data_6JW7
#
_model_server_result.job_id            0bIeckp1Ozjv8ADGGMtB2g 
_model_server_result.datetime_utc      '2025-05-18 07:13:36' 
_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          6jw7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    6JW7 
#
_exptl.entry_id    6JW7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              485.483 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol 
_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         120 
_cell.entry_id            6JW7 
_cell.length_a            120.01 
_cell.length_b            120.01 
_cell.length_c            132.86 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JW7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 88.573333 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C18 H35 N3 O12' 
_chem_comp.formula_weight    485.483 
_chem_comp.id                CJX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3S,4S,5R,6R)-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-bis(azanyl)-3-[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-oxane-3,4,5-triol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '3"-deamino-3"-hydroxykanamycin A' 
#
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
O4 C4 CJX sing 70 n n 
O3 C3 CJX sing 71 n n 
C4 C3 CJX sing 72 n n 
C4 C5 CJX sing 73 n n 
C3 C2 CJX sing 74 n n 
C5 C6 CJX sing 75 n n 
C5 O5 CJX sing 76 n n 
C6 O6 CJX sing 77 n n 
C2 O2 CJX sing 78 n n 
C2 C1 CJX sing 79 n n 
O5 C1 CJX sing 80 n n 
C1 O1 CJX sing 81 n n 
O1 CBG CJX sing 82 n n 
OAK CBA CJX sing 83 n n 
CBA CBG CJX sing 84 n n 
CBA CBF CJX sing 85 n n 
OAI CAY CJX sing 86 n n 
CBG CAT CJX sing 87 n n 
NAC CAT CJX sing 88 n n 
CAT CAN CJX sing 89 n n 
OAQ CBF CJX sing 90 n n 
OAQ CBD CJX sing 91 n n 
CBF CAS CJX sing 92 n n 
CAY CBD CJX sing 93 n n 
CAY CAU CJX sing 94 n n 
CBD OAO CJX sing 95 n n 
CAS CAN CJX sing 96 n n 
CAS NAB CJX sing 97 n n 
CAU OAE CJX sing 98 n n 
CAU CAW CJX sing 99 n n 
OAO CBB CJX sing 100 n n 
CAW CBB CJX sing 101 n n 
CAW OAG CJX sing 102 n n 
CBB CAL CJX sing 103 n n 
CAL NAA CJX sing 104 n n 
C4 H1 CJX sing 105 n n 
C5 H2 CJX sing 106 n n 
C6 H3 CJX sing 107 n n 
C6 H4 CJX sing 108 n n 
C3 H5 CJX sing 109 n n 
O2 H6 CJX sing 110 n n 
C2 H7 CJX sing 111 n n 
O3 H8 CJX sing 112 n n 
O4 H9 CJX sing 113 n n 
O6 H10 CJX sing 114 n n 
C1 H11 CJX sing 115 n n 
CBG H12 CJX sing 116 n n 
CBA H13 CJX sing 117 n n 
OAK H14 CJX sing 118 n n 
CAT H15 CJX sing 119 n n 
NAC H16 CJX sing 120 n n 
NAC H17 CJX sing 121 n n 
CAN H19 CJX sing 122 n n 
CAN H20 CJX sing 123 n n 
CAS H21 CJX sing 124 n n 
NAB H22 CJX sing 125 n n 
NAB H23 CJX sing 126 n n 
CBF H25 CJX sing 127 n n 
CBD H26 CJX sing 128 n n 
CBB H27 CJX sing 129 n n 
CAL H28 CJX sing 130 n n 
CAL H29 CJX sing 131 n n 
NAA H30 CJX sing 132 n n 
NAA H31 CJX sing 133 n n 
CAW H33 CJX sing 134 n n 
OAG H34 CJX sing 135 n n 
CAU H35 CJX sing 136 n n 
OAE H36 CJX sing 137 n n 
CAY H37 CJX sing 138 n n 
OAI H38 CJX sing 139 n n 
#
_atom_sites.entry_id                     6JW7 
_atom_sites.fract_transf_matrix[1][1]    0.008333 
_atom_sites.fract_transf_matrix[1][2]    0.004811 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009622 
_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]    0.007527 
_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 NAI A 1 401 401 NAI NAI . 
D 3 CJX A 1 402 402 CJX DRG . 
E 2 NAI B 1 401 401 NAI NAI . 
F 4 HOH A 1 501 48 HOH HOH . 
F 4 HOH A 2 502 21 HOH HOH . 
F 4 HOH A 3 503 15 HOH HOH . 
F 4 HOH A 4 504 16 HOH HOH . 
F 4 HOH A 5 505 58 HOH HOH . 
F 4 HOH A 6 506 28 HOH HOH . 
F 4 HOH A 7 507 38 HOH HOH . 
F 4 HOH A 8 508 2 HOH HOH . 
F 4 HOH A 9 509 35 HOH HOH . 
F 4 HOH A 10 510 25 HOH HOH . 
F 4 HOH A 11 511 49 HOH HOH . 
F 4 HOH A 12 512 8 HOH HOH . 
F 4 HOH A 13 513 27 HOH HOH . 
F 4 HOH A 14 514 47 HOH HOH . 
F 4 HOH A 15 515 31 HOH HOH . 
F 4 HOH A 16 516 40 HOH HOH . 
F 4 HOH A 17 517 29 HOH HOH . 
F 4 HOH A 18 518 33 HOH HOH . 
F 4 HOH A 19 519 36 HOH HOH . 
F 4 HOH A 20 520 22 HOH HOH . 
F 4 HOH A 21 521 59 HOH HOH . 
F 4 HOH A 22 522 44 HOH HOH . 
F 4 HOH A 23 523 6 HOH HOH . 
F 4 HOH A 24 524 34 HOH HOH . 
F 4 HOH A 25 525 46 HOH HOH . 
F 4 HOH A 26 526 1 HOH HOH . 
F 4 HOH A 27 527 32 HOH HOH . 
F 4 HOH A 28 528 11 HOH HOH . 
F 4 HOH A 29 529 45 HOH HOH . 
F 4 HOH A 30 530 54 HOH HOH . 
F 4 HOH A 31 531 53 HOH HOH . 
G 4 HOH B 1 501 12 HOH HOH . 
G 4 HOH B 2 502 30 HOH HOH . 
G 4 HOH B 3 503 3 HOH HOH . 
G 4 HOH B 4 504 19 HOH HOH . 
G 4 HOH B 5 505 26 HOH HOH . 
G 4 HOH B 6 506 4 HOH HOH . 
G 4 HOH B 7 507 23 HOH HOH . 
G 4 HOH B 8 508 57 HOH HOH . 
G 4 HOH B 9 509 5 HOH HOH . 
G 4 HOH B 10 510 7 HOH HOH . 
G 4 HOH B 11 511 24 HOH HOH . 
G 4 HOH B 12 512 13 HOH HOH . 
G 4 HOH B 13 513 10 HOH HOH . 
G 4 HOH B 14 514 55 HOH HOH . 
G 4 HOH B 15 515 39 HOH HOH . 
G 4 HOH B 16 516 20 HOH HOH . 
G 4 HOH B 17 517 51 HOH HOH . 
G 4 HOH B 18 518 42 HOH HOH . 
G 4 HOH B 19 519 14 HOH HOH . 
G 4 HOH B 20 520 9 HOH HOH . 
G 4 HOH B 21 521 17 HOH HOH . 
G 4 HOH B 22 522 60 HOH HOH . 
G 4 HOH B 23 523 41 HOH HOH . 
G 4 HOH B 24 524 18 HOH HOH . 
G 4 HOH B 25 525 37 HOH HOH . 
G 4 HOH B 26 526 56 HOH HOH . 
G 4 HOH B 27 527 50 HOH HOH . 
G 4 HOH B 28 528 43 HOH HOH . 
G 4 HOH B 29 529 52 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 C4 CJX . . . D 3 48.637 -3.57 21.189 1 85.21 ? C4 CJX 402 A 1 
HETATM 2 C C5 CJX . . . D 3 49.484 -3.795 22.445 1 77.26 ? C5 CJX 402 A 1 
HETATM 3 C C6 CJX . . . D 3 50.627 -2.782 22.557 1 73.68 ? C6 CJX 402 A 1 
HETATM 4 C C3 CJX . . . D 3 47.262 -4.345 21.328 1 79.28 ? C3 CJX 402 A 1 
HETATM 5 O O2 CJX . . . D 3 45.334 -4.974 23.083 1 57.44 ? O2 CJX 402 A 1 
HETATM 6 C C2 CJX . . . D 3 46.462 -4.085 22.752 1 83.6 ? C2 CJX 402 A 1 
HETATM 7 O O3 CJX . . . D 3 46.477 -4.008 20.208 1 75.72 ? O3 CJX 402 A 1 
HETATM 8 O O4 CJX . . . D 3 49.462 -3.896 19.906 1 83.73 ? O4 CJX 402 A 1 
HETATM 9 O O6 CJX . . . D 3 49.935 -1.512 22.632 1 63.93 ? O6 CJX 402 A 1 
HETATM 10 O O5 CJX . . . D 3 48.712 -3.567 23.665 1 92.86 ? O5 CJX 402 A 1 
HETATM 11 C C1 CJX . . . D 3 47.418 -4.215 23.947 1 90.16 ? C1 CJX 402 A 1 
HETATM 12 O O1 CJX . . . D 3 47.521 -5.635 24.229 1 99.53 ? O1 CJX 402 A 1 
HETATM 13 C CBG CJX . . . D 3 48.058 -6.081 25.431 1 90.59 ? CBG CJX 402 A 1 
HETATM 14 C CBA CJX . . . D 3 49.571 -6.387 25.252 1 93.48 ? CBA CJX 402 A 1 
HETATM 15 O OAK CJX . . . D 3 50.409 -5.325 24.69 1 74.26 ? OAK CJX 402 A 1 
HETATM 16 C CAT CJX . . . D 3 47.313 -7.405 25.877 1 92.84 ? CAT CJX 402 A 1 
HETATM 17 N NAC CJX . . . D 3 45.792 -7.403 25.832 1 96.97 ? NAC CJX 402 A 1 
HETATM 18 C CAN CJX . . . D 3 47.789 -7.716 27.242 1 85.25 ? CAN CJX 402 A 1 
HETATM 19 C CAS CJX . . . D 3 49.287 -7.926 27.156 1 85.21 ? CAS CJX 402 A 1 
HETATM 20 N NAB CJX . . . D 3 49.765 -8.367 28.459 1 85.9 ? NAB CJX 402 A 1 
HETATM 21 C CBF CJX . . . D 3 50.09 -6.696 26.641 1 97.5 ? CBF CJX 402 A 1 
HETATM 22 O OAQ CJX . . . D 3 51.5 -7.038 26.517 1 109.73 ? OAQ CJX 402 A 1 
HETATM 23 C CBD CJX . . . D 3 52.683 -6.185 26.763 1 110.91 ? CBD CJX 402 A 1 
HETATM 24 O OAO CJX . . . D 3 52.76 -5.498 28.06 1 116.11 ? OAO CJX 402 A 1 
HETATM 25 C CBB CJX . . . D 3 52.497 -6.448 29.165 1 116.15 ? CBB CJX 402 A 1 
HETATM 26 C CAL CJX . . . D 3 52.656 -5.88 30.562 1 115.58 ? CAL CJX 402 A 1 
HETATM 27 N NAA CJX . . . D 3 53.925 -5.13 30.632 1 115.05 ? NAA CJX 402 A 1 
HETATM 28 C CAW CJX . . . D 3 53.376 -7.807 29.07 1 108.45 ? CAW CJX 402 A 1 
HETATM 29 O OAG CJX . . . D 3 52.729 -8.88 29.807 1 120.62 ? OAG CJX 402 A 1 
HETATM 30 C CAU CJX . . . D 3 53.597 -8.347 27.649 1 101.06 ? CAU CJX 402 A 1 
HETATM 31 O OAE CJX . . . D 3 54.63 -9.364 27.657 1 86.34 ? OAE CJX 402 A 1 
HETATM 32 C CAY CJX . . . D 3 53.867 -7.181 26.645 1 101.12 ? CAY CJX 402 A 1 
HETATM 33 O OAI CJX . . . D 3 53.919 -7.685 25.307 1 77.84 ? OAI CJX 402 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           336 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           33 
#