data_5U89
#
_model_server_result.job_id            5fFLtZBtyKvucCLapQ6JPQ 
_model_server_result.datetime_utc      '2024-10-28 02:30:22' 
_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          5u89 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1601}' 
#
_entry.id    5U89 
#
_exptl.entry_id    5U89 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              743.747 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-({[(2R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}propyl]sulfonyl}amino)-5'-deoxyadenosine" 
_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            5U89 
_cell.length_a            119.51 
_cell.length_b            119.51 
_cell.length_c            589.647 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5U89 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        179 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            OG 
_struct_conn.ptnr1_label_comp_id            SER 
_struct_conn.ptnr1_label_seq_id             566 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             SER 
_struct_conn.ptnr1_auth_seq_id              999 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            C 
_struct_conn.ptnr2_label_atom_id            P37 
_struct_conn.ptnr2_label_comp_id            MJ8 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             MJ8 
_struct_conn.ptnr2_auth_seq_id              1601 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.631 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C24 H42 N9 O12 P S2' 
_chem_comp.formula_weight    743.747 
_chem_comp.id                MJ8 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-({[(2R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}propyl]sulfonyl}amino)-5'-deoxyadenosine" 
_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
N01 C02 MJ8 sing 235 n n 
N03 C02 MJ8 doub 236 n y 
N03 C04 MJ8 sing 237 n y 
C02 C07 MJ8 sing 238 n y 
C04 N05 MJ8 doub 239 n y 
C33 C32 MJ8 sing 240 n n 
C07 C06 MJ8 doub 241 n y 
C07 N08 MJ8 sing 242 n y 
N05 C06 MJ8 sing 243 n y 
C06 N10 MJ8 sing 244 n y 
N08 C09 MJ8 doub 245 n y 
C26 C27 MJ8 sing 246 n n 
C26 C25 MJ8 sing 247 n n 
O40 C29 MJ8 doub 248 n n 
N28 C29 MJ8 sing 249 n n 
N28 C27 MJ8 sing 250 n n 
C34 C32 MJ8 sing 251 n n 
C32 C35 MJ8 sing 252 n n 
C32 C30 MJ8 sing 253 n n 
C29 C30 MJ8 sing 254 n n 
N10 C09 MJ8 sing 255 n y 
N10 C11 MJ8 sing 256 n n 
N24 C25 MJ8 sing 257 n n 
N24 C23 MJ8 sing 258 n n 
C35 O36 MJ8 sing 259 n n 
C30 O31 MJ8 sing 260 n n 
C25 O41 MJ8 doub 261 n n 
P37 O36 MJ8 sing 262 n n 
P37 O39 MJ8 doub 263 n n 
P37 O38 MJ8 sing 264 n n 
C11 O12 MJ8 sing 265 n n 
C11 C46 MJ8 sing 266 n n 
C23 C22 MJ8 sing 267 n n 
C22 S21 MJ8 sing 268 n n 
O12 C13 MJ8 sing 269 n n 
C46 O47 MJ8 sing 270 n n 
C46 C44 MJ8 sing 271 n n 
O43 S16 MJ8 doub 272 n n 
C17 S16 MJ8 sing 273 n n 
C17 C18 MJ8 sing 274 n n 
C19 C18 MJ8 sing 275 n n 
C19 N20 MJ8 sing 276 n n 
S16 N15 MJ8 sing 277 n n 
S16 O42 MJ8 doub 278 n n 
C18 S21 MJ8 sing 279 n n 
C13 C44 MJ8 sing 280 n n 
C13 C14 MJ8 sing 281 n n 
C44 O45 MJ8 sing 282 n n 
N15 C14 MJ8 sing 283 n n 
P37 O1 MJ8 sing 284 n n 
N15 H1 MJ8 sing 285 n n 
C14 H2 MJ8 sing 286 n n 
C14 H3 MJ8 sing 287 n n 
C13 H4 MJ8 sing 288 n n 
C44 H5 MJ8 sing 289 n n 
O45 H6 MJ8 sing 290 n n 
C46 H7 MJ8 sing 291 n n 
O47 H8 MJ8 sing 292 n n 
C11 H9 MJ8 sing 293 n n 
C04 H10 MJ8 sing 294 n n 
C09 H11 MJ8 sing 295 n n 
N01 H12 MJ8 sing 296 n n 
N01 H13 MJ8 sing 297 n n 
C17 H14 MJ8 sing 298 n n 
C17 H15 MJ8 sing 299 n n 
C18 H16 MJ8 sing 300 n n 
C19 H17 MJ8 sing 301 n n 
C19 H18 MJ8 sing 302 n n 
N20 H19 MJ8 sing 303 n n 
N20 H20 MJ8 sing 304 n n 
C22 H22 MJ8 sing 305 n n 
C22 H23 MJ8 sing 306 n n 
C23 H24 MJ8 sing 307 n n 
C23 H25 MJ8 sing 308 n n 
N24 H26 MJ8 sing 309 n n 
C26 H27 MJ8 sing 310 n n 
C26 H28 MJ8 sing 311 n n 
C27 H29 MJ8 sing 312 n n 
C27 H30 MJ8 sing 313 n n 
N28 H31 MJ8 sing 314 n n 
C30 H32 MJ8 sing 315 n n 
O31 H33 MJ8 sing 316 n n 
C33 H34 MJ8 sing 317 n n 
C33 H35 MJ8 sing 318 n n 
C33 H36 MJ8 sing 319 n n 
C34 H37 MJ8 sing 320 n n 
C34 H38 MJ8 sing 321 n n 
C34 H39 MJ8 sing 322 n n 
C35 H40 MJ8 sing 323 n n 
C35 H41 MJ8 sing 324 n n 
O38 H42 MJ8 sing 325 n n 
O1 H43 MJ8 sing 326 n n 
#
_atom_sites.entry_id                     5U89 
_atom_sites.fract_transf_matrix[1][1]    0.008368 
_atom_sites.fract_transf_matrix[1][2]    0.004831 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009662 
_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]    0.001696 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          C 
_pdbx_nonpoly_scheme.entity_id        3 
_pdbx_nonpoly_scheme.mon_id           MJ8 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      1601 
_pdbx_nonpoly_scheme.auth_seq_num     1 
_pdbx_nonpoly_scheme.pdb_mon_id       MJ8 
_pdbx_nonpoly_scheme.auth_mon_id      MJ8 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 O O43 MJ8 . . . C 3 -53.253 52.613 -3.468 1 116.61 ? O43 MJ8 1601 A 1 
HETATM 2 S S16 MJ8 . . . C 3 -53.101 51.498 -2.576 1 127.56 ? S16 MJ8 1601 A 1 
HETATM 3 O O42 MJ8 . . . C 3 -52.396 51.922 -1.399 1 135.83 ? O42 MJ8 1601 A 1 
HETATM 4 N N15 MJ8 . . . C 3 -54.555 50.945 -2.163 1 113.1 ? N15 MJ8 1601 A 1 
HETATM 5 C C14 MJ8 . . . C 3 -55.284 52.002 -1.448 1 108.83 ? C14 MJ8 1601 A 1 
HETATM 6 C C13 MJ8 . . . C 3 -56.467 52.47 -2.287 1 102.44 ? C13 MJ8 1601 A 1 
HETATM 7 O O12 MJ8 . . . C 3 -56.15 52.498 -3.682 1 101.21 ? O12 MJ8 1601 A 1 
HETATM 8 C C44 MJ8 . . . C 3 -57.667 51.549 -2.177 1 86.67 ? C44 MJ8 1601 A 1 
HETATM 9 O O45 MJ8 . . . C 3 -58.469 51.899 -1.046 1 83.6 ? O45 MJ8 1601 A 1 
HETATM 10 C C46 MJ8 . . . C 3 -58.405 51.795 -3.475 1 82.96 ? C46 MJ8 1601 A 1 
HETATM 11 O O47 MJ8 . . . C 3 -59.377 52.832 -3.308 1 96.95 ? O47 MJ8 1601 A 1 
HETATM 12 C C11 MJ8 . . . C 3 -57.332 52.25 -4.451 1 80.29 ? C11 MJ8 1601 A 1 
HETATM 13 N N10 MJ8 . . . C 3 -57.076 51.155 -5.417 1 67.79 ? N10 MJ8 1601 A 1 
HETATM 14 C C06 MJ8 . . . C 3 -57.772 50.928 -6.535 1 71.01 ? C06 MJ8 1601 A 1 
HETATM 15 N N05 MJ8 . . . C 3 -58.824 51.558 -7.111 1 73.12 ? N05 MJ8 1601 A 1 
HETATM 16 C C04 MJ8 . . . C 3 -59.334 51.105 -8.265 1 74.58 ? C04 MJ8 1601 A 1 
HETATM 17 N N03 MJ8 . . . C 3 -58.82 50.029 -8.877 1 74.73 ? N03 MJ8 1601 A 1 
HETATM 18 C C09 MJ8 . . . C 3 -56.124 50.217 -5.311 1 76.54 ? C09 MJ8 1601 A 1 
HETATM 19 N N08 MJ8 . . . C 3 -56.206 49.387 -6.376 1 88.12 ? N08 MJ8 1601 A 1 
HETATM 20 C C07 MJ8 . . . C 3 -57.226 49.814 -7.148 1 75.03 ? C07 MJ8 1601 A 1 
HETATM 21 C C02 MJ8 . . . C 3 -57.771 49.367 -8.342 1 71.1 ? C02 MJ8 1601 A 1 
HETATM 22 N N01 MJ8 . . . C 3 -57.257 48.279 -8.965 1 73.17 ? N01 MJ8 1601 A 1 
HETATM 23 C C17 MJ8 . . . C 3 -52.267 50.276 -3.334 1 96.96 ? C17 MJ8 1601 A 1 
HETATM 24 C C18 MJ8 . . . C 3 -51.388 49.555 -2.318 1 94.92 ? C18 MJ8 1601 A 1 
HETATM 25 C C19 MJ8 . . . C 3 -51.234 48.086 -2.7 1 93.97 ? C19 MJ8 1601 A 1 
HETATM 26 N N20 MJ8 . . . C 3 -50.772 47.324 -1.527 1 93.25 ? N20 MJ8 1601 A 1 
HETATM 27 S S21 MJ8 . . . C 3 -49.799 50.327 -2.253 1 290.21 ? S21 MJ8 1601 A 1 
HETATM 28 C C22 MJ8 . . . C 3 -49.175 50.61 -3.878 1 90.86 ? C22 MJ8 1601 A 1 
HETATM 29 C C23 MJ8 . . . C 3 -49.407 52.062 -4.28 1 104.41 ? C23 MJ8 1601 A 1 
HETATM 30 N N24 MJ8 . . . C 3 -48.414 52.539 -5.221 1 117.98 ? N24 MJ8 1601 A 1 
HETATM 31 C C25 MJ8 . . . C 3 -47.56 53.497 -4.877 1 136.21 ? C25 MJ8 1601 A 1 
HETATM 32 O O41 MJ8 . . . C 3 -47.379 53.839 -3.719 1 158.93 ? O41 MJ8 1601 A 1 
HETATM 33 C C26 MJ8 . . . C 3 -46.804 54.163 -6.001 1 133.8 ? C26 MJ8 1601 A 1 
HETATM 34 C C27 MJ8 . . . C 3 -45.828 55.166 -5.404 1 138.84 ? C27 MJ8 1601 A 1 
HETATM 35 N N28 MJ8 . . . C 3 -46.091 56.53 -5.822 1 139.86 ? N28 MJ8 1601 A 1 
HETATM 36 C C29 MJ8 . . . C 3 -45.162 57.459 -5.634 1 132.94 ? C29 MJ8 1601 A 1 
HETATM 37 O O40 MJ8 . . . C 3 -44 57.281 -5.964 1 118.58 ? O40 MJ8 1601 A 1 
HETATM 38 C C30 MJ8 . . . C 3 -45.637 58.719 -4.959 1 135.83 ? C30 MJ8 1601 A 1 
HETATM 39 O O31 MJ8 . . . C 3 -47.056 58.64 -4.774 1 132.09 ? O31 MJ8 1601 A 1 
HETATM 40 C C32 MJ8 . . . C 3 -45.319 59.974 -5.764 1 128.96 ? C32 MJ8 1601 A 1 
HETATM 41 C C33 MJ8 . . . C 3 -45.751 59.791 -7.214 1 121.56 ? C33 MJ8 1601 A 1 
HETATM 42 C C34 MJ8 . . . C 3 -43.824 60.264 -5.705 1 119.84 ? C34 MJ8 1601 A 1 
HETATM 43 C C35 MJ8 . . . C 3 -46.09 61.139 -5.134 1 127.82 ? C35 MJ8 1601 A 1 
HETATM 44 O O36 MJ8 . . . C 3 -45.246 61.856 -4.224 1 120.58 ? O36 MJ8 1601 A 1 
HETATM 45 P P37 MJ8 . . . C 3 -44.523 63.302 -4.433 1 222.87 ? P37 MJ8 1601 A 1 
HETATM 46 O O39 MJ8 . . . C 3 -45.355 64.399 -3.797 1 222.12 ? O39 MJ8 1601 A 1 
HETATM 47 O O38 MJ8 . . . C 3 -43.221 63.17 -3.68 1 224.74 ? O38 MJ8 1601 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           47 
#