data_5MRA
#
_model_server_result.job_id            1EFM7rgLPBwgR-Hycrs1uQ 
_model_server_result.datetime_utc      '2024-11-05 01:28:23' 
_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          5mra 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":204}' 
#
_entry.id    5MRA 
#
_exptl.entry_id    5MRA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              543.519 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            DOXORUBICIN 
_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            5MRA 
_cell.length_a            92.229 
_cell.length_b            104.831 
_cell.length_c            113.273 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MRA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,J,K 1 1 
C,D,L,M,N,O,P,Q 2 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             K 
_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 OD1 ASP 52 A ASP 83 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc2 A OD2 ASP 54 A ASP 85 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? 
metalc ? metalc3 A O THR 58 A THR 89 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc4 A OD2 ASP 84 A ASP 115 1_555 E MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc5 B OG SER 56 B SER 87 1_555 H MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? 
metalc ? metalc6 B O THR 58 B THR 89 1_555 H MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc7 B OD1 ASP 82 B ASP 113 1_555 I MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? 
metalc ? metalc8 C O ALA 12 C ALA 43 1_555 L MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? 
metalc ? metalc9 C OD1 ASP 15 C ASP 46 1_555 L MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? 
metalc ? metalc10 C O GLN 17 C GLN 48 1_555 L MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
metalc ? metalc11 C OD1 ASP 52 C ASP 83 1_555 M MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
metalc ? metalc12 C O ARG 53 C ARG 84 1_555 M MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc13 C OG1 THR 58 C THR 89 1_555 M MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? 
metalc ? metalc14 C OE2 GLU 93 C GLU 124 1_555 N MG MG . C MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc15 L MG MG . C MG 201 1_555 Q O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? 
metalc ? metalc16 D OD1 ASP 54 D ASP 85 1_555 P MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc17 D O THR 58 D THR 89 1_555 P MG MG . D MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc18 D OD1 ASP 84 D ASP 115 1_555 O MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? 
metalc ? metalc19 D OE1 GLU 93 D GLU 124 1_555 O MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
#
_chem_comp.formula           'C27 H29 N O11' 
_chem_comp.formula_weight    543.519 
_chem_comp.id                DM2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              DOXORUBICIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ADRIAMYCIN 
#
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 C2 DM2 doub 83 n y 
C1 C20 DM2 sing 84 n y 
C1 H1 DM2 sing 85 n n 
C2 C3 DM2 sing 86 n y 
C2 H2 DM2 sing 87 n n 
C3 C4 DM2 doub 88 n y 
C3 H3 DM2 sing 89 n n 
C4 O4 DM2 sing 90 n n 
C4 C5 DM2 sing 91 n y 
O4 C21 DM2 sing 92 n n 
C5 C6 DM2 sing 93 n n 
C5 C20 DM2 doub 94 n y 
C6 O6 DM2 doub 95 n n 
C6 C7 DM2 sing 96 n n 
C7 C8 DM2 doub 97 n y 
C7 C18 DM2 sing 98 n y 
C8 O8 DM2 sing 99 n n 
C8 C9 DM2 sing 100 n y 
O8 HO8 DM2 sing 101 n n 
C9 C10 DM2 sing 102 n n 
C9 C16 DM2 doub 103 n y 
C10 O10 DM2 sing 104 n n 
C10 C11 DM2 sing 105 n n 
C10 H10 DM2 sing 106 n n 
O10 C1' DM2 sing 107 n n 
C11 C12 DM2 sing 108 n n 
C11 H111 DM2 sing 109 n n 
C11 H112 DM2 sing 110 n n 
C12 O12 DM2 sing 111 n n 
C12 C13 DM2 sing 112 n n 
C12 C15 DM2 sing 113 n n 
O12 HO12 DM2 sing 114 n n 
C13 O13 DM2 doub 115 n n 
C13 C14 DM2 sing 116 n n 
C14 O14 DM2 sing 117 n n 
C14 H141 DM2 sing 118 n n 
C14 H142 DM2 sing 119 n n 
O14 HO14 DM2 sing 120 n n 
C15 C16 DM2 sing 121 n n 
C15 H151 DM2 sing 122 n n 
C15 H152 DM2 sing 123 n n 
C16 C17 DM2 sing 124 n y 
C17 O17 DM2 sing 125 n n 
C17 C18 DM2 doub 126 n y 
O17 HO17 DM2 sing 127 n n 
C18 C19 DM2 sing 128 n n 
C19 O19 DM2 doub 129 n n 
C19 C20 DM2 sing 130 n n 
C21 H211 DM2 sing 131 n n 
C21 H212 DM2 sing 132 n n 
C21 H213 DM2 sing 133 n n 
C1' C2' DM2 sing 134 n n 
C1' O5' DM2 sing 135 n n 
C1' H1' DM2 sing 136 n n 
C2' C3' DM2 sing 137 n n 
C2' "H2'1" DM2 sing 138 n n 
C2' "H2'2" DM2 sing 139 n n 
C3' N3' DM2 sing 140 n n 
C3' C4' DM2 sing 141 n n 
C3' H3' DM2 sing 142 n n 
N3' "HN'1" DM2 sing 143 n n 
N3' "HN'2" DM2 sing 144 n n 
C4' O4' DM2 sing 145 n n 
C4' C5' DM2 sing 146 n n 
C4' H4' DM2 sing 147 n n 
O4' HO4' DM2 sing 148 n n 
C5' O5' DM2 sing 149 n n 
C5' C6' DM2 sing 150 n n 
C5' H5' DM2 sing 151 n n 
C6' "H6'1" DM2 sing 152 n n 
C6' "H6'2" DM2 sing 153 n n 
C6' "H6'3" DM2 sing 154 n n 
#
_atom_sites.entry_id                     5MRA 
_atom_sites.fract_transf_matrix[1][1]    0.010843 
_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]    0.009539 
_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]    0.008828 
_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
E 2 MG A 1 201 5 MG MG . 
F 2 MG A 1 202 12 MG MG . 
G 2 MG A 1 203 13 MG MG . 
H 2 MG B 1 201 3 MG MG . 
I 2 MG B 1 202 6 MG MG . 
J 3 DMS B 1 203 1 DMS DMS . 
K 4 DM2 B 1 204 1 DM2 DM2 . 
L 2 MG C 1 201 1 MG MG . 
M 2 MG C 1 202 4 MG MG . 
N 2 MG C 1 203 11 MG MG . 
O 2 MG D 1 201 2 MG MG . 
P 2 MG D 1 202 9 MG MG . 
Q 5 HOH C 1 301 1 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 DM2 . . . K 4 -18.297 -31.706 17.825 1 233.11 ? C1 DM2 204 B 1 
HETATM 2 C C2 DM2 . . . K 4 -17.261 -31.301 18.647 1 232.31 ? C2 DM2 204 B 1 
HETATM 3 C C3 DM2 . . . K 4 -15.927 -31.41 18.242 1 238.21 ? C3 DM2 204 B 1 
HETATM 4 C C4 DM2 . . . K 4 -15.554 -31.922 17.014 1 241.93 ? C4 DM2 204 B 1 
HETATM 5 O O4 DM2 . . . K 4 -14.228 -32.007 16.693 1 245.23 ? O4 DM2 204 B 1 
HETATM 6 C C5 DM2 . . . K 4 -16.613 -32.369 16.089 1 240.46 ? C5 DM2 204 B 1 
HETATM 7 C C6 DM2 . . . K 4 -16.292 -32.931 14.747 1 240.51 ? C6 DM2 204 B 1 
HETATM 8 O O6 DM2 . . . K 4 -15.115 -33.049 14.351 1 236.28 ? O6 DM2 204 B 1 
HETATM 9 C C7 DM2 . . . K 4 -17.401 -33.367 13.863 1 255.25 ? C7 DM2 204 B 1 
HETATM 10 C C8 DM2 . . . K 4 -17.103 -33.933 12.511 1 267.13 ? C8 DM2 204 B 1 
HETATM 11 O O8 DM2 . . . K 4 -15.813 -34.056 12.085 1 249.86 ? O8 DM2 204 B 1 
HETATM 12 C C9 DM2 . . . K 4 -18.238 -34.367 11.643 1 291.11 ? C9 DM2 204 B 1 
HETATM 13 C C10 DM2 . . . K 4 -18.073 -34.965 10.294 1 297.2 ? C10 DM2 204 B 1 
HETATM 14 O O10 DM2 . . . K 4 -18.385 -36.377 10.357 1 309.06 ? O10 DM2 204 B 1 
HETATM 15 C C11 DM2 . . . K 4 -19.047 -34.294 9.309 1 289.84 ? C11 DM2 204 B 1 
HETATM 16 C C12 DM2 . . . K 4 -20.483 -34.003 9.83 1 281.75 ? C12 DM2 204 B 1 
HETATM 17 O O12 DM2 . . . K 4 -21.415 -34.617 8.936 1 252.83 ? O12 DM2 204 B 1 
HETATM 18 C C13 DM2 . . . K 4 -20.778 -32.498 9.815 1 271.7 ? C13 DM2 204 B 1 
HETATM 19 O O13 DM2 . . . K 4 -20.568 -31.881 8.78 1 286.94 ? O13 DM2 204 B 1 
HETATM 20 C C14 DM2 . . . K 4 -21.337 -31.678 10.974 1 250.97 ? C14 DM2 204 B 1 
HETATM 21 O O14 DM2 . . . K 4 -20.286 -31.091 11.754 1 223.5 ? O14 DM2 204 B 1 
HETATM 22 C C15 DM2 . . . K 4 -20.742 -34.675 11.19 1 285.97 ? C15 DM2 204 B 1 
HETATM 23 C C16 DM2 . . . K 4 -19.636 -34.241 12.126 1 292.09 ? C16 DM2 204 B 1 
HETATM 24 C C17 DM2 . . . K 4 -19.928 -33.671 13.461 1 282.96 ? C17 DM2 204 B 1 
HETATM 25 O O17 DM2 . . . K 4 -21.212 -33.561 13.876 1 285.92 ? O17 DM2 204 B 1 
HETATM 26 C C18 DM2 . . . K 4 -18.814 -33.232 14.34 1 268.71 ? C18 DM2 204 B 1 
HETATM 27 C C19 DM2 . . . K 4 -19.124 -32.668 15.686 1 263.01 ? C19 DM2 204 B 1 
HETATM 28 O O19 DM2 . . . K 4 -20.302 -32.561 16.086 1 272.38 ? O19 DM2 204 B 1 
HETATM 29 C C20 DM2 . . . K 4 -18.02 -32.233 16.565 1 246.01 ? C20 DM2 204 B 1 
HETATM 30 C C21 DM2 . . . K 4 -13.569 -30.921 16.066 1 252.46 ? C21 DM2 204 B 1 
HETATM 31 C C1' DM2 . . . K 4 -17.413 -37.35 10.797 1 290.53 ? C1' DM2 204 B 1 
HETATM 32 C C2' DM2 . . . K 4 -17.417 -37.579 12.318 1 276.75 ? C2' DM2 204 B 1 
HETATM 33 C C3' DM2 . . . K 4 -18.733 -38.183 12.799 1 261.21 ? C3' DM2 204 B 1 
HETATM 34 N N3' DM2 . . . K 4 -18.676 -38.405 14.233 1 231.58 ? N3' DM2 204 B 1 
HETATM 35 C C4' DM2 . . . K 4 -19.014 -39.483 12.041 1 275.31 ? C4' DM2 204 B 1 
HETATM 36 O O4' DM2 . . . K 4 -18.09 -40.498 12.459 1 278 ? O4' DM2 204 B 1 
HETATM 37 C C5' DM2 . . . K 4 -18.926 -39.251 10.522 1 279.42 ? C5' DM2 204 B 1 
HETATM 38 O O5' DM2 . . . K 4 -17.679 -38.619 10.162 1 284.64 ? O5' DM2 204 B 1 
HETATM 39 C C6' DM2 . . . K 4 -19.109 -40.545 9.723 1 262.19 ? C6' DM2 204 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#