data_8DJM
#
_model_server_result.job_id            P2vIfEEw4HAJHE59l2X0nw 
_model_server_result.datetime_utc      '2025-07-07 06:38:36' 
_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          8djm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":402}' 
#
_entry.id    8DJM 
#
_exptl.entry_id    8DJM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1229.312 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            Digitonin 
_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            8DJM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DJM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,M 
_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    ? 
_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
? 7 J N N 
? 7 L 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 D SG CYS 23 L CYS 42 1_555 D SG CYS 88 L CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf2 E SG CYS 22 H CYS 41 1_555 E SG CYS 96 H CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C56 H92 O29' 
_chem_comp.formula_weight    1229.312 
_chem_comp.id                AJP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Digitonin 
_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
C01 C02 AJP sing 1 n n 
C02 C85 AJP sing 2 n n 
C02 C03 AJP sing 3 n n 
C85 O84 AJP sing 4 n n 
C03 C04 AJP sing 5 n n 
O84 C05 AJP sing 6 n n 
C05 C04 AJP sing 7 n n 
C05 O09 AJP sing 8 n n 
C05 C06 AJP sing 9 n n 
O09 C08 AJP sing 10 n n 
C08 C10 AJP sing 11 n n 
C08 C07 AJP sing 12 n n 
C83 C06 AJP sing 13 n n 
C06 C07 AJP sing 14 n n 
C10 O82 AJP sing 15 n n 
C10 C11 AJP sing 16 n n 
C07 C12 AJP sing 17 n n 
C11 C12 AJP sing 18 n n 
C11 C16 AJP sing 19 n n 
C12 C81 AJP sing 20 n n 
C12 C13 AJP sing 21 n n 
C17 C16 AJP sing 22 n n 
C17 C18 AJP sing 23 n n 
C13 C14 AJP sing 24 n n 
C16 C15 AJP sing 25 n n 
C15 C14 AJP sing 26 n n 
C15 C20 AJP sing 27 n n 
C18 C19 AJP sing 28 n n 
C19 C20 AJP sing 29 n n 
C19 C24 AJP sing 30 n n 
C20 C21 AJP sing 31 n n 
C20 C80 AJP sing 32 n n 
C21 C22 AJP sing 33 n n 
C24 C23 AJP sing 34 n n 
O33 C32 AJP sing 35 n n 
C23 C22 AJP sing 36 n n 
C23 O25 AJP sing 37 n n 
C32 C30 AJP sing 38 n n 
C22 O79 AJP sing 39 n n 
C30 O31 AJP sing 40 n n 
C30 C29 AJP sing 41 n n 
O31 C26 AJP sing 42 n n 
C26 O25 AJP sing 43 n n 
C26 C27 AJP sing 44 n n 
C29 C28 AJP sing 45 n n 
C29 O34 AJP sing 46 n n 
C41 C39 AJP sing 47 n n 
C41 O42 AJP sing 48 n n 
C28 C27 AJP sing 49 n n 
C28 O77 AJP sing 50 n n 
C27 O78 AJP sing 51 n n 
O40 C39 AJP sing 52 n n 
O40 C35 AJP sing 53 n n 
C39 C38 AJP sing 54 n n 
O34 C35 AJP sing 55 n n 
C35 C36 AJP sing 56 n n 
C38 O43 AJP sing 57 n n 
C38 C37 AJP sing 58 n n 
C36 C37 AJP sing 59 n n 
C36 O54 AJP sing 60 n n 
C37 O44 AJP sing 61 n n 
O54 C55 AJP sing 62 n n 
O76 C56 AJP sing 63 n n 
O50 C49 AJP sing 64 n n 
O50 C45 AJP sing 65 n n 
C56 C55 AJP sing 66 n n 
C56 C57 AJP sing 67 n n 
O44 C45 AJP sing 68 n n 
C55 O60 AJP sing 69 n n 
C49 C48 AJP sing 70 n n 
C45 C46 AJP sing 71 n n 
O60 C59 AJP sing 72 n n 
O63 C58 AJP sing 73 n n 
O75 C66 AJP sing 74 n n 
O64 C57 AJP sing 75 n n 
O64 C65 AJP sing 76 n n 
C57 C58 AJP sing 77 n n 
O62 C61 AJP sing 78 n n 
C48 O51 AJP sing 79 n n 
C48 C47 AJP sing 80 n n 
C58 C59 AJP sing 81 n n 
C59 C61 AJP sing 82 n n 
C46 C47 AJP sing 83 n n 
C46 O53 AJP sing 84 n n 
C66 C65 AJP sing 85 n n 
C66 C67 AJP sing 86 n n 
C65 O70 AJP sing 87 n n 
C47 O52 AJP sing 88 n n 
O74 C67 AJP sing 89 n n 
C67 C68 AJP sing 90 n n 
O70 C69 AJP sing 91 n n 
C68 C69 AJP sing 92 n n 
C68 O73 AJP sing 93 n n 
C69 C71 AJP sing 94 n n 
C71 O72 AJP sing 95 n n 
C01 H1 AJP sing 96 n n 
C01 H2 AJP sing 97 n n 
C01 H3 AJP sing 98 n n 
C02 H4 AJP sing 99 n n 
C03 H5 AJP sing 100 n n 
C03 H6 AJP sing 101 n n 
C04 H7 AJP sing 102 n n 
C04 H8 AJP sing 103 n n 
C06 H9 AJP sing 104 n n 
C07 H10 AJP sing 105 n n 
C08 H11 AJP sing 106 n n 
C10 H12 AJP sing 107 n n 
C11 H13 AJP sing 108 n n 
C13 H14 AJP sing 109 n n 
C13 H15 AJP sing 110 n n 
C14 H16 AJP sing 111 n n 
C14 H17 AJP sing 112 n n 
C15 H18 AJP sing 113 n n 
C16 H19 AJP sing 114 n n 
C17 H20 AJP sing 115 n n 
C17 H21 AJP sing 116 n n 
C18 H22 AJP sing 117 n n 
C18 H23 AJP sing 118 n n 
C19 H24 AJP sing 119 n n 
C21 H25 AJP sing 120 n n 
C21 H26 AJP sing 121 n n 
C22 H27 AJP sing 122 n n 
C23 H28 AJP sing 123 n n 
C24 H29 AJP sing 124 n n 
C24 H30 AJP sing 125 n n 
C26 H31 AJP sing 126 n n 
C27 H32 AJP sing 127 n n 
C28 H33 AJP sing 128 n n 
C29 H34 AJP sing 129 n n 
C30 H35 AJP sing 130 n n 
C32 H36 AJP sing 131 n n 
C32 H37 AJP sing 132 n n 
O33 H38 AJP sing 133 n n 
C35 H39 AJP sing 134 n n 
C36 H40 AJP sing 135 n n 
C37 H41 AJP sing 136 n n 
C38 H42 AJP sing 137 n n 
C39 H43 AJP sing 138 n n 
C41 H44 AJP sing 139 n n 
C41 H45 AJP sing 140 n n 
O42 H46 AJP sing 141 n n 
O43 H47 AJP sing 142 n n 
C45 H48 AJP sing 143 n n 
C46 H49 AJP sing 144 n n 
C47 H50 AJP sing 145 n n 
C48 H51 AJP sing 146 n n 
C49 H52 AJP sing 147 n n 
C49 H53 AJP sing 148 n n 
O51 H54 AJP sing 149 n n 
O52 H55 AJP sing 150 n n 
O53 H56 AJP sing 151 n n 
C55 H57 AJP sing 152 n n 
C56 H58 AJP sing 153 n n 
C57 H59 AJP sing 154 n n 
C58 H60 AJP sing 155 n n 
C59 H61 AJP sing 156 n n 
C61 H62 AJP sing 157 n n 
C61 H63 AJP sing 158 n n 
O62 H64 AJP sing 159 n n 
O63 H65 AJP sing 160 n n 
C65 H66 AJP sing 161 n n 
C66 H67 AJP sing 162 n n 
C67 H68 AJP sing 163 n n 
C68 H69 AJP sing 164 n n 
C69 H70 AJP sing 165 n n 
C71 H71 AJP sing 166 n n 
C71 H72 AJP sing 167 n n 
O72 H73 AJP sing 168 n n 
O73 H74 AJP sing 169 n n 
O74 H75 AJP sing 170 n n 
O75 H76 AJP sing 171 n n 
O76 H77 AJP sing 172 n n 
O77 H78 AJP sing 173 n n 
O78 H79 AJP sing 174 n n 
O79 H80 AJP sing 175 n n 
C80 H81 AJP sing 176 n n 
C80 H82 AJP sing 177 n n 
C80 H83 AJP sing 178 n n 
C81 H84 AJP sing 179 n n 
C81 H85 AJP sing 180 n n 
C81 H86 AJP sing 181 n n 
O82 H87 AJP sing 182 n n 
C83 H88 AJP sing 183 n n 
C83 H89 AJP sing 184 n n 
C83 H90 AJP sing 185 n n 
C85 H91 AJP sing 186 n n 
C85 H92 AJP sing 187 n n 
#
_atom_sites.entry_id                     8DJM 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
F 6 Y01 A 1 401 1 Y01 Y01 . 
G 6 Y01 A 1 402 2 Y01 Y01 . 
H 6 Y01 A 1 403 3 Y01 Y01 . 
I 6 Y01 A 1 404 5 Y01 Y01 . 
J 7 AJP A 1 405 7 AJP AJP . 
K 6 Y01 B 1 401 4 Y01 Y01 . 
L 7 AJP B 1 402 6 AJP AJP . 
M 6 Y01 B 1 403 8 Y01 Y01 . 
#
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 C C01 AJP . . . L 7 126.519 135.715 124.216 1 73.93 ? C01 AJP 402 B 1 
HETATM 2 C C02 AJP . . . L 7 125.475 134.605 122.985 1 73.59 ? C02 AJP 402 B 1 
HETATM 3 C C03 AJP . . . L 7 124.545 134.288 123.488 1 73.07 ? C03 AJP 402 B 1 
HETATM 4 C C04 AJP . . . L 7 123.516 133.719 122.583 1 72.14 ? C04 AJP 402 B 1 
HETATM 5 C C05 AJP . . . L 7 123.346 134.321 121.541 1 70.94 ? C05 AJP 402 B 1 
HETATM 6 C C06 AJP . . . L 7 122.407 133.644 120.442 1 69.56 ? C06 AJP 402 B 1 
HETATM 7 C C07 AJP . . . L 7 121.705 134.753 119.909 1 67.67 ? C07 AJP 402 B 1 
HETATM 8 C C08 AJP . . . L 7 121.641 135.899 121.557 1 67.74 ? C08 AJP 402 B 1 
HETATM 9 O O09 AJP . . . L 7 122.556 135.888 121.954 1 69.43 ? O09 AJP 402 B 1 
HETATM 10 C C10 AJP . . . L 7 121.112 137.035 121.122 1 66.39 ? C10 AJP 402 B 1 
HETATM 11 C C11 AJP . . . L 7 120.692 136.73 119.482 1 64.49 ? C11 AJP 402 B 1 
HETATM 12 C C12 AJP . . . L 7 120.606 134.916 119.414 1 65.58 ? C12 AJP 402 B 1 
HETATM 13 C C13 AJP . . . L 7 120.246 134.375 118.134 1 64.11 ? C13 AJP 402 B 1 
HETATM 14 C C14 AJP . . . L 7 118.956 134.994 117.495 1 62.34 ? C14 AJP 402 B 1 
HETATM 15 C C15 AJP . . . L 7 119.042 136.635 117.366 1 60.33 ? C15 AJP 402 B 1 
HETATM 16 C C16 AJP . . . L 7 119.699 137.516 118.758 1 61.57 ? C16 AJP 402 B 1 
HETATM 17 C C17 AJP . . . L 7 120.223 138.785 118.246 1 59.9 ? C17 AJP 402 B 1 
HETATM 18 C C18 AJP . . . L 7 119.075 139.614 117.506 1 57.96 ? C18 AJP 402 B 1 
HETATM 19 C C19 AJP . . . L 7 118.216 138.727 116.409 1 55.65 ? C19 AJP 402 B 1 
HETATM 20 C C20 AJP . . . L 7 117.788 137.288 116.936 1 56.97 ? C20 AJP 402 B 1 
HETATM 21 C C21 AJP . . . L 7 117.006 136.511 115.822 1 54.38 ? C21 AJP 402 B 1 
HETATM 22 C C22 AJP . . . L 7 115.789 137.284 115.221 1 51.23 ? C22 AJP 402 B 1 
HETATM 23 C C23 AJP . . . L 7 115.967 138.83 114.993 1 48.25 ? C23 AJP 402 B 1 
HETATM 24 C C24 AJP . . . L 7 117.086 139.579 115.863 1 51.74 ? C24 AJP 402 B 1 
HETATM 25 O O25 AJP . . . L 7 114.804 139.456 115.372 1 39.32 ? O25 AJP 402 B 1 
HETATM 26 C C26 AJP . . . L 7 113.75 139.447 114.46 1 31.9 ? C26 AJP 402 B 1 
HETATM 27 C C27 AJP . . . L 7 113.62 140.869 113.909 1 29.18 ? C27 AJP 402 B 1 
HETATM 28 C C28 AJP . . . L 7 112.272 141.14 113.347 1 25.79 ? C28 AJP 402 B 1 
HETATM 29 C C29 AJP . . . L 7 111.217 140.889 114.334 1 23.77 ? C29 AJP 402 B 1 
HETATM 30 C C30 AJP . . . L 7 111.24 139.445 114.859 1 25.54 ? C30 AJP 402 B 1 
HETATM 31 O O31 AJP . . . L 7 112.591 138.943 115.213 1 29 ? O31 AJP 402 B 1 
HETATM 32 C C32 AJP . . . L 7 110.415 139.344 116.112 1 26.31 ? C32 AJP 402 B 1 
HETATM 33 O O33 AJP . . . L 7 109.127 139.874 115.916 1 26.38 ? O33 AJP 402 B 1 
HETATM 34 O O34 AJP . . . L 7 109.91 141.148 113.697 1 22.59 ? O34 AJP 402 B 1 
HETATM 35 O O77 AJP . . . L 7 112.207 142.546 112.92 1 26.23 ? O77 AJP 402 B 1 
HETATM 36 O O78 AJP . . . L 7 114.601 141.046 112.876 1 29.26 ? O78 AJP 402 B 1 
HETATM 37 O O79 AJP . . . L 7 115.511 136.688 114.005 1 51.77 ? O79 AJP 402 B 1 
HETATM 38 C C80 AJP . . . L 7 116.798 137.393 118.128 1 57.37 ? C80 AJP 402 B 1 
HETATM 39 C C81 AJP . . . L 7 119.398 134.568 120.367 1 65.9 ? C81 AJP 402 B 1 
HETATM 40 O O82 AJP . . . L 7 119.986 137.41 121.868 1 66.67 ? O82 AJP 402 B 1 
HETATM 41 C C83 AJP . . . L 7 121.576 132.355 120.851 1 69.93 ? C83 AJP 402 B 1 
HETATM 42 O O84 AJP . . . L 7 124.25 134.598 121.086 1 72.3 ? O84 AJP 402 B 1 
HETATM 43 C C85 AJP . . . L 7 125.303 135.222 121.964 1 73.29 ? C85 AJP 402 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           43 
#