data_4F8V # _model_server_result.job_id gAG8-EHZRJBIccokFFdlSQ _model_server_result.datetime_utc '2024-11-12 21:08:47' _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 4f8v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 4F8V # _exptl.entry_id 4F8V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 447.526 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside' _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 4F8V _cell.length_a 31.65 _cell.length_b 107.65 _cell.length_c 48.86 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4F8V _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 N1 G 1 A G 3 1_555 B N3 C 21 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 3 1_555 B O2 C 21 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 3 1_555 B N4 C 21 B C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 C 2 A C 4 1_555 B N1 G 20 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 C 2 A C 4 1_555 B O6 G 20 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 C 2 A C 4 1_555 B N2 G 20 B G 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 3 A G 5 1_555 B N3 C 19 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 3 A G 5 1_555 B O2 C 19 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 3 A G 5 1_555 B N4 C 19 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog10 A O4 U 4 A U 6 1_555 B N3 U 18 B U 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 C 5 A C 7 1_555 B N1 G 17 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N4 C 5 A C 7 1_555 B O6 G 17 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O2 C 5 A C 7 1_555 B N2 G 17 B G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 C 7 A C 9 1_555 B N1 G 14 B G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N4 C 7 A C 9 1_555 B O6 G 14 B G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O2 C 7 A C 9 1_555 B N2 G 14 B G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 A 8 A A 10 1_555 B N3 U 13 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N6 A 8 A A 10 1_555 B O4 U 13 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 C 9 A C 11 1_555 B N1 G 12 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N4 C 9 A C 11 1_555 B O6 G 12 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 C 9 A C 11 1_555 B N2 G 12 B G 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 10 A C 12 1_555 B N1 G 11 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 10 A C 12 1_555 B O6 G 11 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 10 A C 12 1_555 B N2 G 11 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 G 11 A G 13 1_555 B N3 C 10 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N2 G 11 A G 13 1_555 B O2 C 10 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O6 G 11 A G 13 1_555 B N4 C 10 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N1 G 12 A G 14 1_555 B N3 C 9 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N2 G 12 A G 14 1_555 B O2 C 9 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O6 G 12 A G 14 1_555 B N4 C 9 B C 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N3 U 13 A U 15 1_555 B N1 A 8 B A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A O4 U 13 A U 15 1_555 B N6 A 8 B A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N1 G 14 A G 16 1_555 B N3 C 7 B C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N2 G 14 A G 16 1_555 B O2 C 7 B C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A O6 G 14 A G 16 1_555 B N4 C 7 B C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N1 G 17 A G 19 1_555 B N3 C 5 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N2 G 17 A G 19 1_555 B O2 C 5 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A O6 G 17 A G 19 1_555 B N4 C 5 B C 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A N3 C 19 A C 21 1_555 B N1 G 3 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 A N4 C 19 A C 21 1_555 B O6 G 3 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 A O2 C 19 A C 21 1_555 B N2 G 3 B G 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 A N1 G 20 A G 22 1_555 B N3 C 2 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 A N2 G 20 A G 22 1_555 B O2 C 2 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A O6 G 20 A G 22 1_555 B N4 C 2 B C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog45 A O2 C 21 A C 23 1_555 B N2 G 1 B G 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C19 H37 N5 O7' _chem_comp.formula_weight 447.526 _chem_comp.id SIS _chem_comp.mon_nstd_flag . _chem_comp.name '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Sisomicin # 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 O43 C43 SIS sing 118 n n C83 C43 SIS sing 119 n n C43 C53 SIS sing 120 n n C43 C33 SIS sing 121 n n N33 C33 SIS sing 122 n n N33 C93 SIS sing 123 n n C53 O53 SIS sing 124 n n C33 C23 SIS sing 125 n n O53 C13 SIS sing 126 n n C23 C13 SIS sing 127 n n C23 O23 SIS sing 128 n n C13 O62 SIS sing 129 n n O62 C62 SIS sing 130 n n O52 C52 SIS sing 131 n n C62 C52 SIS sing 132 n n C62 C12 SIS sing 133 n n N12 C12 SIS sing 134 n n C52 C42 SIS sing 135 n n C12 C22 SIS sing 136 n n C42 O11 SIS sing 137 n n C42 C32 SIS sing 138 n n C22 C32 SIS sing 139 n n C11 O11 SIS sing 140 n n C11 O51 SIS sing 141 n n C11 C21 SIS sing 142 n n N21 C21 SIS sing 143 n n O51 C51 SIS sing 144 n n C32 N32 SIS sing 145 n n C21 C31 SIS sing 146 n n C51 C61 SIS sing 147 n n C51 C41 SIS doub 148 n n N61 C61 SIS sing 149 n n C31 C41 SIS sing 150 n n C11 H1 SIS sing 151 n n C12 H2 SIS sing 152 n n C13 H3 SIS sing 153 n n C21 H4 SIS sing 154 n n C22 H5 SIS sing 155 n n C22 H6 SIS sing 156 n n C23 H7 SIS sing 157 n n C31 H8 SIS sing 158 n n C31 H9 SIS sing 159 n n C32 H10 SIS sing 160 n n C33 H11 SIS sing 161 n n C41 H12 SIS sing 162 n n C42 H13 SIS sing 163 n n C52 H14 SIS sing 164 n n C53 H15 SIS sing 165 n n C53 H16 SIS sing 166 n n C61 H17 SIS sing 167 n n C61 H18 SIS sing 168 n n C62 H19 SIS sing 169 n n C83 H20 SIS sing 170 n n C83 H21 SIS sing 171 n n C83 H22 SIS sing 172 n n C93 H23 SIS sing 173 n n C93 H24 SIS sing 174 n n C93 H25 SIS sing 175 n n N12 H26 SIS sing 176 n n N12 H27 SIS sing 177 n n N21 H29 SIS sing 178 n n N21 H30 SIS sing 179 n n N32 H32 SIS sing 180 n n N32 H33 SIS sing 181 n n N33 H35 SIS sing 182 n n N61 H37 SIS sing 183 n n N61 H38 SIS sing 184 n n O23 H40 SIS sing 185 n n O43 H41 SIS sing 186 n n O52 H42 SIS sing 187 n n # _atom_sites.entry_id 4F8V _atom_sites.fract_transf_matrix[1][1] 0.031596 _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] 0.009289 _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] 0.020467 _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 SIS A 1 101 52 SIS SIS . D 2 SIS B 1 101 51 SIS SIS . E 3 HOH A 1 201 1 HOH HOH . E 3 HOH A 2 202 3 HOH HOH . F 3 HOH B 1 201 2 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 C11 SIS . . . C 2 6.856 -20.812 -27.898 1 75.72 ? C11 SIS 101 A 1 HETATM 2 C C12 SIS . . . C 2 3.371 -20.05 -31.89 1 83.21 ? C12 SIS 101 A 1 HETATM 3 C C13 SIS . . . C 2 4.01 -16.551 -31.804 1 94.41 ? C13 SIS 101 A 1 HETATM 4 C C21 SIS . . . C 2 8.364 -21.056 -28.226 1 75.51 ? C21 SIS 101 A 1 HETATM 5 C C22 SIS . . . C 2 2.95 -21.256 -30.961 1 80.96 ? C22 SIS 101 A 1 HETATM 6 C C23 SIS . . . C 2 4.017 -16.002 -33.261 1 96.47 ? C23 SIS 101 A 1 HETATM 7 C C31 SIS . . . C 2 8.705 -22.611 -28.217 1 74.67 ? C31 SIS 101 A 1 HETATM 8 C C32 SIS . . . C 2 4.254 -21.887 -30.334 1 78.42 ? C32 SIS 101 A 1 HETATM 9 C C33 SIS . . . C 2 5.518 -16.076 -33.775 1 97.4 ? C33 SIS 101 A 1 HETATM 10 C C41 SIS . . . C 2 7.771 -23.436 -27.257 1 74.65 ? C41 SIS 101 A 1 HETATM 11 C C42 SIS . . . C 2 5.016 -20.781 -29.51 1 78.62 ? C42 SIS 101 A 1 HETATM 12 C C43 SIS . . . C 2 6.445 -15.137 -32.838 1 99.44 ? C43 SIS 101 A 1 HETATM 13 C C51 SIS . . . C 2 6.779 -22.843 -26.557 1 75.72 ? C51 SIS 101 A 1 HETATM 14 C C52 SIS . . . C 2 5.41 -19.575 -30.459 1 81.09 ? C52 SIS 101 A 1 HETATM 15 C C53 SIS . . . C 2 6.342 -15.637 -31.352 1 99.69 ? C53 SIS 101 A 1 HETATM 16 C C61 SIS . . . C 2 5.83 -23.641 -25.611 1 78.74 ? C61 SIS 101 A 1 HETATM 17 C C62 SIS . . . C 2 4.125 -18.96 -31.068 1 83.51 ? C62 SIS 101 A 1 HETATM 18 C C83 SIS . . . C 2 7.95 -15.097 -33.2 1 101.04 ? C83 SIS 101 A 1 HETATM 19 C C93 SIS . . . C 2 5.993 -16.584 -36.191 1 100.4 ? C93 SIS 101 A 1 HETATM 20 N N12 SIS . . . C 2 2.189 -19.478 -32.466 1 81.52 ? N12 SIS 101 A 1 HETATM 21 N N21 SIS . . . C 2 8.654 -20.431 -29.522 1 72.78 ? N21 SIS 101 A 1 HETATM 22 N N32 SIS . . . C 2 3.889 -23.016 -29.454 1 78.04 ? N32 SIS 101 A 1 HETATM 23 N N33 SIS . . . C 2 5.62 -15.587 -35.177 1 98.02 ? N33 SIS 101 A 1 HETATM 24 N N61 SIS . . . C 2 4.813 -22.763 -25.032 1 78.43 ? N61 SIS 101 A 1 HETATM 25 O O11 SIS . . . C 2 6.147 -21.373 -28.993 1 78.91 ? O11 SIS 101 A 1 HETATM 26 O O23 SIS . . . C 2 3.164 -16.811 -34.054 1 98.46 ? O23 SIS 101 A 1 HETATM 27 O O43 SIS . . . C 2 6.037 -13.777 -32.883 1 101.3 ? O43 SIS 101 A 1 HETATM 28 O O51 SIS . . . C 2 6.525 -21.445 -26.642 1 74.91 ? O51 SIS 101 A 1 HETATM 29 O O52 SIS . . . C 2 6.089 -18.551 -29.718 1 78.64 ? O52 SIS 101 A 1 HETATM 30 O O53 SIS . . . C 2 4.893 -15.716 -30.932 1 94.84 ? O53 SIS 101 A 1 HETATM 31 O O62 SIS . . . C 2 4.517 -17.906 -31.909 1 89.99 ? O62 SIS 101 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #