data_306D
#
_model_server_result.job_id            7HOa9vgIxidPMBpIbHX-8Q 
_model_server_result.datetime_utc      '2025-08-31 16:29:41' 
_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          306d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":9}' 
#
_entry.id    306D 
#
_exptl.entry_id    306D 
_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            306D 
_cell.length_a            28.03 
_cell.length_b            28.03 
_cell.length_c            58.04 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 306D 
_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 29.02 
#
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc2 C MG MG . A MG 10 1_555 D O HOH . A HOH 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc3 C MG MG . A MG 10 1_555 D O HOH . A HOH 12 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc4 C MG MG . A MG 10 1_555 D O HOH . A HOH 13 4_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc5 C MG MG . A MG 10 1_555 D O HOH . A HOH 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc6 C MG MG . A MG 10 1_555 D O HOH . A HOH 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
hydrog WATSON-CRICK hydrog1 A N3 DT 4 A DT 4 1_555 A N1 DA 5 A DA 5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A O4 DT 4 A DT 4 1_555 A N6 DA 5 A DA 5 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N1 DA 5 A DA 5 1_555 A N3 DT 4 A DT 4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N6 DA 5 A DA 5 1_555 A O4 DT 4 A DT 4 6_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 111 n n 
C1 N1 DMY sing 112 n n 
C1 H1 DMY sing 113 n n 
N1 C2 DMY sing 114 n n 
N1 HN1 DMY sing 115 n n 
C2 C3 DMY sing 116 n y 
C2 C5 DMY doub 117 n y 
C3 C4 DMY doub 118 n y 
C3 H3 DMY sing 119 n n 
C4 N2 DMY sing 120 n y 
C4 C7 DMY sing 121 n n 
N2 C5 DMY sing 122 n y 
N2 C6 DMY sing 123 n n 
C5 H5 DMY sing 124 n n 
C6 H61 DMY sing 125 n n 
C6 H62 DMY sing 126 n n 
C6 H63 DMY sing 127 n n 
C7 O2 DMY doub 128 n n 
C7 N3 DMY sing 129 n n 
N3 C8 DMY sing 130 n n 
N3 HN3 DMY sing 131 n n 
C8 C9 DMY sing 132 n y 
C8 C11 DMY doub 133 n y 
C9 C10 DMY doub 134 n y 
C9 H9 DMY sing 135 n n 
C10 N4 DMY sing 136 n y 
C10 C13 DMY sing 137 n n 
N4 C11 DMY sing 138 n y 
N4 C12 DMY sing 139 n n 
C11 H11 DMY sing 140 n n 
C12 H121 DMY sing 141 n n 
C12 H122 DMY sing 142 n n 
C12 H123 DMY sing 143 n n 
C13 O3 DMY doub 144 n n 
C13 N5 DMY sing 145 n n 
N5 C14 DMY sing 146 n n 
N5 HN5 DMY sing 147 n n 
C14 C15 DMY sing 148 n y 
C14 C17 DMY doub 149 n y 
C15 C16 DMY doub 150 n y 
C15 H15 DMY sing 151 n n 
C16 N6 DMY sing 152 n y 
C16 C19 DMY sing 153 n n 
N6 C17 DMY sing 154 n y 
N6 C18 DMY sing 155 n n 
C17 H17 DMY sing 156 n n 
C18 H181 DMY sing 157 n n 
C18 H182 DMY sing 158 n n 
C18 H183 DMY sing 159 n n 
C19 O4 DMY doub 160 n n 
C19 N7 DMY sing 161 n n 
N7 C20 DMY sing 162 n n 
N7 HN7 DMY sing 163 n n 
C20 C21 DMY sing 164 n n 
C20 H201 DMY sing 165 n n 
C20 H202 DMY sing 166 n n 
C21 C22 DMY sing 167 n n 
C21 H211 DMY sing 168 n n 
C21 H212 DMY sing 169 n n 
C22 N8 DMY doub 170 n n 
C22 N9 DMY sing 171 n n 
N8 HN8 DMY sing 172 n n 
N9 HN91 DMY sing 173 n n 
N9 HN92 DMY sing 174 n n 
#
_atom_sites.entry_id                     306D 
_atom_sites.fract_transf_matrix[1][1]    0.035676 
_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]    0.035676 
_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]    0.017229 
_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 . 
#
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 10.42 -3.234 19.861 1 11.08 ? C1 DMY 9 A 1 
HETATM 2 O O1 DMY . . . B 2 11.017 -3.517 20.901 1 11.76 ? O1 DMY 9 A 1 
HETATM 3 N N1 DMY . . . B 2 10.827 -2.445 18.853 1 10.68 ? N1 DMY 9 A 1 
HETATM 4 C C2 DMY . . . B 2 12.003 -1.799 18.756 1 10.26 ? C2 DMY 9 A 1 
HETATM 5 C C3 DMY . . . B 2 12.369 -0.979 17.709 1 9.91 ? C3 DMY 9 A 1 
HETATM 6 C C4 DMY . . . B 2 13.66 -0.518 17.908 1 9.82 ? C4 DMY 9 A 1 
HETATM 7 N N2 DMY . . . B 2 14.119 -1.056 19.067 1 9.93 ? N2 DMY 9 A 1 
HETATM 8 C C5 DMY . . . B 2 13.157 -1.836 19.601 1 10.18 ? C5 DMY 9 A 1 
HETATM 9 C C6 DMY . . . B 2 15.486 -0.879 19.739 1 9.95 ? C6 DMY 9 A 1 
HETATM 10 C C7 DMY . . . B 2 14.462 0.284 17.014 1 9.59 ? C7 DMY 9 A 1 
HETATM 11 O O2 DMY . . . B 2 15.697 0.25 17.05 1 9.63 ? O2 DMY 9 A 1 
HETATM 12 N N3 DMY . . . B 2 13.736 1.076 16.17 1 9.37 ? N3 DMY 9 A 1 
HETATM 13 C C8 DMY . . . B 2 14.288 1.753 15.116 1 9.09 ? C8 DMY 9 A 1 
HETATM 14 C C9 DMY . . . B 2 13.633 2.589 14.217 1 8.87 ? C9 DMY 9 A 1 
HETATM 15 C C10 DMY . . . B 2 14.529 3.114 13.301 1 8.81 ? C10 DMY 9 A 1 
HETATM 16 N N4 DMY . . . B 2 15.748 2.603 13.596 1 8.88 ? N4 DMY 9 A 1 
HETATM 17 C C11 DMY . . . B 2 15.64 1.796 14.657 1 9.02 ? C11 DMY 9 A 1 
HETATM 18 C C12 DMY . . . B 2 17.104 2.782 12.916 1 8.88 ? C12 DMY 9 A 1 
HETATM 19 C C13 DMY . . . B 2 14.259 3.942 12.139 1 8.72 ? C13 DMY 9 A 1 
HETATM 20 O O3 DMY . . . B 2 15.039 4.008 11.185 1 8.35 ? O3 DMY 9 A 1 
HETATM 21 N N5 DMY . . . B 2 13.093 4.637 12.213 1 8.82 ? N5 DMY 9 A 1 
HETATM 22 C C14 DMY . . . B 2 12.577 5.374 11.186 1 8.91 ? C14 DMY 9 A 1 
HETATM 23 C C15 DMY . . . B 2 11.405 6.105 11.204 1 9.02 ? C15 DMY 9 A 1 
HETATM 24 C C16 DMY . . . B 2 11.21 6.7 9.961 1 9.23 ? C16 DMY 9 A 1 
HETATM 25 N N6 DMY . . . B 2 12.239 6.337 9.155 1 8.98 ? N6 DMY 9 A 1 
HETATM 26 C C17 DMY . . . B 2 13.075 5.557 9.85 1 9.11 ? C17 DMY 9 A 1 
HETATM 27 C C18 DMY . . . B 2 12.437 6.6 7.638 1 9.11 ? C18 DMY 9 A 1 
HETATM 28 C C19 DMY . . . B 2 10.093 7.5 9.518 1 9.38 ? C19 DMY 9 A 1 
HETATM 29 O O4 DMY . . . B 2 9.727 7.613 8.334 1 9.46 ? O4 DMY 9 A 1 
HETATM 30 N N7 DMY . . . B 2 9.481 8.156 10.512 1 9.38 ? N7 DMY 9 A 1 
HETATM 31 C C20 DMY . . . B 2 8.358 9.051 10.27 1 9.47 ? C20 DMY 9 A 1 
HETATM 32 C C21 DMY . . . B 2 7.018 8.335 10.184 1 9.5 ? C21 DMY 9 A 1 
HETATM 33 C C22 DMY . . . B 2 5.904 9.322 9.845 1 9.64 ? C22 DMY 9 A 1 
HETATM 34 N N8 DMY . . . B 2 5.72 9.708 8.575 1 9.49 ? N8 DMY 9 A 1 
HETATM 35 N N9 DMY . . . B 2 5.131 9.804 10.825 1 9.46 ? N9 DMY 9 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           4 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           369 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           35 
#