data_8JUR
#
_model_server_result.job_id            SiZoBAZZHZNQlNKgtIpYuQ 
_model_server_result.datetime_utc      '2025-01-23 17:42:58' 
_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          8jur 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":405}' 
#
_entry.id    8JUR 
#
_exptl.entry_id    8JUR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              449.542 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL' 
_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            8JUR 
_cell.length_a            86.326 
_cell.length_b            134.103 
_cell.length_c            145.787 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8JUR 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,O,P,Q,R 
_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                             H 
_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 O ASP 43 A ASP 43 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? 
metalc ? metalc2 A O ASN 44 A ASN 44 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc3 A O GLY 46 A GLY 46 1_555 F NA NA . A NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
metalc ? metalc4 A OE1 GLN 107 A GLN 107 1_555 G NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? 
metalc ? metalc5 A OE1 GLN 146 A GLN 146 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc6 A OE1 GLN 149 A GLN 149 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc7 A O ARG 154 A ARG 154 1_555 G NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? 
metalc ? metalc8 A OD2 ASP 156 A ASP 156 1_555 G NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? 
metalc ? metalc9 A OD1 ASP 174 A ASP 174 1_555 E NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? 
metalc ? metalc10 F NA NA . A NA 403 1_555 C O GLY 181 C GLY 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? 
metalc ? metalc11 B O ASN 44 B ASN 44 1_555 K NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.022 ? 
metalc ? metalc12 B O GLY 46 B GLY 46 1_555 K NA NA . B NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? 
metalc ? metalc13 B O PRO 82 B PRO 82 1_555 J NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? 
metalc ? metalc14 B O GLY 85 B GLY 85 1_555 J NA NA . B NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? 
metalc ? metalc15 B OD1 ASP 174 B ASP 174 1_555 L NA NA . B NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? 
metalc ? metalc16 B O GLY 181 B GLY 181 1_555 O NA NA . C NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
metalc ? metalc17 C O ASP 43 C ASP 43 1_555 O NA NA . C NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? 
metalc ? metalc18 C O ASN 44 C ASN 44 1_555 O NA NA . C NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? 
metalc ? metalc19 C O GLY 46 C GLY 46 1_555 O NA NA . C NA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc20 C OE1 GLN 146 C GLN 146 1_555 N NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? 
metalc ? metalc21 C OE1 GLN 149 C GLN 149 1_555 N NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc22 C OD1 ASP 174 C ASP 174 1_555 N NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? 
metalc ? metalc23 C OD2 ASP 174 C ASP 174 1_555 N NA NA . C NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? 
#
_chem_comp.formula           'C19 H39 N5 O7' 
_chem_comp.formula_weight    449.542 
_chem_comp.id                LLL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'GENTAMICIN C1A' 
#
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 LLL sing 235 n n 
C11 C21 LLL sing 236 n n 
C11 O51 LLL sing 237 n n 
C11 H11 LLL sing 238 n n 
O11 C42 LLL sing 239 n n 
C21 N21 LLL sing 240 n n 
C21 C31 LLL sing 241 n n 
C21 H21 LLL sing 242 n n 
N21 H211 LLL sing 243 n n 
N21 H212 LLL sing 244 n n 
C31 C41 LLL sing 245 n n 
C31 H311 LLL sing 246 n n 
C31 H312 LLL sing 247 n n 
C41 C51 LLL sing 248 n n 
C41 H411 LLL sing 249 n n 
C41 H412 LLL sing 250 n n 
C51 O51 LLL sing 251 n n 
C51 C61 LLL sing 252 n n 
C51 H51 LLL sing 253 n n 
C61 N61 LLL sing 254 n n 
C61 H611 LLL sing 255 n n 
C61 H612 LLL sing 256 n n 
N61 H11A LLL sing 257 n n 
N61 H12A LLL sing 258 n n 
C12 N12 LLL sing 259 n n 
C12 C22 LLL sing 260 n n 
C12 C62 LLL sing 261 n n 
C12 H12 LLL sing 262 n n 
N12 H121 LLL sing 263 n n 
N12 H122 LLL sing 264 n n 
C22 C32 LLL sing 265 n n 
C22 H221 LLL sing 266 n n 
C22 H222 LLL sing 267 n n 
C32 N32 LLL sing 268 n n 
C32 C42 LLL sing 269 n n 
C32 H32 LLL sing 270 n n 
N32 H321 LLL sing 271 n n 
N32 H322 LLL sing 272 n n 
C42 C52 LLL sing 273 n n 
C42 H42 LLL sing 274 n n 
C52 O52 LLL sing 275 n n 
C52 C62 LLL sing 276 n n 
C52 H52 LLL sing 277 n n 
O52 H3 LLL sing 278 n n 
C62 O62 LLL sing 279 n n 
C62 H62 LLL sing 280 n n 
O62 C13 LLL sing 281 n n 
C13 C23 LLL sing 282 n n 
C13 O53 LLL sing 283 n n 
C13 H13 LLL sing 284 n n 
C23 O23 LLL sing 285 n n 
C23 C33 LLL sing 286 n n 
C23 H23 LLL sing 287 n n 
O23 H2 LLL sing 288 n n 
C33 N33 LLL sing 289 n n 
C33 C43 LLL sing 290 n n 
C33 H1 LLL sing 291 n n 
N33 C93 LLL sing 292 n n 
N33 H33 LLL sing 293 n n 
C43 O43 LLL sing 294 n n 
C43 C53 LLL sing 295 n n 
C43 C83 LLL sing 296 n n 
O43 H43 LLL sing 297 n n 
C53 O53 LLL sing 298 n n 
C53 H531 LLL sing 299 n n 
C53 H532 LLL sing 300 n n 
C83 H831 LLL sing 301 n n 
C83 H832 LLL sing 302 n n 
C83 H833 LLL sing 303 n n 
C93 H931 LLL sing 304 n n 
C93 H932 LLL sing 305 n n 
C93 H933 LLL sing 306 n n 
#
_atom_sites.entry_id                     8JUR 
_atom_sites.fract_transf_matrix[1][1]    0.011584 
_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]    0.007457 
_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]    0.006859 
_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
D 2 C8E A 1 401 507 C8E C8E . 
E 3 NA A 1 402 2 NA NA . 
F 3 NA A 1 403 4 NA NA . 
G 3 NA A 1 404 8 NA NA . 
H 4 LLL A 1 405 51 LLL LLL . 
I 2 C8E B 1 401 506 C8E C8E . 
J 3 NA B 1 402 3 NA NA . 
K 3 NA B 1 403 5 NA NA . 
L 3 NA B 1 404 7 NA NA . 
M 2 C8E C 1 401 509 C8E C8E . 
N 3 NA C 1 402 1 NA NA . 
O 3 NA C 1 403 6 NA NA . 
P 5 HOH A 1 501 20 HOH HOH . 
P 5 HOH A 2 502 12 HOH HOH . 
P 5 HOH A 3 503 22 HOH HOH . 
P 5 HOH A 4 504 14 HOH HOH . 
P 5 HOH A 5 505 21 HOH HOH . 
P 5 HOH A 6 506 26 HOH HOH . 
P 5 HOH A 7 507 25 HOH HOH . 
P 5 HOH A 8 508 17 HOH HOH . 
P 5 HOH A 9 509 24 HOH HOH . 
Q 5 HOH B 1 501 19 HOH HOH . 
Q 5 HOH B 2 502 16 HOH HOH . 
Q 5 HOH B 3 503 18 HOH HOH . 
R 5 HOH C 1 501 13 HOH HOH . 
R 5 HOH C 2 502 15 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 C11 LLL . . . H 4 -3.456 -14.797 20.716 1 121.27 ? C11 LLL 405 A 1 
HETATM 2 O O11 LLL . . . H 4 -3.93 -13.861 21.68 1 119.64 ? O11 LLL 405 A 1 
HETATM 3 C C21 LLL . . . H 4 -3.411 -16.211 21.324 1 101.65 ? C21 LLL 405 A 1 
HETATM 4 N N21 LLL . . . H 4 -4.704 -16.643 21.876 1 99.02 ? N21 LLL 405 A 1 
HETATM 5 C C31 LLL . . . H 4 -2.281 -16.356 22.341 1 100.18 ? C31 LLL 405 A 1 
HETATM 6 C C41 LLL . . . H 4 -0.964 -15.898 21.722 1 116.42 ? C41 LLL 405 A 1 
HETATM 7 C C51 LLL . . . H 4 -1.1 -14.486 21.184 1 102.62 ? C51 LLL 405 A 1 
HETATM 8 O O51 LLL . . . H 4 -2.167 -14.428 20.206 1 117.99 ? O51 LLL 405 A 1 
HETATM 9 C C61 LLL . . . H 4 0.163 -13.949 20.531 1 81.52 ? C61 LLL 405 A 1 
HETATM 10 N N61 LLL . . . H 4 1.319 -13.791 21.447 1 86.38 ? N61 LLL 405 A 1 
HETATM 11 C C12 LLL . . . H 4 -6.534 -10.449 21.505 1 99.29 ? C12 LLL 405 A 1 
HETATM 12 N N12 LLL . . . H 4 -7.1 -9.183 20.94 1 70.24 ? N12 LLL 405 A 1 
HETATM 13 C C22 LLL . . . H 4 -5.048 -10.25 21.792 1 93.84 ? C22 LLL 405 A 1 
HETATM 14 C C32 LLL . . . H 4 -4.349 -11.531 22.236 1 106.51 ? C32 LLL 405 A 1 
HETATM 15 N N32 LLL . . . H 4 -2.889 -11.256 22.421 1 94.79 ? N32 LLL 405 A 1 
HETATM 16 C C42 LLL . . . H 4 -4.56 -12.647 21.214 1 110.48 ? C42 LLL 405 A 1 
HETATM 17 C C52 LLL . . . H 4 -6.073 -12.865 21.054 1 109.41 ? C52 LLL 405 A 1 
HETATM 18 O O52 LLL . . . H 4 -6.336 -13.954 20.168 1 129.46 ? O52 LLL 405 A 1 
HETATM 19 C C62 LLL . . . H 4 -6.778 -11.604 20.535 1 101.31 ? C62 LLL 405 A 1 
HETATM 20 O O62 LLL . . . H 4 -8.203 -11.802 20.434 1 99.59 ? O62 LLL 405 A 1 
HETATM 21 C C13 LLL . . . H 4 -8.745 -12.038 19.15 1 98.68 ? C13 LLL 405 A 1 
HETATM 22 C C23 LLL . . . H 4 -10.184 -11.519 19.079 1 97.85 ? C23 LLL 405 A 1 
HETATM 23 O O23 LLL . . . H 4 -10.244 -10.214 19.684 1 100.13 ? O23 LLL 405 A 1 
HETATM 24 C C33 LLL . . . H 4 -11.232 -12.455 19.699 1 94.6 ? C33 LLL 405 A 1 
HETATM 25 N N33 LLL . . . H 4 -12.6 -12.121 19.268 1 93.63 ? N33 LLL 405 A 1 
HETATM 26 C C43 LLL . . . H 4 -10.947 -13.955 19.422 1 83.54 ? C43 LLL 405 A 1 
HETATM 27 O O43 LLL . . . H 4 -11.3 -14.236 18.056 1 72.63 ? O43 LLL 405 A 1 
HETATM 28 C C53 LLL . . . H 4 -9.463 -14.266 19.608 1 81.87 ? C53 LLL 405 A 1 
HETATM 29 O O53 LLL . . . H 4 -8.665 -13.417 18.771 1 102.14 ? O53 LLL 405 A 1 
HETATM 30 C C83 LLL . . . H 4 -11.78 -14.857 20.327 1 120.6 ? C83 LLL 405 A 1 
HETATM 31 C C93 LLL . . . H 4 -13.121 -10.874 19.778 1 52.88 ? C93 LLL 405 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#