data_159D
#
_model_server_result.job_id            1OOLoV9VDhg8NYLg-XQIdQ 
_model_server_result.datetime_utc      '2025-08-20 22:21:00' 
_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          159d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":9}' 
#
_entry.id    159D 
#
_exptl.entry_id    159D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              481.508 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DISTAMYCIN A' 
_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            159D 
_cell.length_a            27.93 
_cell.length_b            27.93 
_cell.length_c            57.67 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 159D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        91 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 2 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_555 x,-y,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 0 28.835 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 A OP2 DC 6 A DC 6 1_555 C MG MG . A MG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? 
metalc ? metalc2 C MG MG . A MG 10 1_555 D O HOH . A HOH 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc3 C MG MG . A MG 10 1_555 D O HOH . A HOH 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc4 C MG MG . A MG 10 1_555 D O HOH . A HOH 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
#
_chem_comp.formula           'C22 H27 N9 O4' 
_chem_comp.formula_weight    481.508 
_chem_comp.id                DMY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DISTAMYCIN A' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DISTAMYCIN;STALLIMYCIN 
#
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
C1 O1 DMY doub 73 n n 
C1 N1 DMY sing 74 n n 
C1 H1 DMY sing 75 n n 
N1 C2 DMY sing 76 n n 
N1 HN1 DMY sing 77 n n 
C2 C3 DMY sing 78 n y 
C2 C5 DMY doub 79 n y 
C3 C4 DMY doub 80 n y 
C3 H3 DMY sing 81 n n 
C4 N2 DMY sing 82 n y 
C4 C7 DMY sing 83 n n 
N2 C5 DMY sing 84 n y 
N2 C6 DMY sing 85 n n 
C5 H5 DMY sing 86 n n 
C6 H61 DMY sing 87 n n 
C6 H62 DMY sing 88 n n 
C6 H63 DMY sing 89 n n 
C7 O2 DMY doub 90 n n 
C7 N3 DMY sing 91 n n 
N3 C8 DMY sing 92 n n 
N3 HN3 DMY sing 93 n n 
C8 C9 DMY sing 94 n y 
C8 C11 DMY doub 95 n y 
C9 C10 DMY doub 96 n y 
C9 H9 DMY sing 97 n n 
C10 N4 DMY sing 98 n y 
C10 C13 DMY sing 99 n n 
N4 C11 DMY sing 100 n y 
N4 C12 DMY sing 101 n n 
C11 H11 DMY sing 102 n n 
C12 H121 DMY sing 103 n n 
C12 H122 DMY sing 104 n n 
C12 H123 DMY sing 105 n n 
C13 O3 DMY doub 106 n n 
C13 N5 DMY sing 107 n n 
N5 C14 DMY sing 108 n n 
N5 HN5 DMY sing 109 n n 
C14 C15 DMY sing 110 n y 
C14 C17 DMY doub 111 n y 
C15 C16 DMY doub 112 n y 
C15 H15 DMY sing 113 n n 
C16 N6 DMY sing 114 n y 
C16 C19 DMY sing 115 n n 
N6 C17 DMY sing 116 n y 
N6 C18 DMY sing 117 n n 
C17 H17 DMY sing 118 n n 
C18 H181 DMY sing 119 n n 
C18 H182 DMY sing 120 n n 
C18 H183 DMY sing 121 n n 
C19 O4 DMY doub 122 n n 
C19 N7 DMY sing 123 n n 
N7 C20 DMY sing 124 n n 
N7 HN7 DMY sing 125 n n 
C20 C21 DMY sing 126 n n 
C20 H201 DMY sing 127 n n 
C20 H202 DMY sing 128 n n 
C21 C22 DMY sing 129 n n 
C21 H211 DMY sing 130 n n 
C21 H212 DMY sing 131 n n 
C22 N8 DMY doub 132 n n 
C22 N9 DMY sing 133 n n 
N8 HN8 DMY sing 134 n n 
N9 HN91 DMY sing 135 n n 
N9 HN92 DMY sing 136 n n 
#
_atom_sites.entry_id                     159D 
_atom_sites.fract_transf_matrix[1][1]    0.035804 
_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]    0.035804 
_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]    0.01734 
_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
B 2 DMY A 1 9 9 DMY DMY . 
C 3 MG A 1 10 10 MG MG . 
D 4 HOH A 1 11 11 HOH HOH . 
D 4 HOH A 2 12 12 HOH HOH . 
D 4 HOH A 3 13 13 HOH HOH . 
D 4 HOH A 4 14 14 HOH HOH . 
D 4 HOH A 5 15 15 HOH HOH . 
D 4 HOH A 6 16 16 HOH HOH . 
D 4 HOH A 7 17 17 HOH HOH . 
D 4 HOH A 8 18 18 HOH HOH . 
D 4 HOH A 9 19 19 HOH HOH . 
D 4 HOH A 10 20 20 HOH HOH . 
D 4 HOH A 11 21 21 HOH HOH . 
D 4 HOH A 12 22 22 HOH HOH . 
D 4 HOH A 13 23 23 HOH HOH . 
D 4 HOH A 14 24 24 HOH HOH . 
D 4 HOH A 15 25 25 HOH HOH . 
D 4 HOH A 16 26 26 HOH HOH . 
D 4 HOH A 17 27 27 HOH HOH . 
D 4 HOH A 18 28 28 HOH HOH . 
D 4 HOH A 19 29 29 HOH HOH . 
D 4 HOH A 20 30 30 HOH HOH . 
D 4 HOH A 21 31 31 HOH HOH . 
D 4 HOH A 22 32 32 HOH HOH . 
D 4 HOH A 23 33 33 HOH HOH . 
D 4 HOH A 24 34 34 HOH HOH . 
D 4 HOH A 25 35 35 HOH HOH . 
D 4 HOH A 26 36 36 HOH HOH . 
D 4 HOH A 27 37 37 HOH HOH . 
D 4 HOH A 28 38 38 HOH HOH . 
D 4 HOH A 29 39 39 HOH HOH . 
D 4 HOH A 30 40 40 HOH HOH . 
D 4 HOH A 31 41 41 HOH HOH . 
D 4 HOH A 32 42 42 HOH HOH . 
D 4 HOH A 33 43 43 HOH HOH . 
D 4 HOH A 34 44 44 HOH HOH . 
D 4 HOH A 35 45 45 HOH HOH . 
D 4 HOH A 36 46 46 HOH HOH . 
D 4 HOH A 37 47 47 HOH HOH . 
D 4 HOH A 38 48 48 HOH HOH . 
D 4 HOH A 39 49 49 HOH HOH . 
D 4 HOH A 40 50 50 HOH HOH . 
D 4 HOH A 41 51 51 HOH HOH . 
D 4 HOH A 42 52 52 HOH HOH . 
D 4 HOH A 43 53 53 HOH HOH . 
D 4 HOH A 44 54 54 HOH HOH . 
D 4 HOH A 45 55 55 HOH HOH . 
D 4 HOH A 46 56 56 HOH HOH . 
D 4 HOH A 47 57 57 HOH HOH . 
D 4 HOH A 48 58 58 HOH HOH . 
D 4 HOH A 49 59 59 HOH HOH . 
D 4 HOH A 50 60 60 HOH HOH . 
D 4 HOH A 51 61 61 HOH HOH . 
D 4 HOH A 52 62 62 HOH HOH . 
D 4 HOH A 53 63 63 HOH HOH . 
D 4 HOH A 54 64 64 HOH HOH . 
D 4 HOH A 55 65 65 HOH HOH . 
D 4 HOH A 56 66 66 HOH HOH . 
D 4 HOH A 57 67 67 HOH HOH . 
D 4 HOH A 58 68 68 HOH HOH . 
D 4 HOH A 59 69 69 HOH HOH . 
D 4 HOH A 60 70 70 HOH HOH . 
D 4 HOH A 61 71 71 HOH HOH . 
D 4 HOH A 62 72 72 HOH HOH . 
D 4 HOH A 63 73 73 HOH HOH . 
D 4 HOH A 64 74 74 HOH HOH . 
D 4 HOH A 65 75 75 HOH HOH . 
#
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 C1 DMY . . . B 2 10.092 -3.209 19.679 1 9.07 ? C1 DMY 9 A 1 
HETATM 2 O O1 DMY . . . B 2 10.67 -3.523 20.725 1 9.29 ? O1 DMY 9 A 1 
HETATM 3 N N1 DMY . . . B 2 10.487 -2.391 18.677 1 8.68 ? N1 DMY 9 A 1 
HETATM 4 C C2 DMY . . . B 2 11.681 -1.712 18.633 1 8.39 ? C2 DMY 9 A 1 
HETATM 5 C C3 DMY . . . B 2 12.061 -0.843 17.609 1 8.18 ? C3 DMY 9 A 1 
HETATM 6 C C4 DMY . . . B 2 13.414 -0.532 17.764 1 8.26 ? C4 DMY 9 A 1 
HETATM 7 N N2 DMY . . . B 2 13.852 -1.177 18.943 1 8.43 ? N2 DMY 9 A 1 
HETATM 8 C C5 DMY . . . B 2 12.829 -1.851 19.437 1 8.48 ? C5 DMY 9 A 1 
HETATM 9 C C6 DMY . . . B 2 15.193 -0.985 19.634 1 8.45 ? C6 DMY 9 A 1 
HETATM 10 C C7 DMY . . . B 2 14.173 0.285 16.893 1 8.2 ? C7 DMY 9 A 1 
HETATM 11 O O2 DMY . . . B 2 15.398 0.404 17.006 1 8.22 ? O2 DMY 9 A 1 
HETATM 12 N N3 DMY . . . B 2 13.561 1.059 15.969 1 8.05 ? N3 DMY 9 A 1 
HETATM 13 C C8 DMY . . . B 2 14.176 1.793 14.986 1 7.88 ? C8 DMY 9 A 1 
HETATM 14 C C9 DMY . . . B 2 13.529 2.676 14.13 1 7.75 ? C9 DMY 9 A 1 
HETATM 15 C C10 DMY . . . B 2 14.449 3.154 13.187 1 7.84 ? C10 DMY 9 A 1 
HETATM 16 N N4 DMY . . . B 2 15.685 2.59 13.515 1 7.76 ? N4 DMY 9 A 1 
HETATM 17 C C11 DMY . . . B 2 15.502 1.774 14.531 1 7.97 ? C11 DMY 9 A 1 
HETATM 18 C C12 DMY . . . B 2 17.033 2.837 12.837 1 8.19 ? C12 DMY 9 A 1 
HETATM 19 C C13 DMY . . . B 2 14.105 3.921 12.05 1 7.85 ? C13 DMY 9 A 1 
HETATM 20 O O3 DMY . . . B 2 14.891 4.139 11.126 1 7.92 ? O3 DMY 9 A 1 
HETATM 21 N N5 DMY . . . B 2 12.942 4.575 12.026 1 7.95 ? N5 DMY 9 A 1 
HETATM 22 C C14 DMY . . . B 2 12.472 5.364 11.016 1 8.16 ? C14 DMY 9 A 1 
HETATM 23 C C15 DMY . . . B 2 11.338 6.161 11.094 1 8.38 ? C15 DMY 9 A 1 
HETATM 24 C C16 DMY . . . B 2 11.053 6.635 9.8 1 8.72 ? C16 DMY 9 A 1 
HETATM 25 N N6 DMY . . . B 2 12.146 6.29 8.982 1 8.81 ? N6 DMY 9 A 1 
HETATM 26 C C17 DMY . . . B 2 12.919 5.492 9.686 1 8.52 ? C17 DMY 9 A 1 
HETATM 27 C C18 DMY . . . B 2 12.303 6.583 7.482 1 8.8 ? C18 DMY 9 A 1 
HETATM 28 C C19 DMY . . . B 2 9.939 7.451 9.448 1 8.88 ? C19 DMY 9 A 1 
HETATM 29 O O4 DMY . . . B 2 9.599 7.686 8.267 1 8.99 ? O4 DMY 9 A 1 
HETATM 30 N N7 DMY . . . B 2 9.253 8.108 10.393 1 8.6 ? N7 DMY 9 A 1 
HETATM 31 C C20 DMY . . . B 2 8.123 8.969 10.117 1 8.68 ? C20 DMY 9 A 1 
HETATM 32 C C21 DMY . . . B 2 6.823 8.218 9.962 1 8.49 ? C21 DMY 9 A 1 
HETATM 33 C C22 DMY . . . B 2 5.723 9.207 9.658 1 8.64 ? C22 DMY 9 A 1 
HETATM 34 N N8 DMY . . . B 2 5.624 9.665 8.416 1 8.43 ? N8 DMY 9 A 1 
HETATM 35 N N9 DMY . . . B 2 4.992 9.724 10.644 1 8.52 ? N9 DMY 9 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           35 
#