data_4JD6
#
_model_server_result.job_id            GXSDAwbsFTnFQRKeUYbL-g 
_model_server_result.datetime_utc      '2024-10-15 13:17:48' 
_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":"H","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 . H 3 -10.262 -21.463 36.743 0.5 127.81 ? C11 TOY 501 A 1 
HETATM 2 C C11 TOY . B . H 3 -10.834 -18.222 30.879 0.5 149.11 ? C11 TOY 501 A 1 
HETATM 3 O O11 TOY . A . H 3 -9.285 -20.421 36.835 0.5 130.66 ? O11 TOY 501 A 1 
HETATM 4 O O11 TOY . B . H 3 -10.007 -17.227 31.476 0.5 149.94 ? O11 TOY 501 A 1 
HETATM 5 C C21 TOY . A . H 3 -11.528 -21.087 37.51 0.5 126.52 ? C21 TOY 501 A 1 
HETATM 6 C C21 TOY . B . H 3 -11.114 -17.82 29.419 0.5 148.47 ? C21 TOY 501 A 1 
HETATM 7 N N21 TOY . A . H 3 -11.884 -19.711 37.215 0.5 125.5 ? N21 TOY 501 A 1 
HETATM 8 N N21 TOY . B . H 3 -9.87 -17.318 28.841 0.5 148 ? N21 TOY 501 A 1 
HETATM 9 C C31 TOY . A . H 3 -11.316 -21.241 39.006 0.5 124.92 ? C31 TOY 501 A 1 
HETATM 10 C C31 TOY . B . H 3 -12.18 -16.736 29.241 0.5 148.22 ? C31 TOY 501 A 1 
HETATM 11 C C41 TOY . A . H 3 -10.851 -22.651 39.32 0.5 124.47 ? C41 TOY 501 A 1 
HETATM 12 C C41 TOY . B . H 3 -13.071 -16.571 30.466 0.5 148.54 ? C41 TOY 501 A 1 
HETATM 13 O O41 TOY . A . H 3 -10.645 -22.792 40.729 0.5 123.85 ? O41 TOY 501 A 1 
HETATM 14 O O41 TOY . B . H 3 -12.503 -15.609 31.36 0.5 148.92 ? O41 TOY 501 A 1 
HETATM 15 C C51 TOY . A . H 3 -9.565 -22.952 38.57 0.5 124.99 ? C51 TOY 501 A 1 
HETATM 16 C C51 TOY . B . H 3 -13.205 -17.891 31.191 0.5 148.25 ? C51 TOY 501 A 1 
HETATM 17 O O51 TOY . A . H 3 -9.725 -22.728 37.165 0.5 126.76 ? O51 TOY 501 A 1 
HETATM 18 O O51 TOY . B . H 3 -11.982 -18.37 31.719 0.5 148.9 ? O51 TOY 501 A 1 
HETATM 19 C C61 TOY . A . H 3 -9.21 -24.419 38.775 0.5 124.73 ? C61 TOY 501 A 1 
HETATM 20 C C61 TOY . B . H 3 -13.709 -18.887 30.215 0.5 147.32 ? C61 TOY 501 A 1 
HETATM 21 N N61 TOY . A . H 3 -9.192 -24.727 40.216 0.5 123.66 ? N61 TOY 501 A 1 
HETATM 22 N N61 TOY . B . H 3 -15.173 -18.681 30.3 0.5 146.14 ? N61 TOY 501 A 1 
HETATM 23 C C12 TOY . A . H 3 -7.712 -18.172 33.573 0.5 133 ? C12 TOY 501 A 1 
HETATM 24 C C12 TOY . B . H 3 -7.627 -19.452 34.249 0.5 147.91 ? C12 TOY 501 A 1 
HETATM 25 N N12 TOY . A . H 3 -7.162 -17.932 32.252 0.5 132.48 ? N12 TOY 501 A 1 
HETATM 26 N N12 TOY . B . H 3 -6.813 -19.682 35.43 0.5 147.96 ? N12 TOY 501 A 1 
HETATM 27 C C22 TOY . A . H 3 -6.784 -19.111 34.339 0.5 132.24 ? C22 TOY 501 A 1 
HETATM 28 C C22 TOY . B . H 3 -6.985 -18.378 33.381 0.5 147.27 ? C22 TOY 501 A 1 
HETATM 29 C C32 TOY . A . H 3 -7.356 -19.505 35.696 0.5 132.08 ? C32 TOY 501 A 1 
HETATM 30 C C32 TOY . B . H 3 -7.847 -18.117 32.152 0.5 147.49 ? C32 TOY 501 A 1 
HETATM 31 N N32 TOY . A . H 3 -6.486 -20.486 36.317 0.5 130.78 ? N32 TOY 501 A 1 
HETATM 32 N N32 TOY . B . H 3 -7.236 -17.093 31.328 0.5 147.58 ? N32 TOY 501 A 1 
HETATM 33 C C42 TOY . A . H 3 -8.754 -20.095 35.547 0.5 132.38 ? C42 TOY 501 A 1 
HETATM 34 C C42 TOY . B . H 3 -9.233 -17.674 32.596 0.5 149.18 ? C42 TOY 501 A 1 
HETATM 35 C C52 TOY . A . H 3 -9.676 -19.122 34.816 0.5 133.66 ? C52 TOY 501 A 1 
HETATM 36 C C52 TOY . B . H 3 -9.891 -18.767 33.431 0.5 149.34 ? C52 TOY 501 A 1 
HETATM 37 O O52 TOY . A . H 3 -10.973 -19.708 34.663 0.5 134.58 ? O52 TOY 501 A 1 
HETATM 38 O O52 TOY . B . H 3 -11.215 -18.378 33.815 0.5 150 ? O52 TOY 501 A 1 
HETATM 39 C C62 TOY . A . H 3 -9.115 -18.759 33.444 0.5 134.02 ? C62 TOY 501 A 1 
HETATM 40 C C62 TOY . B . H 3 -9.027 -19.018 34.664 0.5 148.51 ? C62 TOY 501 A 1 
HETATM 41 O O62 TOY . A . H 3 -9.986 -17.822 32.804 0.5 135.44 ? O62 TOY 501 A 1 
HETATM 42 O O62 TOY . B . H 3 -9.599 -20.023 35.495 0.5 147.48 ? O62 TOY 501 A 1 
HETATM 43 C C13 TOY . A . H 3 -10.559 -18.348 31.603 0.5 135.67 ? C13 TOY 501 A 1 
HETATM 44 C C13 TOY . B . H 3 -10.013 -19.478 36.746 0.5 144.6 ? C13 TOY 501 A 1 
HETATM 45 C C23 TOY . A . H 3 -10.568 -17.277 30.508 0.5 135.96 ? C23 TOY 501 A 1 
HETATM 46 C C23 TOY . B . H 3 -9.553 -20.386 37.882 0.5 143.75 ? C23 TOY 501 A 1 
HETATM 47 O O23 TOY . A . H 3 -9.297 -16.617 30.474 0.5 136.72 ? O23 TOY 501 A 1 
HETATM 48 O O23 TOY . B . H 3 -8.131 -20.544 37.822 0.5 143.47 ? O23 TOY 501 A 1 
HETATM 49 C C33 TOY . A . H 3 -11.664 -16.239 30.714 0.5 135.77 ? C33 TOY 501 A 1 
HETATM 50 C C33 TOY . B . H 3 -10.214 -21.754 37.797 0.5 142.6 ? C33 TOY 501 A 1 
HETATM 51 N N33 TOY . A . H 3 -11.781 -15.409 29.53 0.5 135.62 ? N33 TOY 501 A 1 
HETATM 52 N N33 TOY . B . H 3 -9.995 -22.481 39.033 0.5 142.1 ? N33 TOY 501 A 1 
HETATM 53 C C43 TOY . A . H 3 -12.989 -16.931 30.985 0.5 135.55 ? C43 TOY 501 A 1 
HETATM 54 C C43 TOY . B . H 3 -11.706 -21.617 37.542 0.5 140.88 ? C43 TOY 501 A 1 
HETATM 55 O O43 TOY . A . H 3 -13.99 -15.955 31.263 0.5 135.87 ? O43 TOY 501 A 1 
HETATM 56 O O43 TOY . B . H 3 -12.164 -22.915 37.177 0.5 139.01 ? O43 TOY 501 A 1 
HETATM 57 C C53 TOY . A . H 3 -12.839 -17.858 32.179 0.5 135.22 ? C53 TOY 501 A 1 
HETATM 58 C C53 TOY . B . H 3 -11.987 -20.647 36.4 0.5 140.75 ? C53 TOY 501 A 1 
HETATM 59 O O53 TOY . A . H 3 -11.874 -18.857 31.857 0.5 135.27 ? O53 TOY 501 A 1 
HETATM 60 O O53 TOY . B . H 3 -11.431 -19.39 36.751 0.5 142.5 ? O53 TOY 501 A 1 
HETATM 61 C C63 TOY . A . H 3 -14.165 -18.524 32.53 0.5 134.72 ? C63 TOY 501 A 1 
HETATM 62 C C63 TOY . B . H 3 -13.465 -20.439 36.102 0.5 138.8 ? C63 TOY 501 A 1 
HETATM 63 O O63 TOY . A . H 3 -13.978 -19.414 33.636 0.5 133.45 ? O63 TOY 501 A 1 
HETATM 64 O O63 TOY . B . H 3 -13.619 -20.075 34.67 0.5 138.67 ? O63 TOY 501 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           64 
#