2 FAD 502 B 1 
HETATM 26 N N3 FAD . . . I 2 25.383 48.625 -1.908 1 99.44 ? N3 FAD 502 B 1 
HETATM 27 C C4 FAD . . . I 2 26.537 48.01 -1.586 1 100.42 ? C4 FAD 502 B 1 
HETATM 28 O O4 FAD . . . I 2 26.558 46.798 -1.274 1 100.32 ? O4 FAD 502 B 1 
HETATM 29 C C4X FAD . . . I 2 27.797 48.799 -1.605 1 99.37 ? C4X FAD 502 B 1 
HETATM 30 N N5 FAD . . . I 2 28.982 48.245 -1.293 1 96.25 ? N5 FAD 502 B 1 
HETATM 31 C C5X FAD . . . I 2 30.126 48.952 -1.302 1 92.94 ? C5X FAD 502 B 1 
HETATM 32 C C6 FAD . . . I 2 31.297 48.291 -0.964 1 91.64 ? C6 FAD 502 B 1 
HETATM 33 C C7 FAD . . . I 2 32.517 48.947 -0.957 1 90.43 ? C7 FAD 502 B 1 
HETATM 34 C C7M FAD . . . I 2 33.764 48.184 -0.584 1 88.11 ? C7M FAD 502 B 1 
HETATM 35 C C8 FAD . . . I 2 32.552 50.391 -1.319 1 92.95 ? C8 FAD 502 B 1 
HETATM 36 C C8M FAD . . . I 2 33.857 51.139 -1.319 1 93.83 ? C8M FAD 502 B 1 
HETATM 37 C C9 FAD . . . I 2 31.373 51.062 -1.657 1 93.84 ? C9 FAD 502 B 1 
HETATM 38 C C9A FAD . . . I 2 30.136 50.399 -1.671 1 93.66 ? C9A FAD 502 B 1 
HETATM 39 N N10 FAD . . . I 2 28.892 51.015 -2.016 1 99.23 ? N10 FAD 502 B 1 
HETATM 40 C C10 FAD . . . I 2 27.703 50.232 -1.981 1 99.02 ? C10 FAD 502 B 1 
HETATM 41 C C1' FAD . . . I 2 28.786 52.441 -2.368 1 107.68 ? C1' FAD 502 B 1 
HETATM 42 C C2' FAD . . . I 2 28.975 52.728 -3.859 1 113.26 ? C2' FAD 502 B 1 
HETATM 43 O O2' FAD . . . I 2 30.201 52.148 -4.324 1 111.12 ? O2' FAD 502 B 1 
HETATM 44 C C3' FAD . . . I 2 28.988 54.239 -4.129 1 121.27 ? C3' FAD 502 B 1 
HETATM 45 O O3' FAD . . . I 2 28.324 54.923 -3.061 1 121.84 ? O3' FAD 502 B 1 
HETATM 46 C C4' FAD . . . I 2 28.298 54.641 -5.436 1 128.26 ? C4' FAD 502 B 1 
HETATM 47 O O4' FAD . . . I 2 28.977 54.046 -6.55 1 133.42 ? O4' FAD 502 B 1 
HETATM 48 C C5' FAD . . . I 2 28.247 56.167 -5.576 1 132.48 ? C5' FAD 502 B 1 
HETATM 49 O O5' FAD . . . I 2 27.969 56.582 -6.914 1 130.4 ? O5' FAD 502 B 1 
HETATM 50 P P FAD . . . I 2 28.575 57.954 -7.515 1 131.35 ? P FAD 502 B 1 
HETATM 51 O O1P FAD . . . I 2 28.199 58.039 -8.98 1 135.89 ? O1P FAD 502 B 1 
HETATM 52 O O2P FAD . . . I 2 28.295 59.109 -6.588 1 130.78 ? O2P FAD 502 B 1 
HETATM 53 O O3P FAD . . . I 2 30.16 57.753 -7.401 1 121.25 ? O3P FAD 502 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           395 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           53 
#