data_1NAB
#
_model_server_result.job_id            L07hEhbNGrSxqcOeWkURgg 
_model_server_result.datetime_utc      '2024-10-11 06:22:50' 
_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          1nab 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":40}' 
#
_entry.id    1NAB 
#
_exptl.entry_id    1NAB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              643.635 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            7-[5-(4-AMINO-5-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY)-4-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY]-6,9,11-TRIHYDROXY-9-(2-HYDROXY-ACETYL)-7,8,9,10-TETRAHYDRO-NAPHTHACENE-5,12-DIONE 
_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            1NAB 
_cell.length_a            37.813 
_cell.length_b            37.813 
_cell.length_c            63.02 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NAB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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,D,E,F 
_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    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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D 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
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 DA 3 A DA 3 1_555 B N3 DT 4 B DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N6 DA 3 A DA 3 1_555 B O4 DT 4 B DT 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 DT 4 A DT 4 1_555 B N1 DA 3 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O4 DT 4 A DT 4 1_555 B N6 DA 3 B DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'C32 H37 N O13' 
_chem_comp.formula_weight    643.635 
_chem_comp.id                44D 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              7-[5-(4-AMINO-5-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY)-4-HYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YLOXY]-6,9,11-TRIHYDROXY-9-(2-HYDROXY-ACETYL)-7,8,9,10-TETRAHYDRO-NAPHTHACENE-5,12-DIONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "4'-(O-ALPHA-L-DAUNOSAMINYL)-4-DEMETHOXYDOXORUBICIN" 
#
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 44D doub 1 n y 
C1 C15 44D sing 2 n y 
C1 HC1 44D sing 3 n n 
C2 C3 44D sing 4 n y 
C2 HC2 44D sing 5 n n 
C3 C4 44D doub 6 n y 
C3 HC3 44D sing 7 n n 
C4 C16 44D sing 8 n y 
C4 HC4 44D sing 9 n n 
C5 C16 44D sing 10 n n 
C5 C17 44D sing 11 n n 
C5 O5 44D doub 12 n n 
C6 C17 44D doub 13 n y 
C6 C20 44D sing 14 n y 
C6 O6 44D sing 15 n n 
C7 C8 44D sing 16 n n 
C7 C20 44D sing 17 n n 
C7 O7 44D sing 18 n n 
C7 HC7 44D sing 19 n n 
C8 C9 44D sing 20 n n 
C8 HC81 44D sing 21 n n 
C8 HC82 44D sing 22 n n 
C9 C10 44D sing 23 n n 
C9 C13 44D sing 24 n n 
C9 O9 44D sing 25 n n 
C10 C19 44D sing 26 n n 
C10 H101 44D sing 27 n n 
C10 H102 44D sing 28 n n 
C11 C18 44D doub 29 n y 
C11 C19 44D sing 30 n y 
C11 O11 44D sing 31 n n 
C12 C15 44D sing 32 n n 
C12 C18 44D sing 33 n n 
C12 O12 44D doub 34 n n 
C13 C14 44D sing 35 n n 
C13 O13 44D doub 36 n n 
C14 O14 44D sing 37 n n 
C14 H141 44D sing 38 n n 
C14 H142 44D sing 39 n n 
C15 C16 44D doub 40 n y 
C17 C18 44D sing 41 n y 
C19 C20 44D doub 42 n y 
O6 HO6 44D sing 43 n n 
O7 C1B 44D sing 44 n n 
O9 HO9 44D sing 45 n n 
O11 H11 44D sing 46 n n 
O14 H14 44D sing 47 n n 
C1B C2B 44D sing 48 n n 
C1B O5B 44D sing 49 n n 
C1B H1B 44D sing 50 n n 
C2B C3B 44D sing 51 n n 
C2B "H2'1" 44D sing 52 n n 
C2B "H2'2" 44D sing 53 n n 
C3B C4B 44D sing 54 n n 
C3B O3' 44D sing 55 n n 
C3B H3B 44D sing 56 n n 
C4B C5B 44D sing 57 n n 
C4B O4B 44D sing 58 n n 
C4B H4B 44D sing 59 n n 
C5B C6B 44D sing 60 n n 
C5B O5B 44D sing 61 n n 
C5B H5B 44D sing 62 n n 
C6B "H6'1" 44D sing 63 n n 
C6B "H6'2" 44D sing 64 n n 
C6B "H6'3" 44D sing 65 n n 
O3' "H3'O" 44D sing 66 n n 
O4B C1' 44D sing 67 n n 
C1' C2' 44D sing 68 n n 
C1' O5' 44D sing 69 n n 
C1' H1' 44D sing 70 n n 
C2' C3' 44D sing 71 n n 
C2' H2B 44D sing 72 n n 
C2' H2D 44D sing 73 n n 
C3' C4' 44D sing 74 n n 
C3' N3' 44D sing 75 n n 
C3' H3' 44D sing 76 n n 
C4' C5' 44D sing 77 n n 
C4' O4' 44D sing 78 n n 
C4' H4' 44D sing 79 n n 
C5' C6' 44D sing 80 n n 
C5' O5' 44D sing 81 n n 
C5' H5' 44D sing 82 n n 
C6' H6B 44D sing 83 n n 
C6' H6D 44D sing 84 n n 
C6' H6E 44D sing 85 n n 
O4' "H4'O" 44D sing 86 n n 
N3' "H3'1" 44D sing 87 n n 
N3' "H3'2" 44D sing 88 n n 
#
_atom_sites.entry_id                     1NAB 
_atom_sites.fract_transf_matrix[1][1]    0.026446 
_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]    0.026446 
_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]    0.015868 
_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
C 2 44D A 1 41 14 44D MEN . 
D 2 44D B 1 40 13 44D MEN . 
E 3 HOH A 1 42 6 HOH HOH . 
E 3 HOH A 2 43 8 HOH HOH . 
E 3 HOH A 3 44 10 HOH HOH . 
E 3 HOH A 4 45 11 HOH HOH . 
E 3 HOH A 5 46 12 HOH HOH . 
E 3 HOH A 6 47 13 HOH HOH . 
E 3 HOH A 7 48 17 HOH HOH . 
E 3 HOH A 8 49 18 HOH HOH . 
E 3 HOH A 9 50 26 HOH HOH . 
E 3 HOH A 10 51 29 HOH HOH . 
E 3 HOH A 11 52 30 HOH HOH . 
E 3 HOH A 12 53 31 HOH HOH . 
F 3 HOH B 1 41 1 HOH HOH . 
F 3 HOH B 2 42 2 HOH HOH . 
F 3 HOH B 3 43 3 HOH HOH . 
F 3 HOH B 4 44 5 HOH HOH . 
F 3 HOH B 5 45 7 HOH HOH . 
F 3 HOH B 6 46 9 HOH HOH . 
F 3 HOH B 7 47 14 HOH HOH . 
F 3 HOH B 8 48 15 HOH HOH . 
F 3 HOH B 9 49 16 HOH HOH . 
F 3 HOH B 10 50 20 HOH HOH . 
F 3 HOH B 11 51 21 HOH HOH . 
F 3 HOH B 12 52 22 HOH HOH . 
F 3 HOH B 13 53 23 HOH HOH . 
F 3 HOH B 14 54 24 HOH HOH . 
F 3 HOH B 15 55 25 HOH HOH . 
F 3 HOH B 16 56 27 HOH HOH . 
F 3 HOH B 17 57 28 HOH HOH . 
F 3 HOH B 18 58 33 HOH HOH . 
F 3 HOH B 19 59 34 HOH HOH . 
F 3 HOH B 20 60 35 HOH HOH . 
F 3 HOH B 21 61 36 HOH HOH . 
F 3 HOH B 22 62 37 HOH HOH . 
F 3 HOH B 23 63 38 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 44D . . . D 2 2.56 18.262 20.318 1 19.44 ? C1 44D 40 B 1 
HETATM 2 C C2 44D . . . D 2 3.535 19.117 20.992 1 19.97 ? C2 44D 40 B 1 
HETATM 3 C C3 44D . . . D 2 4.337 19.899 20.16 1 19.79 ? C3 44D 40 B 1 
HETATM 4 C C4 44D . . . D 2 4.22 19.873 18.755 1 19.61 ? C4 44D 40 B 1 
HETATM 5 C C5 44D . . . D 2 3.161 18.992 16.776 1 18.3 ? C5 44D 40 B 1 
HETATM 6 C C6 44D . . . D 2 2.125 18.039 14.86 1 17.08 ? C6 44D 40 B 1 
HETATM 7 C C7 44D . . . D 2 1.085 17.23 12.825 1 18.12 ? C7 44D 40 B 1 
HETATM 8 C C8 44D . . . D 2 0.064 16.217 12.327 1 17.64 ? C8 44D 40 B 1 
HETATM 9 C C9 44D . . . D 2 0.076 14.886 13.02 1 17.63 ? C9 44D 40 B 1 
HETATM 10 C C10 44D . . . D 2 -0.423 15.234 14.488 1 17.34 ? C10 44D 40 B 1 
HETATM 11 C C11 44D . . . D 2 0.518 16.394 16.461 1 17.05 ? C11 44D 40 B 1 
HETATM 12 C C12 44D . . . D 2 1.573 17.381 18.389 1 18.49 ? C12 44D 40 B 1 
HETATM 13 C C13 44D . . . D 2 -1.032 14.031 12.327 1 17.63 ? C13 44D 40 B 1 
HETATM 14 C C14 44D . . . D 2 -0.794 12.61 12.018 1 17.63 ? C14 44D 40 B 1 
HETATM 15 C C15 44D . . . D 2 2.492 18.281 18.925 1 18.81 ? C15 44D 40 B 1 
HETATM 16 C C16 44D . . . D 2 3.259 19.068 18.143 1 18.64 ? C16 44D 40 B 1 
HETATM 17 C C17 44D . . . D 2 2.238 18.111 16.234 1 17.65 ? C17 44D 40 B 1 
HETATM 18 C C18 44D . . . D 2 1.422 17.275 17.009 1 17.51 ? C18 44D 40 B 1 
HETATM 19 C C19 44D . . . D 2 0.386 16.345 15.068 1 17.16 ? C19 44D 40 B 1 
HETATM 20 C C20 44D . . . D 2 1.183 17.162 14.324 1 17.27 ? C20 44D 40 B 1 
HETATM 21 O O5 44D . . . D 2 4.015 19.729 16.032 1 18.8 ? O5 44D 40 B 1 
HETATM 22 O O6 44D . . . D 2 2.945 18.829 14.098 1 16.76 ? O6 44D 40 B 1 
HETATM 23 O O7 44D . . . D 2 2.31 17.067 12.232 1 20.3 ? O7 44D 40 B 1 
HETATM 24 O O9 44D . . . D 2 1.304 14.111 12.787 1 17.97 ? O9 44D 40 B 1 
HETATM 25 O O11 44D . . . D 2 -0.295 15.563 17.23 1 16.63 ? O11 44D 40 B 1 
HETATM 26 O O12 44D . . . D 2 0.934 16.693 19.297 1 19.62 ? O12 44D 40 B 1 
HETATM 27 O O13 44D . . . D 2 -2.272 14.519 12.446 1 17.9 ? O13 44D 40 B 1 
HETATM 28 O O14 44D . . . D 2 -1.989 11.933 11.558 1 17.45 ? O14 44D 40 B 1 
HETATM 29 C C1B 44D . . . D 2 2.892 17.812 11.218 1 22.48 ? C1B 44D 40 B 1 
HETATM 30 C C2B 44D . . . D 2 4.363 17.657 10.94 1 23.45 ? C2B 44D 40 B 1 
HETATM 31 C C3B 44D . . . D 2 4.371 16.239 10.348 1 24.9 ? C3B 44D 40 B 1 
HETATM 32 C C4B 44D . . . D 2 3.671 16.239 8.98 1 25.21 ? C4B 44D 40 B 1 
HETATM 33 C C5B 44D . . . D 2 2.201 16.557 9.289 1 24.53 ? C5B 44D 40 B 1 
HETATM 34 C C6B 44D . . . D 2 1.312 16.508 8.079 1 23.74 ? C6B 44D 40 B 1 
HETATM 35 O O3' 44D . . . D 2 5.792 15.687 10.184 1 25.99 ? O3' 44D 40 B 1 
HETATM 36 O O4B 44D . . . D 2 4.235 17.117 8.029 1 26.88 ? O4B 44D 40 B 1 
HETATM 37 O O5B 44D . . . D 2 2.174 17.824 9.989 1 23.63 ? O5B 44D 40 B 1 
HETATM 38 C C1' 44D . . . D 2 4.946 17.154 6.882 1 28.18 ? C1' 44D 40 B 1 
HETATM 39 C C2' 44D . . . D 2 4.677 18.447 6.17 1 28.67 ? C2' 44D 40 B 1 
HETATM 40 C C3' 44D . . . D 2 5.781 19.412 6.378 1 29.62 ? C3' 44D 40 B 1 
HETATM 41 C C4' 44D . . . D 2 7.267 18.954 6.516 1 30.17 ? C4' 44D 40 B 1 
HETATM 42 C C5' 44D . . . D 2 7.248 17.672 7.405 1 29.79 ? C5' 44D 40 B 1 
HETATM 43 C C6' 44D . . . D 2 8.67 17.283 7.783 1 29.98 ? C6' 44D 40 B 1 
HETATM 44 O O4' 44D . . . D 2 8.209 18.792 5.401 1 31.25 ? O4' 44D 40 B 1 
HETATM 45 O O5' 44D . . . D 2 6.348 16.754 6.794 1 29.39 ? O5' 44D 40 B 1 
HETATM 46 N N3' 44D . . . D 2 5.766 20.308 5.212 1 30.38 ? N3' 44D 40 B 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#