data_1L8T
#
_model_server_result.job_id            v_sav3hB2dEDgKxaXtjHqw 
_model_server_result.datetime_utc      '2025-01-09 18:57:49' 
_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          1l8t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1}' 
#
_entry.id    1L8T 
#
_exptl.entry_id    1L8T 
_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    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            1L8T 
_cell.length_a            46.629 
_cell.length_b            46.629 
_cell.length_c            301.289 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1L8T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        95 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_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
metalc ? metalc1 A OD1 ASN 194 A ASN 195 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? 
metalc ? metalc2 A OD2 ASP 207 A ASP 208 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc3 A OD2 ASP 207 A ASP 208 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc4 A OD1 ASP 207 A ASP 208 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc5 D O2A ADP . A ADP 300 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? 
metalc ? metalc6 D O3B ADP . A ADP 300 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc7 D O1B ADP . A ADP 300 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc8 B MG MG . A MG 301 1_555 F O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? 
metalc ? metalc9 B MG MG . A MG 301 1_555 F O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc10 C MG MG . A MG 302 1_555 F O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? 
metalc ? metalc11 C MG MG . A MG 302 1_555 F O HOH . A HOH 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? 
metalc ? metalc12 C MG MG . A MG 302 1_555 F O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
#
_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 217 n n 
C1 O5 KAN sing 218 n n 
C1 O9 KAN sing 219 n n 
C1 H1 KAN sing 220 n n 
C2 C3 KAN sing 221 n n 
C2 O6 KAN sing 222 n n 
C2 H2 KAN sing 223 n n 
C3 C4 KAN sing 224 n n 
C3 O7 KAN sing 225 n n 
C3 H3 KAN sing 226 n n 
C4 C5 KAN sing 227 n n 
C4 O8 KAN sing 228 n n 
C4 H4 KAN sing 229 n n 
C5 C6 KAN sing 230 n n 
C5 O5 KAN sing 231 n n 
C5 H5 KAN sing 232 n n 
C6 N1 KAN sing 233 n n 
C6 H61 KAN sing 234 n n 
C6 H62 KAN sing 235 n n 
C7 C8 KAN sing 236 n n 
C7 C12 KAN sing 237 n n 
C7 N3 KAN sing 238 n n 
C7 H7 KAN sing 239 n n 
C8 C9 KAN sing 240 n n 
C8 O11 KAN sing 241 n n 
C8 H8 KAN sing 242 n n 
C9 C10 KAN sing 243 n n 
C9 O10 KAN sing 244 n n 
C9 H9 KAN sing 245 n n 
C10 C11 KAN sing 246 n n 
C10 O9 KAN sing 247 n n 
C10 H10 KAN sing 248 n n 
C11 C12 KAN sing 249 n n 
C11 N2 KAN sing 250 n n 
C11 H11 KAN sing 251 n n 
C12 H121 KAN sing 252 n n 
C12 H122 KAN sing 253 n n 
C13 C14 KAN sing 254 n n 
C13 O11 KAN sing 255 n n 
C13 O12 KAN sing 256 n n 
C13 H13 KAN sing 257 n n 
C14 C15 KAN sing 258 n n 
C14 O13 KAN sing 259 n n 
C14 H14 KAN sing 260 n n 
C15 C16 KAN sing 261 n n 
C15 N4 KAN sing 262 n n 
C15 H15 KAN sing 263 n n 
C16 C17 KAN sing 264 n n 
C16 O14 KAN sing 265 n n 
C16 H16 KAN sing 266 n n 
C17 C18 KAN sing 267 n n 
C17 O12 KAN sing 268 n n 
C17 H17 KAN sing 269 n n 
C18 O15 KAN sing 270 n n 
C18 H181 KAN sing 271 n n 
C18 H182 KAN sing 272 n n 
N1 HN11 KAN sing 273 n n 
N1 HN12 KAN sing 274 n n 
N2 HN21 KAN sing 275 n n 
N2 HN22 KAN sing 276 n n 
N3 HN31 KAN sing 277 n n 
N3 HN32 KAN sing 278 n n 
N4 HN41 KAN sing 279 n n 
N4 HN42 KAN sing 280 n n 
O6 HO6 KAN sing 281 n n 
O7 HO7 KAN sing 282 n n 
O8 HO8 KAN sing 283 n n 
O10 HO1 KAN sing 284 n n 
O13 HO3 KAN sing 285 n n 
O14 HO4 KAN sing 286 n n 
O15 HO5 KAN sing 287 n n 
#
_atom_sites.entry_id                     1L8T 
_atom_sites.fract_transf_matrix[1][1]    0.021446 
_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]    0.021446 
_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]    0.003319 
_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 MG A 1 301 301 MG MG2 . 
C 2 MG A 1 302 302 MG MG2 . 
D 3 ADP A 1 300 300 ADP ADP . 
E 4 KAN A 1 1 1 KAN KAN . 
F 5 HOH A 1 501 501 HOH WAT . 
F 5 HOH A 2 502 502 HOH WAT . 
F 5 HOH A 3 503 503 HOH WAT . 
F 5 HOH A 4 504 504 HOH WAT . 
F 5 HOH A 5 505 505 HOH WAT . 
F 5 HOH A 6 506 506 HOH WAT . 
F 5 HOH A 7 507 507 HOH WAT . 
F 5 HOH A 8 508 508 HOH WAT . 
F 5 HOH A 9 509 509 HOH WAT . 
F 5 HOH A 10 510 510 HOH WAT . 
F 5 HOH A 11 511 511 HOH WAT . 
F 5 HOH A 12 512 512 HOH WAT . 
F 5 HOH A 13 513 513 HOH WAT . 
F 5 HOH A 14 514 514 HOH WAT . 
F 5 HOH A 15 515 515 HOH WAT . 
F 5 HOH A 16 516 516 HOH WAT . 
F 5 HOH A 17 517 517 HOH WAT . 
F 5 HOH A 18 518 518 HOH WAT . 
F 5 HOH A 19 519 519 HOH WAT . 
F 5 HOH A 20 520 520 HOH WAT . 
F 5 HOH A 21 521 521 HOH WAT . 
F 5 HOH A 22 522 522 HOH WAT . 
F 5 HOH A 23 523 523 HOH WAT . 
F 5 HOH A 24 524 524 HOH WAT . 
F 5 HOH A 25 525 525 HOH WAT . 
F 5 HOH A 26 526 526 HOH WAT . 
F 5 HOH A 27 527 527 HOH WAT . 
F 5 HOH A 28 528 528 HOH WAT . 
F 5 HOH A 29 529 529 HOH WAT . 
F 5 HOH A 30 530 530 HOH WAT . 
F 5 HOH A 31 531 531 HOH WAT . 
F 5 HOH A 32 532 532 HOH WAT . 
F 5 HOH A 33 533 533 HOH WAT . 
F 5 HOH A 34 534 534 HOH WAT . 
F 5 HOH A 35 535 535 HOH WAT . 
F 5 HOH A 36 536 536 HOH WAT . 
F 5 HOH A 37 537 537 HOH WAT . 
F 5 HOH A 38 538 538 HOH WAT . 
F 5 HOH A 39 539 539 HOH WAT . 
F 5 HOH A 40 540 540 HOH WAT . 
F 5 HOH A 41 541 541 HOH WAT . 
F 5 HOH A 42 542 542 HOH WAT . 
F 5 HOH A 43 543 543 HOH WAT . 
F 5 HOH A 44 544 544 HOH WAT . 
F 5 HOH A 45 545 545 HOH WAT . 
F 5 HOH A 46 546 546 HOH WAT . 
F 5 HOH A 47 547 547 HOH WAT . 
F 5 HOH A 48 548 548 HOH WAT . 
F 5 HOH A 49 549 549 HOH WAT . 
F 5 HOH A 50 550 550 HOH WAT . 
F 5 HOH A 51 551 551 HOH WAT . 
F 5 HOH A 52 552 552 HOH WAT . 
F 5 HOH A 53 553 553 HOH WAT . 
F 5 HOH A 54 554 554 HOH WAT . 
F 5 HOH A 55 555 555 HOH WAT . 
F 5 HOH A 56 556 556 HOH WAT . 
F 5 HOH A 57 557 557 HOH WAT . 
F 5 HOH A 58 558 558 HOH WAT . 
F 5 HOH A 59 559 559 HOH WAT . 
F 5 HOH A 60 560 560 HOH WAT . 
F 5 HOH A 61 561 561 HOH WAT . 
F 5 HOH A 62 562 562 HOH WAT . 
F 5 HOH A 63 563 563 HOH WAT . 
F 5 HOH A 64 564 564 HOH WAT . 
F 5 HOH A 65 565 565 HOH WAT . 
#
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 . . . E 4 58.646 14.74 -275.631 1 39.67 ? C1 KAN 1 A 1 
HETATM 2 C C2 KAN . . . E 4 59.982 14.003 -275.551 1 42.01 ? C2 KAN 1 A 1 
HETATM 3 C C3 KAN . . . E 4 59.82 12.594 -276.061 1 42.86 ? C3 KAN 1 A 1 
HETATM 4 C C4 KAN . . . E 4 58.733 11.897 -275.27 1 42.8 ? C4 KAN 1 A 1 
HETATM 5 C C5 KAN . . . E 4 57.435 12.657 -275.481 1 41.78 ? C5 KAN 1 A 1 
HETATM 6 C C6 KAN . . . E 4 56.312 11.988 -274.699 1 42.88 ? C6 KAN 1 A 1 
HETATM 7 C C7 KAN . . . E 4 56.739 18.282 -278.948 1 40.25 ? C7 KAN 1 A 1 
HETATM 8 C C8 KAN . . . E 4 57.791 18.511 -277.847 1 41.81 ? C8 KAN 1 A 1 
HETATM 9 C C9 KAN . . . E 4 58.525 17.176 -277.544 1 41.45 ? C9 KAN 1 A 1 
HETATM 10 C C10 KAN . . . E 4 57.53 16.068 -277.176 1 39.17 ? C10 KAN 1 A 1 
HETATM 11 C C11 KAN . . . E 4 56.561 15.88 -278.345 1 40.67 ? C11 KAN 1 A 1 
HETATM 12 C C12 KAN . . . E 4 55.774 17.165 -278.569 1 39.23 ? C12 KAN 1 A 1 
HETATM 13 C C13 KAN . . . E 4 59.22 20.281 -277.285 1 50.11 ? C13 KAN 1 A 1 
HETATM 14 C C14 KAN . . . E 4 59.268 21.758 -277.698 1 51.49 ? C14 KAN 1 A 1 
HETATM 15 C C15 KAN . . . E 4 60.255 21.979 -278.829 1 53.35 ? C15 KAN 1 A 1 
HETATM 16 C C16 KAN . . . E 4 61.599 21.397 -278.473 1 54.12 ? C16 KAN 1 A 1 
HETATM 17 C C17 KAN . . . E 4 61.413 19.913 -278.18 1 54.59 ? C17 KAN 1 A 1 
HETATM 18 C C18 KAN . . . E 4 62.745 19.26 -277.843 1 56.73 ? C18 KAN 1 A 1 
HETATM 19 N N1 KAN . . . E 4 55.039 12.67 -274.968 1 42.39 ? N1 KAN 1 A 1 
HETATM 20 N N2 KAN . . . E 4 55.625 14.78 -278.053 1 39.79 ? N2 KAN 1 A 1 
HETATM 21 N N3 KAN . . . E 4 55.98 19.521 -279.175 1 35.81 ? N3 KAN 1 A 1 
HETATM 22 N N4 KAN . . . E 4 60.392 23.42 -279.07 1 55.56 ? N4 KAN 1 A 1 
HETATM 23 O O5 KAN . . . E 4 57.58 14.005 -274.989 1 39.74 ? O5 KAN 1 A 1 
HETATM 24 O O6 KAN . . . E 4 60.94 14.674 -276.369 1 42.27 ? O6 KAN 1 A 1 
HETATM 25 O O7 KAN . . . E 4 61.038 11.912 -275.862 1 45.56 ? O7 KAN 1 A 1 
HETATM 26 O O8 KAN . . . E 4 58.58 10.578 -275.782 1 44.6 ? O8 KAN 1 A 1 
HETATM 27 O O9 KAN . . . E 4 58.221 14.845 -276.992 1 38.44 ? O9 KAN 1 A 1 
HETATM 28 O O10 KAN . . . E 4 59.402 17.374 -276.438 1 44.45 ? O10 KAN 1 A 1 
HETATM 29 O O11 KAN . . . E 4 58.732 19.455 -278.352 1 45.86 ? O11 KAN 1 A 1 
HETATM 30 O O12 KAN . . . E 4 60.541 19.756 -277.045 1 51.51 ? O12 KAN 1 A 1 
HETATM 31 O O13 KAN . . . E 4 57.988 22.141 -278.154 1 54.43 ? O13 KAN 1 A 1 
HETATM 32 O O14 KAN . . . E 4 62.446 21.559 -279.6 1 53.35 ? O14 KAN 1 A 1 
HETATM 33 O O15 KAN . . . E 4 62.72 17.941 -278.381 1 56.67 ? O15 KAN 1 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           33 
#