data_1KNY # _model_server_result.job_id jdnz5u7LLoSizvSswvesHQ _model_server_result.datetime_utc '2025-02-27 06:26:14' _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 1kny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":559}' # _entry.id 1KNY # _exptl.entry_id 1KNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.499 _entity.id 4 _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 90 _cell.entry_id 1KNY _cell.length_a 57.3 _cell.length_b 102.2 _cell.length_c 108.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G,H,I,J _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 ? 4 E N N ? 4 H 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 metalc ? metalc1 A OE2 GLU 52 A GLU 52 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 A OE1 GLU 52 A GLU 52 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc3 D O1G APC . A APC 556 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc4 D O2B APC . A APC 556 1_555 C MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.646 ? metalc ? metalc5 B OE1 GLU 52 B GLU 52 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.018 ? metalc ? metalc6 B OE2 GLU 52 B GLU 52 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc7 G O1G APC . B APC 557 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc8 G O2B APC . B APC 557 1_555 F MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? # _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 224 n n C1 O5 KAN sing 225 n n C1 O9 KAN sing 226 n n C1 H1 KAN sing 227 n n C2 C3 KAN sing 228 n n C2 O6 KAN sing 229 n n C2 H2 KAN sing 230 n n C3 C4 KAN sing 231 n n C3 O7 KAN sing 232 n n C3 H3 KAN sing 233 n n C4 C5 KAN sing 234 n n C4 O8 KAN sing 235 n n C4 H4 KAN sing 236 n n C5 C6 KAN sing 237 n n C5 O5 KAN sing 238 n n C5 H5 KAN sing 239 n n C6 N1 KAN sing 240 n n C6 H61 KAN sing 241 n n C6 H62 KAN sing 242 n n C7 C8 KAN sing 243 n n C7 C12 KAN sing 244 n n C7 N3 KAN sing 245 n n C7 H7 KAN sing 246 n n C8 C9 KAN sing 247 n n C8 O11 KAN sing 248 n n C8 H8 KAN sing 249 n n C9 C10 KAN sing 250 n n C9 O10 KAN sing 251 n n C9 H9 KAN sing 252 n n C10 C11 KAN sing 253 n n C10 O9 KAN sing 254 n n C10 H10 KAN sing 255 n n C11 C12 KAN sing 256 n n C11 N2 KAN sing 257 n n C11 H11 KAN sing 258 n n C12 H121 KAN sing 259 n n C12 H122 KAN sing 260 n n C13 C14 KAN sing 261 n n C13 O11 KAN sing 262 n n C13 O12 KAN sing 263 n n C13 H13 KAN sing 264 n n C14 C15 KAN sing 265 n n C14 O13 KAN sing 266 n n C14 H14 KAN sing 267 n n C15 C16 KAN sing 268 n n C15 N4 KAN sing 269 n n C15 H15 KAN sing 270 n n C16 C17 KAN sing 271 n n C16 O14 KAN sing 272 n n C16 H16 KAN sing 273 n n C17 C18 KAN sing 274 n n C17 O12 KAN sing 275 n n C17 H17 KAN sing 276 n n C18 O15 KAN sing 277 n n C18 H181 KAN sing 278 n n C18 H182 KAN sing 279 n n N1 HN11 KAN sing 280 n n N1 HN12 KAN sing 281 n n N2 HN21 KAN sing 282 n n N2 HN22 KAN sing 283 n n N3 HN31 KAN sing 284 n n N3 HN32 KAN sing 285 n n N4 HN41 KAN sing 286 n n N4 HN42 KAN sing 287 n n O6 HO6 KAN sing 288 n n O7 HO7 KAN sing 289 n n O8 HO8 KAN sing 290 n n O10 HO1 KAN sing 291 n n O13 HO3 KAN sing 292 n n O14 HO4 KAN sing 293 n n O15 HO5 KAN sing 294 n n # _atom_sites.entry_id 1KNY _atom_sites.fract_transf_matrix[1][1] 0.017452 _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] 0.009785 _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] 0.009191 _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 MG A 1 603 603 MG MG . D 3 APC A 1 556 556 APC APC . E 4 KAN A 1 558 558 KAN KAN . F 2 MG B 1 604 604 MG MG . G 3 APC B 1 557 557 APC APC . H 4 KAN B 1 559 559 KAN KAN . I 5 HOH A 1 604 1 HOH HOH . I 5 HOH A 2 605 2 HOH HOH . I 5 HOH A 3 606 3 HOH HOH . I 5 HOH A 4 607 4 HOH HOH . I 5 HOH A 5 608 5 HOH HOH . I 5 HOH A 6 609 6 HOH HOH . I 5 HOH A 7 610 7 HOH HOH . I 5 HOH A 8 611 12 HOH HOH . I 5 HOH A 9 612 14 HOH HOH . I 5 HOH A 10 613 15 HOH HOH . I 5 HOH A 11 614 16 HOH HOH . I 5 HOH A 12 615 17 HOH HOH . I 5 HOH A 13 616 18 HOH HOH . I 5 HOH A 14 617 19 HOH HOH . I 5 HOH A 15 618 20 HOH HOH . I 5 HOH A 16 619 21 HOH HOH . I 5 HOH A 17 620 22 HOH HOH . I 5 HOH A 18 621 23 HOH HOH . I 5 HOH A 19 622 24 HOH HOH . I 5 HOH A 20 623 25 HOH HOH . I 5 HOH A 21 624 34 HOH HOH . I 5 HOH A 22 625 35 HOH HOH . I 5 HOH A 23 626 36 HOH HOH . I 5 HOH A 24 627 37 HOH HOH . I 5 HOH A 25 628 38 HOH HOH . I 5 HOH A 26 629 39 HOH HOH . I 5 HOH A 27 630 40 HOH HOH . I 5 HOH A 28 631 42 HOH HOH . J 5 HOH B 1 605 8 HOH HOH . J 5 HOH B 2 606 9 HOH HOH . J 5 HOH B 3 607 10 HOH HOH . J 5 HOH B 4 608 11 HOH HOH . J 5 HOH B 5 609 13 HOH HOH . J 5 HOH B 6 610 26 HOH HOH . J 5 HOH B 7 611 27 HOH HOH . J 5 HOH B 8 612 28 HOH HOH . J 5 HOH B 9 613 29 HOH HOH . J 5 HOH B 10 614 30 HOH HOH . J 5 HOH B 11 615 31 HOH HOH . J 5 HOH B 12 616 32 HOH HOH . J 5 HOH B 13 617 33 HOH HOH . J 5 HOH B 14 618 41 HOH HOH . J 5 HOH B 15 619 43 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 . . . H 4 19.8 47.345 42.542 1 44.62 ? C1 KAN 559 B 1 HETATM 2 C C2 KAN . . . H 4 18.676 47.083 43.509 1 30.45 ? C2 KAN 559 B 1 HETATM 3 C C3 KAN . . . H 4 18.123 45.67 43.398 1 62.78 ? C3 KAN 559 B 1 HETATM 4 C C4 KAN . . . H 4 17.981 45.156 41.969 1 35.07 ? C4 KAN 559 B 1 HETATM 5 C C5 KAN . . . H 4 19.041 45.708 41.011 1 100 ? C5 KAN 559 B 1 HETATM 6 C C6 KAN . . . H 4 18.54 45.634 39.585 1 43.59 ? C6 KAN 559 B 1 HETATM 7 C C7 KAN . . . H 4 24.992 47.643 42.634 1 100 ? C7 KAN 559 B 1 HETATM 8 C C8 KAN . . . H 4 24.417 46.315 42.126 1 100 ? C8 KAN 559 B 1 HETATM 9 C C9 KAN . . . H 4 22.984 46.495 41.649 1 32.78 ? C9 KAN 559 B 1 HETATM 10 C C10 KAN . . . H 4 22.234 46.836 42.939 1 40.69 ? C10 KAN 559 B 1 HETATM 11 C C11 KAN . . . H 4 22.648 48.204 43.48 1 42.74 ? C11 KAN 559 B 1 HETATM 12 C C12 KAN . . . H 4 24.147 48.166 43.796 1 58.07 ? C12 KAN 559 B 1 HETATM 13 C C13 KAN . . . H 4 25.64 44.363 41.501 1 82.66 ? C13 KAN 559 B 1 HETATM 14 C C14 KAN . . . H 4 27.143 44.209 41.794 1 100 ? C14 KAN 559 B 1 HETATM 15 C C15 KAN . . . H 4 27.998 44.307 40.533 1 100 ? C15 KAN 559 B 1 HETATM 16 C C16 KAN . . . H 4 27.456 43.411 39.419 1 100 ? C16 KAN 559 B 1 HETATM 17 C C17 KAN . . . H 4 25.969 43.684 39.266 1 100 ? C17 KAN 559 B 1 HETATM 18 C C18 KAN . . . H 4 25.345 42.817 38.21 1 100 ? C18 KAN 559 B 1 HETATM 19 N N1 KAN . . . H 4 17.194 45.001 39.462 1 37.17 ? N1 KAN 559 B 1 HETATM 20 N N2 KAN . . . H 4 21.868 48.49 44.676 1 41.71 ? N2 KAN 559 B 1 HETATM 21 N N3 KAN . . . H 4 26.401 47.524 43.035 1 34.54 ? N3 KAN 559 B 1 HETATM 22 N N4 KAN . . . H 4 29.408 43.917 40.843 1 61.94 ? N4 KAN 559 B 1 HETATM 23 O O5 KAN . . . H 4 19.323 47.093 41.24 1 38.59 ? O5 KAN 559 B 1 HETATM 24 O O6 KAN . . . H 4 19.208 47.294 44.791 1 100 ? O6 KAN 559 B 1 HETATM 25 O O7 KAN . . . H 4 16.877 45.568 44.075 1 100 ? O7 KAN 559 B 1 HETATM 26 O O8 KAN . . . H 4 18.008 43.74 41.9 1 100 ? O8 KAN 559 B 1 HETATM 27 O O9 KAN . . . H 4 20.837 46.454 42.911 1 50.9 ? O9 KAN 559 B 1 HETATM 28 O O10 KAN . . . H 4 22.542 45.273 41.083 1 65.82 ? O10 KAN 559 B 1 HETATM 29 O O11 KAN . . . H 4 25.291 45.687 41.156 1 100 ? O11 KAN 559 B 1 HETATM 30 O O12 KAN . . . H 4 25.289 43.439 40.513 1 91 ? O12 KAN 559 B 1 HETATM 31 O O13 KAN . . . H 4 27.581 45.134 42.781 1 90.25 ? O13 KAN 559 B 1 HETATM 32 O O14 KAN . . . H 4 28.138 43.741 38.212 1 100 ? O14 KAN 559 B 1 HETATM 33 O O15 KAN . . . H 4 25.669 41.45 38.488 1 100 ? O15 KAN 559 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 353 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 33 #