data_277D # _model_server_result.job_id ZRK3YnaKa0QoQOckOmcitw _model_server_result.datetime_utc '2024-10-18 15:26:49' _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 277d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":7}' # _entry.id 277D # _exptl.entry_id 277D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 606.416 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-BROMO-4'-EPIDAUNORUBICIN" _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 277D _cell.length_a 28.19 _cell.length_b 28.19 _cell.length_c 52.66 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 277D _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 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 _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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 28.19 28.19 26.33 # _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 covale ? covale1 A O3' DC 3 A DC 3 1_555 A P G49 4 A G49 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.713 ? covale ? covale2 A O3' G49 4 A G49 4 1_555 A P DC 5 A DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 A CM2 G49 4 A G49 4 1_555 B N3' DM8 . A DM8 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 A N1 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 A O6 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 A N2 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 A N1 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 A O6 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 A N2 G49 4 A G49 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 G49 4 A G49 4 1_555 A N3 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 G49 4 A G49 4 1_555 A O2 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 G49 4 A G49 4 1_555 A N4 DC 3 A DC 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 A N3 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 A O2 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 A N4 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C27 H28 Br N O10' _chem_comp.formula_weight 606.416 _chem_comp.id DM8 _chem_comp.mon_nstd_flag . _chem_comp.name "2'-BROMO-4'-EPIDAUNORUBICIN" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'WP401;DAUNOMYCIN DERIVATIVE;DAUNORUBICIN DERIVATIVE' # 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 DM8 doub 75 n y C1 C15 DM8 sing 76 n y C1 H1 DM8 sing 77 n n C2 C3 DM8 sing 78 n y C2 H2 DM8 sing 79 n n C3 C4 DM8 doub 80 n y C3 H3 DM8 sing 81 n n C4 C16 DM8 sing 82 n y C4 O4 DM8 sing 83 n n C5 C16 DM8 sing 84 n n C5 C17 DM8 sing 85 n n C5 O5 DM8 doub 86 n n C6 C17 DM8 doub 87 n y C6 C20 DM8 sing 88 n y C6 O6 DM8 sing 89 n n C7 C8 DM8 sing 90 n n C7 C20 DM8 sing 91 n n C7 O7 DM8 sing 92 n n C7 H7 DM8 sing 93 n n C8 C9 DM8 sing 94 n n C8 H81 DM8 sing 95 n n C8 H82 DM8 sing 96 n n C9 C10 DM8 sing 97 n n C9 C13 DM8 sing 98 n n C9 O9 DM8 sing 99 n n C10 C19 DM8 sing 100 n n C10 H101 DM8 sing 101 n n C10 H102 DM8 sing 102 n n C11 C18 DM8 doub 103 n y C11 C19 DM8 sing 104 n y C11 O11 DM8 sing 105 n n C12 C15 DM8 sing 106 n n C12 C18 DM8 sing 107 n n C12 O12 DM8 doub 108 n n C13 C14 DM8 sing 109 n n C13 O13 DM8 doub 110 n n C14 H141 DM8 sing 111 n n C14 H142 DM8 sing 112 n n C14 H143 DM8 sing 113 n n C15 C16 DM8 doub 114 n y C17 C18 DM8 sing 115 n y C19 C20 DM8 doub 116 n y C21 O4 DM8 sing 117 n n C21 H211 DM8 sing 118 n n C21 H212 DM8 sing 119 n n C21 H213 DM8 sing 120 n n O6 H6 DM8 sing 121 n n O7 C1' DM8 sing 122 n n O9 H9 DM8 sing 123 n n O11 H11 DM8 sing 124 n n C1' C2' DM8 sing 125 n n C1' O5' DM8 sing 126 n n C1' H1' DM8 sing 127 n n C2' C3' DM8 sing 128 n n C2' BR DM8 sing 129 n n C2' H2' DM8 sing 130 n n C3' C4' DM8 sing 131 n n C3' N3' DM8 sing 132 n n C3' H3' DM8 sing 133 n n C4' C5' DM8 sing 134 n n C4' O4' DM8 sing 135 n n C4' H4' DM8 sing 136 n n C5' C6' DM8 sing 137 n n C5' O5' DM8 sing 138 n n C5' H5' DM8 sing 139 n n C6' "H6'1" DM8 sing 140 n n C6' "H6'2" DM8 sing 141 n n C6' "H6'3" DM8 sing 142 n n O4' HO4' DM8 sing 143 n n N3' "HN'1" DM8 sing 144 n n N3' "HN'2" DM8 sing 145 n n # _atom_sites.entry_id 277D _atom_sites.fract_transf_matrix[1][1] 0.035474 _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] 0.035474 _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] 0.018989 _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 DM8 A 1 7 4 DM8 DM8 . C 3 HOH A 1 8 8 HOH HOH . C 3 HOH A 2 9 9 HOH HOH . C 3 HOH A 3 10 10 HOH HOH . C 3 HOH A 4 11 11 HOH HOH . C 3 HOH A 5 12 12 HOH HOH . C 3 HOH A 6 13 13 HOH HOH . C 3 HOH A 7 14 14 HOH HOH . C 3 HOH A 8 15 15 HOH HOH . C 3 HOH A 9 16 16 HOH HOH . C 3 HOH A 10 17 17 HOH HOH . C 3 HOH A 11 18 18 HOH HOH . C 3 HOH A 12 19 19 HOH HOH . C 3 HOH A 13 20 20 HOH HOH . C 3 HOH A 14 21 21 HOH HOH . C 3 HOH A 15 22 22 HOH HOH . C 3 HOH A 16 23 23 HOH HOH . C 3 HOH A 17 24 24 HOH HOH . C 3 HOH A 18 25 25 HOH HOH . C 3 HOH A 19 26 26 HOH HOH . C 3 HOH A 20 27 27 HOH HOH . C 3 HOH A 21 28 28 HOH HOH . C 3 HOH A 22 29 29 HOH HOH . C 3 HOH A 23 30 30 HOH HOH . C 3 HOH A 24 31 31 HOH HOH . C 3 HOH A 25 32 32 HOH HOH . C 3 HOH A 26 33 33 HOH HOH . C 3 HOH A 27 34 34 HOH HOH . C 3 HOH A 28 35 35 HOH HOH . C 3 HOH A 29 36 36 HOH HOH . C 3 HOH A 30 37 37 HOH HOH . C 3 HOH A 31 38 38 HOH HOH . C 3 HOH A 32 39 39 HOH HOH . C 3 HOH A 33 40 40 HOH HOH . C 3 HOH A 34 41 41 HOH HOH . C 3 HOH A 35 42 42 HOH HOH . C 3 HOH A 36 43 43 HOH HOH . C 3 HOH A 37 44 44 HOH HOH . C 3 HOH A 38 45 45 HOH HOH . C 3 HOH A 39 46 46 HOH HOH . C 3 HOH A 40 47 47 HOH HOH . C 3 HOH A 41 48 48 HOH HOH . C 3 HOH A 42 49 49 HOH HOH . C 3 HOH A 43 50 50 HOH HOH . C 3 HOH A 44 51 51 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 DM8 . . . B 2 15.642 18.48 5.061 1 17.42 ? C1 DM8 7 A 1 HETATM 2 C C2 DM8 . . . B 2 16.8 19.204 5.092 1 17.57 ? C2 DM8 7 A 1 HETATM 3 C C3 DM8 . . . B 2 18.116 18.57 5.024 1 17.9 ? C3 DM8 7 A 1 HETATM 4 C C4 DM8 . . . B 2 18.224 17.13 4.934 1 17.6 ? C4 DM8 7 A 1 HETATM 5 C C5 DM8 . . . B 2 17.057 14.92 4.866 1 17.11 ? C5 DM8 7 A 1 HETATM 6 C C6 DM8 . . . B 2 15.774 12.845 4.861 1 16.87 ? C6 DM8 7 A 1 HETATM 7 C C7 DM8 . . . B 2 14.503 10.658 4.892 1 18.16 ? C7 DM8 7 A 1 HETATM 8 C C8 DM8 . . . B 2 13.169 10.004 4.987 1 18.55 ? C8 DM8 7 A 1 HETATM 9 C C9 DM8 . . . B 2 12.028 10.858 5.508 1 18.4 ? C9 DM8 7 A 1 HETATM 10 C C10 DM8 . . . B 2 11.971 12.301 4.945 1 17.79 ? C10 DM8 7 A 1 HETATM 11 C C11 DM8 . . . B 2 13.322 14.26 4.971 1 16.81 ? C11 DM8 7 A 1 HETATM 12 C C12 DM8 . . . B 2 14.463 16.434 4.992 1 16.63 ? C12 DM8 7 A 1 HETATM 13 C C13 DM8 . . . B 2 10.692 10.198 5.324 1 18.92 ? C13 DM8 7 A 1 HETATM 14 C C14 DM8 . . . B 2 9.928 9.232 6.23 1 19.77 ? C14 DM8 7 A 1 HETATM 15 C C15 DM8 . . . B 2 15.774 17.059 4.955 1 17.13 ? C15 DM8 7 A 1 HETATM 16 C C16 DM8 . . . B 2 16.992 16.439 4.919 1 17.44 ? C16 DM8 7 A 1 HETATM 17 C C17 DM8 . . . B 2 15.763 14.238 4.908 1 16.82 ? C17 DM8 7 A 1 HETATM 18 C C18 DM8 . . . B 2 14.48 15.01 4.971 1 16.63 ? C18 DM8 7 A 1 HETATM 19 C C19 DM8 . . . B 2 13.285 12.862 4.919 1 17.05 ? C19 DM8 7 A 1 HETATM 20 C C20 DM8 . . . B 2 14.508 12.208 4.855 1 17.32 ? C20 DM8 7 A 1 HETATM 21 C C21 DM8 . . . B 2 20.701 17.011 4.871 1 17.89 ? C21 DM8 7 A 1 HETATM 22 O O4 DM8 . . . B 2 19.407 16.482 4.876 1 18.15 ? O4 DM8 7 A 1 HETATM 23 O O5 DM8 . . . B 2 18.105 14.232 4.813 1 17.53 ? O5 DM8 7 A 1 HETATM 24 O O6 DM8 . . . B 2 16.879 12.172 4.818 1 17.18 ? O6 DM8 7 A 1 HETATM 25 O O7 DM8 . . . B 2 15.224 10.5 6.193 1 19.51 ? O7 DM8 7 A 1 HETATM 26 O O9 DM8 . . . B 2 12.129 10.957 7.02 1 19.08 ? O9 DM8 7 A 1 HETATM 27 O O11 DM8 . . . B 2 12.121 14.985 4.998 1 16.91 ? O11 DM8 7 A 1 HETATM 28 O O12 DM8 . . . B 2 13.457 17.161 5.034 1 16.89 ? O12 DM8 7 A 1 HETATM 29 O O13 DM8 . . . B 2 10.122 10.596 4.297 1 20.12 ? O13 DM8 7 A 1 HETATM 30 C C1' DM8 . . . B 2 16.076 9.418 6.419 1 20.86 ? C1' DM8 7 A 1 HETATM 31 C C2' DM8 . . . B 2 17.054 9.77 7.567 1 20.94 ? C2' DM8 7 A 1 HETATM 32 C C3' DM8 . . . B 2 16.338 9.849 8.905 1 20.85 ? C3' DM8 7 A 1 HETATM 33 C C4' DM8 . . . B 2 15.681 8.476 9.174 1 20.86 ? C4' DM8 7 A 1 HETATM 34 C C5' DM8 . . . B 2 14.517 8.349 8.147 1 21.01 ? C5' DM8 7 A 1 HETATM 35 C C6' DM8 . . . B 2 13.846 6.962 8.231 1 21.05 ? C6' DM8 7 A 1 HETATM 36 O O5' DM8 . . . B 2 15.207 8.273 6.804 1 20.98 ? O5' DM8 7 A 1 HETATM 37 O O4' DM8 . . . B 2 15.137 8.389 10.553 1 21.59 ? O4' DM8 7 A 1 HETATM 38 N N3' DM8 . . . B 2 17.358 10.162 10.006 1 19.82 ? N3' DM8 7 A 1 HETATM 39 BR BR DM8 . . . B 2 18.452 8.609 7.483 1 24.12 ? BR DM8 7 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 39 #