data_4JD6
#
_model_server_result.job_id            L4N6Ig2A9jkv48GsgvEr7w 
_model_server_result.datetime_utc      '2024-10-15 13:18:32' 
_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          4jd6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    4JD6 
#
_exptl.entry_id    4JD6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              467.514 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            TOBRAMYCIN 
_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          104.7 
_cell.angle_gamma         90 
_cell.entry_id            4JD6 
_cell.length_a            82.226 
_cell.length_b            154.908 
_cell.length_c            115.286 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JD6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,K,L,M,N 
_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
? 3 H N N 
? 3 J N N 
#
_chem_comp.formula           'C18 H37 N5 O9' 
_chem_comp.formula_weight    467.514 
_chem_comp.id                TOY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              TOBRAMYCIN 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL 
#
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
C11 O11 TOY sing 390 n n 
C11 C21 TOY sing 391 n n 
C11 O51 TOY sing 392 n n 
C11 H11 TOY sing 393 n n 
O11 C42 TOY sing 394 n n 
C21 N21 TOY sing 395 n n 
C21 C31 TOY sing 396 n n 
C21 H21 TOY sing 397 n n 
N21 HN21 TOY sing 398 n n 
N21 HN22 TOY sing 399 n n 
C31 C41 TOY sing 400 n n 
C31 H311 TOY sing 401 n n 
C31 H312 TOY sing 402 n n 
C41 O41 TOY sing 403 n n 
C41 C51 TOY sing 404 n n 
C41 H41 TOY sing 405 n n 
O41 H41O TOY sing 406 n n 
C51 O51 TOY sing 407 n n 
C51 C61 TOY sing 408 n n 
C51 H51 TOY sing 409 n n 
C61 N61 TOY sing 410 n n 
C61 H611 TOY sing 411 n n 
C61 H612 TOY sing 412 n n 
N61 HN61 TOY sing 413 n n 
N61 HN62 TOY sing 414 n n 
C12 N12 TOY sing 415 n n 
C12 C22 TOY sing 416 n n 
C12 C62 TOY sing 417 n n 
C12 H12 TOY sing 418 n n 
N12 HN11 TOY sing 419 n n 
N12 HN12 TOY sing 420 n n 
C22 C32 TOY sing 421 n n 
C22 H221 TOY sing 422 n n 
C22 H222 TOY sing 423 n n 
C32 N32 TOY sing 424 n n 
C32 C42 TOY sing 425 n n 
C32 H32 TOY sing 426 n n 
N32 HN1 TOY sing 427 n n 
N32 HN2 TOY sing 428 n n 
C42 C52 TOY sing 429 n n 
C42 H42 TOY sing 430 n n 
C52 O52 TOY sing 431 n n 
C52 C62 TOY sing 432 n n 
C52 H52 TOY sing 433 n n 
O52 H52O TOY sing 434 n n 
C62 O62 TOY sing 435 n n 
C62 H62 TOY sing 436 n n 
O62 C13 TOY sing 437 n n 
C13 C23 TOY sing 438 n n 
C13 O53 TOY sing 439 n n 
C13 H13 TOY sing 440 n n 
C23 O23 TOY sing 441 n n 
C23 C33 TOY sing 442 n n 
C23 H23 TOY sing 443 n n 
O23 H23O TOY sing 444 n n 
C33 N33 TOY sing 445 n n 
C33 C43 TOY sing 446 n n 
C33 H33 TOY sing 447 n n 
N33 HN31 TOY sing 448 n n 
N33 HN32 TOY sing 449 n n 
C43 O43 TOY sing 450 n n 
C43 C53 TOY sing 451 n n 
C43 H43 TOY sing 452 n n 
O43 H43O TOY sing 453 n n 
C53 O53 TOY sing 454 n n 
C53 C63 TOY sing 455 n n 
C53 H53 TOY sing 456 n n 
C63 O63 TOY sing 457 n n 
C63 H631 TOY sing 458 n n 
C63 H632 TOY sing 459 n n 
O63 H63O TOY sing 460 n n 
#
_atom_sites.entry_id                     4JD6 
_atom_sites.fract_transf_matrix[1][1]    0.012162 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00319 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006455 
_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]    0.008968 
_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
G 2 COA A 1 500 500 COA COA . 
H 3 TOY A 1 501 501 TOY TOY . 
I 2 COA B 1 500 500 COA COA . 
J 3 TOY B 1 501 501 TOY TOY . 
K 2 COA C 1 500 500 COA COA . 
L 2 COA D 1 500 500 COA COA . 
M 2 COA E 1 500 500 COA COA . 
N 2 COA F 1 500 500 COA COA . 
#
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 TOY . A . J 3 -8.317 18.725 48.692 0.5 118.56 ? C11 TOY 501 B 1 
HETATM 2 C C11 TOY . B . J 3 -11.023 11.914 48.453 0.5 145.15 ? C11 TOY 501 B 1 
HETATM 3 O O11 TOY . A . J 3 -7.392 17.993 47.882 0.5 121.31 ? O11 TOY 501 B 1 
HETATM 4 O O11 TOY . B . J 3 -9.808 12.614 48.811 0.5 143.42 ? O11 TOY 501 B 1 
HETATM 5 C C21 TOY . A . J 3 -9.261 19.558 47.827 0.5 116.94 ? C21 TOY 501 B 1 
HETATM 6 C C21 TOY . B . J 3 -11.043 11.133 47.125 0.5 145.54 ? C21 TOY 501 B 1 
HETATM 7 N N21 TOY . A . J 3 -9.713 18.769 46.697 0.5 115.36 ? N21 TOY 501 B 1 
HETATM 8 N N21 TOY . B . J 3 -9.733 10.563 46.853 0.5 145.09 ? N21 TOY 501 B 1 
HETATM 9 C C31 TOY . A . J 3 -8.568 20.808 47.32 0.5 116.46 ? C31 TOY 501 B 1 
HETATM 10 C C31 TOY . B . J 3 -11.522 11.905 45.899 0.5 146.14 ? C31 TOY 501 B 1 
HETATM 11 C C41 TOY . A . J 3 -7.994 21.594 48.484 0.5 116.81 ? C41 TOY 501 B 1 
HETATM 12 C C41 TOY . B . J 3 -12.64 12.884 46.227 0.5 147.01 ? C41 TOY 501 B 1 
HETATM 13 O O41 TOY . A . J 3 -7.323 22.761 47.996 0.5 116.64 ? O41 TOY 501 B 1 
HETATM 14 O O41 TOY . B . J 3 -12.781 13.802 45.14 0.5 147.15 ? O41 TOY 501 B 1 
HETATM 15 C C51 TOY . A . J 3 -7.026 20.73 49.276 0.5 116.6 ? C51 TOY 501 B 1 
HETATM 16 C C51 TOY . B . J 3 -12.303 13.67 47.483 0.5 146.96 ? C51 TOY 501 B 1 
HETATM 17 O O51 TOY . A . J 3 -7.642 19.505 49.692 0.5 118.28 ? O51 TOY 501 B 1 
HETATM 18 O O51 TOY . B . J 3 -12.165 12.768 48.575 0.5 145.98 ? O51 TOY 501 B 1 
HETATM 19 C C61 TOY . A . J 3 -6.591 21.486 50.524 0.5 115.05 ? C61 TOY 501 B 1 
HETATM 20 C C61 TOY . B . J 3 -13.389 14.69 47.798 0.5 147.18 ? C61 TOY 501 B 1 
HETATM 21 N N61 TOY . A . J 3 -5.974 22.748 50.154 0.5 113.13 ? N61 TOY 501 B 1 
HETATM 22 N N61 TOY . B . J 3 -13.149 15.907 47.043 0.5 147.6 ? N61 TOY 501 B 1 
HETATM 23 C C12 TOY . A . J 3 -7.053 13.755 47.659 0.5 123.93 ? C12 TOY 501 B 1 
HETATM 24 C C12 TOY . B . J 3 -6.277 14.504 48.274 0.5 138.48 ? C12 TOY 501 B 1 
HETATM 25 N N12 TOY . A . J 3 -6.992 12.377 48.109 0.5 122.93 ? N12 TOY 501 B 1 
HETATM 26 N N12 TOY . B . J 3 -5.03 15.169 47.949 0.5 138.09 ? N12 TOY 501 B 1 
HETATM 27 C C22 TOY . A . J 3 -5.909 14.547 48.286 0.5 123.08 ? C22 TOY 501 B 1 
HETATM 28 C C22 TOY . B . J 3 -6.35 13.168 47.557 0.5 138.85 ? C22 TOY 501 B 1 
HETATM 29 C C32 TOY . A . J 3 -5.979 16.024 47.911 0.5 122.82 ? C32 TOY 501 B 1 
HETATM 30 C C32 TOY . B . J 3 -7.582 12.399 48.022 0.5 139.38 ? C32 TOY 501 B 1 
HETATM 31 N N32 TOY . A . J 3 -4.93 16.748 48.603 0.5 122.01 ? N32 TOY 501 B 1 
HETATM 32 N N32 TOY . B . J 3 -7.645 11.123 47.33 0.5 139.48 ? N32 TOY 501 B 1 
HETATM 33 C C42 TOY . A . J 3 -7.334 16.62 48.278 0.5 123.03 ? C42 TOY 501 B 1 
HETATM 34 C C42 TOY . B . J 3 -8.904 13.149 47.836 0.5 141.16 ? C42 TOY 501 B 1 
HETATM 35 C C52 TOY . A . J 3 -8.469 15.828 47.632 0.5 124.29 ? C52 TOY 501 B 1 
HETATM 36 C C52 TOY . B . J 3 -8.81 14.667 48.087 0.5 140.72 ? C52 TOY 501 B 1 
HETATM 37 O O52 TOY . A . J 3 -9.729 16.378 48.034 0.5 125.28 ? O52 TOY 501 B 1 
HETATM 38 O O52 TOY . B . J 3 -9.799 15.319 47.279 0.5 141.68 ? O52 TOY 501 B 1 
HETATM 39 C C62 TOY . A . J 3 -8.407 14.355 48.027 0.5 124.43 ? C62 TOY 501 B 1 
HETATM 40 C C62 TOY . B . J 3 -7.459 15.353 47.828 0.5 139.41 ? C62 TOY 501 B 1 
HETATM 41 O O62 TOY . A . J 3 -9.458 13.638 47.373 0.5 124.7 ? O62 TOY 501 B 1 
HETATM 42 O O62 TOY . B . J 3 -7.428 16.622 48.495 0.5 137.24 ? O62 TOY 501 B 1 
HETATM 43 C C13 TOY . A . J 3 -10.389 13.083 48.305 0.5 125.28 ? C13 TOY 501 B 1 
HETATM 44 C C13 TOY . B . J 3 -7.01 17.678 47.62 0.5 134.39 ? C13 TOY 501 B 1 
HETATM 45 C C23 TOY . A . J 3 -10.788 11.668 47.876 0.5 125.66 ? C23 TOY 501 B 1 
HETATM 46 C C23 TOY . B . J 3 -6.163 18.718 48.365 0.5 133.14 ? C23 TOY 501 B 1 
HETATM 47 O O23 TOY . A . J 3 -9.616 10.939 47.495 0.5 125.41 ? O23 TOY 501 B 1 
HETATM 48 O O23 TOY . B . J 3 -5.308 18.043 49.295 0.5 132.33 ? O23 TOY 501 B 1 
HETATM 49 C C33 TOY . A . J 3 -11.776 11.666 46.716 0.5 126 ? C33 TOY 501 B 1 
HETATM 50 C C33 TOY . B . J 3 -6.989 19.777 49.092 0.5 132.56 ? C33 TOY 501 B 1 
HETATM 51 N N33 TOY . A . J 3 -12.297 10.327 46.52 0.5 125.58 ? N33 TOY 501 B 1 
HETATM 52 N N33 TOY . B . J 3 -6.134 20.861 49.538 0.5 131.79 ? N33 TOY 501 B 1 
HETATM 53 C C43 TOY . A . J 3 -12.918 12.626 47.009 0.5 126.29 ? C43 TOY 501 B 1 
HETATM 54 C C43 TOY . B . J 3 -8.052 20.314 48.153 0.5 132.06 ? C43 TOY 501 B 1 
HETATM 55 O O43 TOY . A . J 3 -13.804 12.682 45.891 0.5 126.63 ? O43 TOY 501 B 1 
HETATM 56 O O43 TOY . B . J 3 -8.825 21.319 48.812 0.5 130.92 ? O43 TOY 501 B 1 
HETATM 57 C C53 TOY . A . J 3 -12.353 14.011 47.286 0.5 126.1 ? C53 TOY 501 B 1 
HETATM 58 C C53 TOY . B . J 3 -8.928 19.146 47.731 0.5 131.02 ? C53 TOY 501 B 1 
HETATM 59 O O53 TOY . A . J 3 -11.528 13.944 48.448 0.5 125.4 ? O53 TOY 501 B 1 
HETATM 60 O O53 TOY . B . J 3 -8.138 18.255 46.944 0.5 132.35 ? O53 TOY 501 B 1 
HETATM 61 C C63 TOY . A . J 3 -13.468 15.031 47.498 0.5 126.21 ? C63 TOY 501 B 1 
HETATM 62 C C63 TOY . B . J 3 -10.127 19.614 46.915 0.5 128.64 ? C63 TOY 501 B 1 
HETATM 63 O O63 TOY . A . J 3 -12.908 16.296 47.894 0.5 124.99 ? O63 TOY 501 B 1 
HETATM 64 O O63 TOY . B . J 3 -11.08 18.55 46.813 0.5 127.7 ? O63 TOY 501 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           64 
#