data_5EBK
#
_model_server_result.job_id            lcmiqBrcYUD2bx8ZeZAo6Q 
_model_server_result.datetime_utc      '2024-12-15 03:47:32' 
_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":"C","auth_seq_id":501}' 
#
_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 . . . C 2 -5.119 20.319 7.941 1 101.45 ? PA FAD 501 A 1 
HETATM 2 O O1A FAD . . . C 2 -4.234 19.511 7.042 1 103.6 ? O1A FAD 501 A 1 
HETATM 3 O O2A FAD . . . C 2 -4.489 21.509 8.613 1 99.61 ? O2A FAD 501 A 1 
HETATM 4 O O5B FAD . . . C 2 -5.735 19.348 9.066 1 102.07 ? O5B FAD 501 A 1 
HETATM 5 C C5B FAD . . . C 2 -6.082 17.998 8.786 1 106.4 ? C5B FAD 501 A 1 
HETATM 6 C C4B FAD . . . C 2 -6.168 17.233 10.105 1 112.79 ? C4B FAD 501 A 1 
HETATM 7 O O4B FAD . . . C 2 -7.491 16.72 10.294 1 116.73 ? O4B FAD 501 A 1 
HETATM 8 C C3B FAD . . . C 2 -5.22 16.038 10.165 1 117.92 ? C3B FAD 501 A 1 
HETATM 9 O O3B FAD . . . C 2 -4.364 16.113 11.313 1 122.95 ? O3B FAD 501 A 1 
HETATM 10 C C2B FAD . . . C 2 -6.115 14.812 10.193 1 116.8 ? C2B FAD 501 A 1 
HETATM 11 O O2B FAD . . . C 2 -5.597 13.729 10.976 1 110.88 ? O2B FAD 501 A 1 
HETATM 12 C C1B FAD . . . C 2 -7.415 15.367 10.756 1 119.51 ? C1B FAD 501 A 1 
HETATM 13 N N9A FAD . . . C 2 -8.576 14.55 10.338 1 126.26 ? N9A FAD 501 A 1 
HETATM 14 C C8A FAD . . . C 2 -9.01 14.354 9.081 1 132.51 ? C8A FAD 501 A 1 
HETATM 15 N N7A FAD . . . C 2 -10.096 13.538 9.062 1 133.69 ? N7A FAD 501 A 1 
HETATM 16 C C5A FAD . . . C 2 -10.366 13.2 10.334 1 130.01 ? C5A FAD 501 A 1 
HETATM 17 C C6A FAD . . . C 2 -11.372 12.366 11.035 1 128.89 ? C6A FAD 501 A 1 
HETATM 18 N N6A FAD . . . C 2 -12.334 11.716 10.342 1 132.43 ? N6A FAD 501 A 1 
HETATM 19 N N1A FAD . . . C 2 -11.293 12.283 12.384 1 125.71 ? N1A FAD 501 A 1 
HETATM 20 C C2A FAD . . . C 2 -10.34 12.931 13.09 1 125.57 ? C2A FAD 501 A 1 
HETATM 21 N N3A FAD . . . C 2 -9.4 13.699 12.511 1 124 ? N3A FAD 501 A 1 
HETATM 22 C C4A FAD . . . C 2 -9.359 13.871 11.17 1 126.94 ? C4A FAD 501 A 1 
HETATM 23 N N1 FAD . . . C 2 0.621 25.055 2.21 1 100.3 ? N1 FAD 501 A 1 
HETATM 24 C C2 FAD . . . C 2 1.481 26.117 2.118 1 98.25 ? C2 FAD 501 A 1 
HETATM 25 O O2 FAD . . . C 2 1.072 27.276 2.378 1 88.47 ? O2 FAD 501 A 1 
HETATM 26 N N3 FAD . . . C 2 2.773 25.964 1.753 1 102.38 ? N3 FAD 501 A 1 
HETATM 27 C C4 FAD . . . C 2 3.298 24.762 1.454 1 104.79 ? C4 FAD 501 A 1 
HETATM 28 O O4 FAD . . . C 2 4.497 24.644 1.112 1 105.71 ? O4 FAD 501 A 1 
HETATM 29 C C4X FAD . . . C 2 2.42 23.567 1.534 1 103.92 ? C4X FAD 501 A 1 
HETATM 30 N N5 FAD . . . C 2 2.894 22.344 1.244 1 102.85 ? N5 FAD 501 A 1 
HETATM 31 C C5X FAD . . . C 2 2.113 21.254 1.304 1 98.46 ? C5X FAD 501 A 1 
HETATM 32 C C6 FAD . . . C 2 2.7 20.039 0.983 1 96.93 ? C6 FAD 501 A 1 
HETATM 33 C C7 FAD . . . C 2 1.963 18.869 1.026 1 96.65 ? C7 FAD 501 A 1 
HETATM 34 C C7M FAD . . . C 2 2.649 17.574 0.667 1 94.31 ? C7M FAD 501 A 1 
HETATM 35 C C8 FAD . . . C 2 0.523 18.944 1.42 1 99.85 ? C8 FAD 501 A 1 
HETATM 36 C C8M FAD . . . C 2 -0.308 17.693 1.477 1 103.25 ? C8M FAD 501 A 1 
HETATM 37 C C9 FAD . . . C 2 -0.069 20.17 1.743 1 98.02 ? C9 FAD 501 A 1 
HETATM 38 C C9A FAD . . . C 2 0.673 21.356 1.707 1 97.4 ? C9A FAD 501 A 1 
HETATM 39 N N10 FAD . . . C 2 0.14 22.644 2.034 1 100.4 ? N10 FAD 501 A 1 
HETATM 40 C C10 FAD . . . C 2 1.005 23.774 1.939 1 101.29 ? C10 FAD 501 A 1 
HETATM 41 C C1' FAD . . . C 2 -1.274 22.856 2.402 1 106.08 ? C1' FAD 501 A 1 
HETATM 42 C C2' FAD . . . C 2 -1.632 22.708 3.88 1 109.44 ? C2' FAD 501 A 1 
HETATM 43 O O2' FAD . . . C 2 -1.09 21.485 4.4 1 105.77 ? O2' FAD 501 A 1 
HETATM 44 C C3' FAD . . . C 2 -3.164 22.752 4.05 1 115.3 ? C3' FAD 501 A 1 
HETATM 45 O O3' FAD . . . C 2 -3.743 23.675 3.108 1 112.36 ? O3' FAD 501 A 1 
HETATM 46 C C4' FAD . . . C 2 -3.68 23.15 5.443 1 120.45 ? C4' FAD 501 A 1 
HETATM 47 O O4' FAD . . . C 2 -3.076 22.342 6.463 1 122.79 ? O4' FAD 501 A 1 
HETATM 48 C C5' FAD . . . C 2 -5.218 23.054 5.465 1 123.44 ? C5' FAD 501 A 1 
HETATM 49 O O5' FAD . . . C 2 -5.814 23.149 6.76 1 121.55 ? O5' FAD 501 A 1 
HETATM 50 P P FAD . . . C 2 -7.063 22.215 7.192 1 117.81 ? P FAD 501 A 1 
HETATM 51 O O1P FAD . . . C 2 -7.327 22.501 8.652 1 127.11 ? O1P FAD 501 A 1 
HETATM 52 O O2P FAD . . . C 2 -8.21 22.292 6.207 1 108.2 ? O2P FAD 501 A 1 
HETATM 53 O O3P FAD . . . C 2 -6.414 20.746 7.081 1 110.18 ? O3P FAD 501 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           53 
#