data_3KP5
#
_model_server_result.job_id            alhp55nJfYhfSkTnuEpARg 
_model_server_result.datetime_utc      '2024-10-11 17:24:44' 
_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          3kp5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2002}' 
#
_entry.id    3KP5 
#
_exptl.entry_id    3KP5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              484.499 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'KANAMYCIN A' 
_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         120 
_cell.entry_id            3KP5 
_cell.length_a            107.828 
_cell.length_b            107.828 
_cell.length_c            49.422 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KP5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_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 
#
_chem_comp.formula           'C18 H36 N4 O11' 
_chem_comp.formula_weight    484.499 
_chem_comp.id                KAN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'KANAMYCIN A' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 KAN sing 160 n n 
C1 O5 KAN sing 161 n n 
C1 O9 KAN sing 162 n n 
C1 H1 KAN sing 163 n n 
C2 C3 KAN sing 164 n n 
C2 O6 KAN sing 165 n n 
C2 H2 KAN sing 166 n n 
C3 C4 KAN sing 167 n n 
C3 O7 KAN sing 168 n n 
C3 H3 KAN sing 169 n n 
C4 C5 KAN sing 170 n n 
C4 O8 KAN sing 171 n n 
C4 H4 KAN sing 172 n n 
C5 C6 KAN sing 173 n n 
C5 O5 KAN sing 174 n n 
C5 H5 KAN sing 175 n n 
C6 N1 KAN sing 176 n n 
C6 H61 KAN sing 177 n n 
C6 H62 KAN sing 178 n n 
C7 C8 KAN sing 179 n n 
C7 C12 KAN sing 180 n n 
C7 N3 KAN sing 181 n n 
C7 H7 KAN sing 182 n n 
C8 C9 KAN sing 183 n n 
C8 O11 KAN sing 184 n n 
C8 H8 KAN sing 185 n n 
C9 C10 KAN sing 186 n n 
C9 O10 KAN sing 187 n n 
C9 H9 KAN sing 188 n n 
C10 C11 KAN sing 189 n n 
C10 O9 KAN sing 190 n n 
C10 H10 KAN sing 191 n n 
C11 C12 KAN sing 192 n n 
C11 N2 KAN sing 193 n n 
C11 H11 KAN sing 194 n n 
C12 H121 KAN sing 195 n n 
C12 H122 KAN sing 196 n n 
C13 C14 KAN sing 197 n n 
C13 O11 KAN sing 198 n n 
C13 O12 KAN sing 199 n n 
C13 H13 KAN sing 200 n n 
C14 C15 KAN sing 201 n n 
C14 O13 KAN sing 202 n n 
C14 H14 KAN sing 203 n n 
C15 C16 KAN sing 204 n n 
C15 N4 KAN sing 205 n n 
C15 H15 KAN sing 206 n n 
C16 C17 KAN sing 207 n n 
C16 O14 KAN sing 208 n n 
C16 H16 KAN sing 209 n n 
C17 C18 KAN sing 210 n n 
C17 O12 KAN sing 211 n n 
C17 H17 KAN sing 212 n n 
C18 O15 KAN sing 213 n n 
C18 H181 KAN sing 214 n n 
C18 H182 KAN sing 215 n n 
N1 HN11 KAN sing 216 n n 
N1 HN12 KAN sing 217 n n 
N2 HN21 KAN sing 218 n n 
N2 HN22 KAN sing 219 n n 
N3 HN31 KAN sing 220 n n 
N3 HN32 KAN sing 221 n n 
N4 HN41 KAN sing 222 n n 
N4 HN42 KAN sing 223 n n 
O6 HO6 KAN sing 224 n n 
O7 HO7 KAN sing 225 n n 
O8 HO8 KAN sing 226 n n 
O10 HO1 KAN sing 227 n n 
O13 HO3 KAN sing 228 n n 
O14 HO4 KAN sing 229 n n 
O15 HO5 KAN sing 230 n n 
#
_atom_sites.entry_id                     3KP5 
_atom_sites.fract_transf_matrix[1][1]    0.009274 
_atom_sites.fract_transf_matrix[1][2]    0.005354 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010709 
_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]    0.020234 
_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 KAN A 1 2001 2001 KAN KAN . 
D 2 KAN B 1 2002 2002 KAN KAN . 
E 3 HOH A 1 1002 1002 HOH HOH . 
E 3 HOH A 2 1003 1003 HOH HOH . 
E 3 HOH A 3 1004 1004 HOH HOH . 
E 3 HOH A 4 1008 1008 HOH HOH . 
E 3 HOH A 5 1009 1009 HOH HOH . 
E 3 HOH A 6 1010 1010 HOH HOH . 
E 3 HOH A 7 1011 1011 HOH HOH . 
E 3 HOH A 8 1012 1012 HOH HOH . 
E 3 HOH A 9 1014 1014 HOH HOH . 
E 3 HOH A 10 1016 1016 HOH HOH . 
E 3 HOH A 11 1017 1017 HOH HOH . 
E 3 HOH A 12 1018 1018 HOH HOH . 
E 3 HOH A 13 1020 1020 HOH HOH . 
E 3 HOH A 14 1021 1021 HOH HOH . 
E 3 HOH A 15 1022 1022 HOH HOH . 
E 3 HOH A 16 1024 1024 HOH HOH . 
E 3 HOH A 17 1025 1025 HOH HOH . 
E 3 HOH A 18 1026 1026 HOH HOH . 
E 3 HOH A 19 1027 1027 HOH HOH . 
E 3 HOH A 20 1028 1028 HOH HOH . 
E 3 HOH A 21 1029 1029 HOH HOH . 
E 3 HOH A 22 1030 1030 HOH HOH . 
E 3 HOH A 23 1032 1032 HOH HOH . 
E 3 HOH A 24 1033 1033 HOH HOH . 
E 3 HOH A 25 1038 1038 HOH HOH . 
E 3 HOH A 26 1039 1039 HOH HOH . 
E 3 HOH A 27 1043 1043 HOH HOH . 
E 3 HOH A 28 1046 1046 HOH HOH . 
E 3 HOH A 29 1047 1047 HOH HOH . 
E 3 HOH A 30 1048 1048 HOH HOH . 
E 3 HOH A 31 1051 1051 HOH HOH . 
E 3 HOH A 32 1053 1053 HOH HOH . 
E 3 HOH A 33 1054 1054 HOH HOH . 
E 3 HOH A 34 1055 1055 HOH HOH . 
E 3 HOH A 35 1059 1059 HOH HOH . 
E 3 HOH A 36 1060 1060 HOH HOH . 
E 3 HOH A 37 1061 1061 HOH HOH . 
E 3 HOH A 38 1062 1062 HOH HOH . 
E 3 HOH A 39 1064 1064 HOH HOH . 
E 3 HOH A 40 1065 1065 HOH HOH . 
E 3 HOH A 41 1068 1068 HOH HOH . 
E 3 HOH A 42 1069 1069 HOH HOH . 
E 3 HOH A 43 1070 1070 HOH HOH . 
E 3 HOH A 44 1071 1071 HOH HOH . 
E 3 HOH A 45 1072 1072 HOH HOH . 
E 3 HOH A 46 1073 1073 HOH HOH . 
E 3 HOH A 47 1074 1074 HOH HOH . 
E 3 HOH A 48 1075 1075 HOH HOH . 
E 3 HOH A 49 1080 1080 HOH HOH . 
E 3 HOH A 50 1081 1081 HOH HOH . 
E 3 HOH A 51 1082 1082 HOH HOH . 
E 3 HOH A 52 1084 1084 HOH HOH . 
E 3 HOH A 53 1085 1085 HOH HOH . 
E 3 HOH A 54 1086 1086 HOH HOH . 
E 3 HOH A 55 1087 1087 HOH HOH . 
E 3 HOH A 56 1094 1094 HOH HOH . 
E 3 HOH A 57 1095 1095 HOH HOH . 
E 3 HOH A 58 1096 1096 HOH HOH . 
E 3 HOH A 59 1099 1099 HOH HOH . 
E 3 HOH A 60 1100 1100 HOH HOH . 
E 3 HOH A 61 1104 1104 HOH HOH . 
E 3 HOH A 62 1105 1105 HOH HOH . 
E 3 HOH A 63 1106 1106 HOH HOH . 
E 3 HOH A 64 1110 1110 HOH HOH . 
E 3 HOH A 65 1111 1111 HOH HOH . 
E 3 HOH A 66 1113 1113 HOH HOH . 
E 3 HOH A 67 1114 1114 HOH HOH . 
E 3 HOH A 68 1115 1115 HOH HOH . 
E 3 HOH A 69 1116 1116 HOH HOH . 
E 3 HOH A 70 1117 1117 HOH HOH . 
E 3 HOH A 71 1120 1120 HOH HOH . 
E 3 HOH A 72 1123 1123 HOH HOH . 
E 3 HOH A 73 1126 1126 HOH HOH . 
E 3 HOH A 74 1129 1129 HOH HOH . 
E 3 HOH A 75 1130 1130 HOH HOH . 
E 3 HOH A 76 1132 1132 HOH HOH . 
E 3 HOH A 77 1134 1134 HOH HOH . 
E 3 HOH A 78 1139 1139 HOH HOH . 
E 3 HOH A 79 1140 1140 HOH HOH . 
E 3 HOH A 80 1142 1142 HOH HOH . 
E 3 HOH A 81 1145 1145 HOH HOH . 
F 3 HOH B 1 1001 1001 HOH HOH . 
F 3 HOH B 2 1005 1005 HOH HOH . 
F 3 HOH B 3 1006 1006 HOH HOH . 
F 3 HOH B 4 1007 1007 HOH HOH . 
F 3 HOH B 5 1013 1013 HOH HOH . 
F 3 HOH B 6 1015 1015 HOH HOH . 
F 3 HOH B 7 1019 1019 HOH HOH . 
F 3 HOH B 8 1023 1023 HOH HOH . 
F 3 HOH B 9 1031 1031 HOH HOH . 
F 3 HOH B 10 1034 1034 HOH HOH . 
F 3 HOH B 11 1035 1035 HOH HOH . 
F 3 HOH B 12 1036 1036 HOH HOH . 
F 3 HOH B 13 1037 1037 HOH HOH . 
F 3 HOH B 14 1040 1040 HOH HOH . 
F 3 HOH B 15 1041 1041 HOH HOH . 
F 3 HOH B 16 1042 1042 HOH HOH . 
F 3 HOH B 17 1044 1044 HOH HOH . 
F 3 HOH B 18 1045 1045 HOH HOH . 
F 3 HOH B 19 1049 1049 HOH HOH . 
F 3 HOH B 20 1050 1050 HOH HOH . 
F 3 HOH B 21 1052 1052 HOH HOH . 
F 3 HOH B 22 1056 1056 HOH HOH . 
F 3 HOH B 23 1057 1057 HOH HOH . 
F 3 HOH B 24 1058 1058 HOH HOH . 
F 3 HOH B 25 1063 1063 HOH HOH . 
F 3 HOH B 26 1067 1067 HOH HOH . 
F 3 HOH B 27 1077 1077 HOH HOH . 
F 3 HOH B 28 1078 1078 HOH HOH . 
F 3 HOH B 29 1079 1079 HOH HOH . 
F 3 HOH B 30 1088 1088 HOH HOH . 
F 3 HOH B 31 1089 1089 HOH HOH . 
F 3 HOH B 32 1090 1090 HOH HOH . 
F 3 HOH B 33 1092 1092 HOH HOH . 
F 3 HOH B 34 1093 1093 HOH HOH . 
F 3 HOH B 35 1097 1097 HOH HOH . 
F 3 HOH B 36 1098 1098 HOH HOH . 
F 3 HOH B 37 1101 1101 HOH HOH . 
F 3 HOH B 38 1102 1102 HOH HOH . 
F 3 HOH B 39 1103 1103 HOH HOH . 
F 3 HOH B 40 1107 1107 HOH HOH . 
F 3 HOH B 41 1108 1108 HOH HOH . 
F 3 HOH B 42 1109 1109 HOH HOH . 
F 3 HOH B 43 1112 1112 HOH HOH . 
F 3 HOH B 44 1118 1118 HOH HOH . 
F 3 HOH B 45 1119 1119 HOH HOH . 
F 3 HOH B 46 1121 1121 HOH HOH . 
F 3 HOH B 47 1124 1124 HOH HOH . 
F 3 HOH B 48 1125 1125 HOH HOH . 
F 3 HOH B 49 1127 1127 HOH HOH . 
F 3 HOH B 50 1128 1128 HOH HOH . 
F 3 HOH B 51 1133 1133 HOH HOH . 
F 3 HOH B 52 1135 1135 HOH HOH . 
F 3 HOH B 53 1136 1136 HOH HOH . 
F 3 HOH B 54 1137 1137 HOH HOH . 
F 3 HOH B 55 1138 1138 HOH HOH . 
F 3 HOH B 56 1141 1141 HOH HOH . 
F 3 HOH B 57 1143 1143 HOH HOH . 
F 3 HOH B 58 1144 1144 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 KAN . . . D 2 -31.06 -50.699 -0.247 1 66.7 ? C1 KAN 2002 B 1 
HETATM 2 C C2 KAN . . . D 2 -29.726 -50.897 0.476 1 66.53 ? C2 KAN 2002 B 1 
HETATM 3 C C3 KAN . . . D 2 -29.881 -50.895 2 1 66.79 ? C3 KAN 2002 B 1 
HETATM 4 C C4 KAN . . . D 2 -30.751 -49.723 2.444 1 67.33 ? C4 KAN 2002 B 1 
HETATM 5 C C5 KAN . . . D 2 -32.074 -49.693 1.68 1 66.91 ? C5 KAN 2002 B 1 
HETATM 6 C C6 KAN . . . D 2 -32.851 -48.464 2.166 1 65.87 ? C6 KAN 2002 B 1 
HETATM 7 C C7 KAN . . . D 2 -31.49 -52.102 -4.506 1 65.02 ? C7 KAN 2002 B 1 
HETATM 8 C C8 KAN . . . D 2 -32.759 -51.485 -3.916 1 65.53 ? C8 KAN 2002 B 1 
HETATM 9 C C9 KAN . . . D 2 -32.532 -51.088 -2.455 1 65.45 ? C9 KAN 2002 B 1 
HETATM 10 C C10 KAN . . . D 2 -32.086 -52.283 -1.61 1 64.87 ? C10 KAN 2002 B 1 
HETATM 11 C C11 KAN . . . D 2 -30.768 -52.766 -2.217 1 64.1 ? C11 KAN 2002 B 1 
HETATM 12 C C12 KAN . . . D 2 -31.001 -53.268 -3.643 1 64.94 ? C12 KAN 2002 B 1 
HETATM 13 C C13 KAN . . . D 2 -34.518 -50.103 -4.588 1 68.93 ? C13 KAN 2002 B 1 
HETATM 14 C C14 KAN . . . D 2 -35.129 -50.296 -5.979 1 70.13 ? C14 KAN 2002 B 1 
HETATM 15 C C15 KAN . . . D 2 -34.517 -49.281 -6.945 1 70.49 ? C15 KAN 2002 B 1 
HETATM 16 C C16 KAN . . . D 2 -34.684 -47.871 -6.376 1 69.6 ? C16 KAN 2002 B 1 
HETATM 17 C C17 KAN . . . D 2 -34.117 -47.802 -4.957 1 68.76 ? C17 KAN 2002 B 1 
HETATM 18 C C18 KAN . . . D 2 -34.361 -46.405 -4.379 1 68.17 ? C18 KAN 2002 B 1 
HETATM 19 N N1 KAN . . . D 2 -34.045 -48.262 1.333 1 65.53 ? N1 KAN 2002 B 1 
HETATM 20 N N2 KAN . . . D 2 -30.211 -53.847 -1.388 1 63.3 ? N2 KAN 2002 B 1 
HETATM 21 N N3 KAN . . . D 2 -31.783 -52.584 -5.865 1 63.92 ? N3 KAN 2002 B 1 
HETATM 22 N N4 KAN . . . D 2 -35.172 -49.374 -8.259 1 69.42 ? N4 KAN 2002 B 1 
HETATM 23 O O5 KAN . . . D 2 -31.8 -49.582 0.275 1 66.77 ? O5 KAN 2002 B 1 
HETATM 24 O O6 KAN . . . D 2 -29.07 -52.091 0.044 1 63.69 ? O6 KAN 2002 B 1 
HETATM 25 O O7 KAN . . . D 2 -28.581 -50.721 2.57 1 66.51 ? O7 KAN 2002 B 1 
HETATM 26 O O8 KAN . . . D 2 -31.015 -49.823 3.849 1 68.78 ? O8 KAN 2002 B 1 
HETATM 27 O O9 KAN . . . D 2 -31.869 -51.886 -0.246 1 66.34 ? O9 KAN 2002 B 1 
HETATM 28 O O10 KAN . . . D 2 -33.725 -50.508 -1.915 1 65.44 ? O10 KAN 2002 B 1 
HETATM 29 O O11 KAN . . . D 2 -33.102 -50.315 -4.671 1 67.26 ? O11 KAN 2002 B 1 
HETATM 30 O O12 KAN . . . D 2 -34.776 -48.769 -4.124 1 68.51 ? O12 KAN 2002 B 1 
HETATM 31 O O13 KAN . . . D 2 -34.86 -51.625 -6.44 1 73.37 ? O13 KAN 2002 B 1 
HETATM 32 O O14 KAN . . . D 2 -33.992 -46.945 -7.221 1 70.95 ? O14 KAN 2002 B 1 
HETATM 33 O O15 KAN . . . D 2 -33.806 -46.314 -3.063 1 69.27 ? O15 KAN 2002 B 1 
#
_model_server_stats.io_time_ms              44 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#