data_6UBS
#
_model_server_result.job_id            Kt7esOvXwIptIhfxsbqtEw 
_model_server_result.datetime_utc      '2024-11-28 10:00:30' 
_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          6ubs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":903}' 
#
_entry.id    6UBS 
#
_exptl.entry_id    6UBS 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              746.566 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' 
_entity.pdbx_number_of_molecules    5 
_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            6UBS 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6UBS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_pdbx_struct_assembly.details               author_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,S,T,U,V,W,X,Y 
_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    ? 
_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
? 4 L N N 
? 4 N N N 
? 4 R N N 
? 4 U N N 
? 4 Y N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n F NAG 1 F 1 NAG A 902 NAG 
2 n F NAG 2 F 2 NAG A 903 NAG 
2 n G NAG 1 G 1 NAG B 902 NAG 
2 n G NAG 2 G 2 NAG B 903 NAG 
2 n H NAG 1 H 1 NAG C 902 NAG 
2 n H NAG 2 H 2 NAG C 903 NAG 
2 n I NAG 1 I 1 NAG D 902 NAG 
2 n I NAG 2 I 2 NAG D 903 NAG 
2 n J NAG 1 J 1 NAG E 902 NAG 
2 n J NAG 2 J 2 NAG E 903 NAG 
#
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
covale ? covale1 A ND2 ASN 62 A ASN 62 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale2 B ND2 ASN 62 B ASN 62 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale3 C ND2 ASN 62 C ASN 62 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale4 D ND2 ASN 62 D ASN 62 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale5 E ND2 ASN 62 E ASN 62 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_chem_comp.formula           'C25 H49 O19 P3' 
_chem_comp.formula_weight    746.566 
_chem_comp.id                PIO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' 
#
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
C1 O1 PIO sing 288 n n 
C1 C2 PIO sing 289 n n 
C1 C6 PIO sing 290 n n 
C1 H1 PIO sing 291 n n 
O1 P1 PIO sing 292 n n 
P1 O11 PIO sing 293 n n 
O11 H11 PIO sing 294 n n 
P1 O12 PIO doub 295 n n 
P1 O13 PIO sing 296 n n 
C2 O2 PIO sing 297 n n 
C2 C3 PIO sing 298 n n 
C2 H2 PIO sing 299 n n 
O2 HO2 PIO sing 300 n n 
C3 O3 PIO sing 301 n n 
C3 C4 PIO sing 302 n n 
C3 H3 PIO sing 303 n n 
O3 HO3 PIO sing 304 n n 
C4 O4 PIO sing 305 n n 
C4 C5 PIO sing 306 n n 
C4 H4 PIO sing 307 n n 
O4 P4 PIO sing 308 n n 
P4 O41 PIO sing 309 n n 
O41 H41 PIO sing 310 n n 
P4 O42 PIO doub 311 n n 
P4 O43 PIO sing 312 n n 
O43 H43 PIO sing 313 n n 
C5 O5 PIO sing 314 n n 
C5 C6 PIO sing 315 n n 
C5 H5 PIO sing 316 n n 
O5 P5 PIO sing 317 n n 
P5 O51 PIO sing 318 n n 
O51 H51 PIO sing 319 n n 
P5 O52 PIO sing 320 n n 
O52 H52 PIO sing 321 n n 
P5 O53 PIO doub 322 n n 
C6 O6 PIO sing 323 n n 
C6 H6 PIO sing 324 n n 
O6 HO6 PIO sing 325 n n 
O13 C1C PIO sing 326 n n 
C1A O1A PIO doub 327 n n 
C1A C2A PIO sing 328 n n 
C1A O2C PIO sing 329 n n 
C1B O1B PIO doub 330 n n 
C1B C2B PIO sing 331 n n 
C1B O3C PIO sing 332 n n 
C1C C2C PIO sing 333 n n 
C1C H1C PIO sing 334 n n 
C1C H1CA PIO sing 335 n n 
C2A C3A PIO sing 336 n n 
C2A H2A PIO sing 337 n n 
C2A H2AA PIO sing 338 n n 
C2B C3B PIO sing 339 n n 
C2B H2B PIO sing 340 n n 
C2B H2BA PIO sing 341 n n 
C2C O2C PIO sing 342 n n 
C2C C3C PIO sing 343 n n 
C2C H2C PIO sing 344 n n 
C3A C4A PIO sing 345 n n 
C3A H3A PIO sing 346 n n 
C3A H3AA PIO sing 347 n n 
C3B C4B PIO sing 348 n n 
C3B H3B PIO sing 349 n n 
C3B H3BA PIO sing 350 n n 
C3C O3C PIO sing 351 n n 
C3C H3C PIO sing 352 n n 
C3C H3CA PIO sing 353 n n 
C4A C5A PIO sing 354 n n 
C4A H4A PIO sing 355 n n 
C4A H4AA PIO sing 356 n n 
C4B C5B PIO sing 357 n n 
C4B H4B PIO sing 358 n n 
C4B H4BA PIO sing 359 n n 
C5A C6A PIO sing 360 n n 
C5A H5A PIO sing 361 n n 
C5A H5AA PIO sing 362 n n 
C5B C6B PIO sing 363 n n 
C5B H5B PIO sing 364 n n 
C5B H5BA PIO sing 365 n n 
C6A C7A PIO sing 366 n n 
C6A H6A PIO sing 367 n n 
C6A H6AA PIO sing 368 n n 
C6B C7B PIO sing 369 n n 
C6B H6B PIO sing 370 n n 
C6B H6BA PIO sing 371 n n 
C7A C8A PIO sing 372 n n 
C7A H7A PIO sing 373 n n 
C7A H7AA PIO sing 374 n n 
C7B C8B PIO sing 375 n n 
C7B H7B PIO sing 376 n n 
C7B H7BA PIO sing 377 n n 
C8A H8A PIO sing 378 n n 
C8A H8AA PIO sing 379 n n 
C8A H8AB PIO sing 380 n n 
C8B H8B PIO sing 381 n n 
C8B H8BA PIO sing 382 n n 
C8B H8BB PIO sing 383 n n 
#
_atom_sites.entry_id                     6UBS 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
K 3 PX4 A 1 601 601 PX4 PX4 . 
L 4 PIO A 1 602 801 PIO PIO . 
M 3 PX4 B 1 601 601 PX4 PX4 . 
N 4 PIO B 1 602 801 PIO PIO . 
O 3 PX4 B 1 603 901 PX4 PX4 . 
P 3 PX4 B 1 606 901 PX4 PX4 . 
Q 3 PX4 C 1 601 601 PX4 PX4 . 
R 4 PIO C 1 602 801 PIO PIO . 
S 3 PX4 C 1 605 901 PX4 PX4 . 
T 3 PX4 D 1 601 601 PX4 PX4 . 
U 4 PIO D 1 602 801 PIO PIO . 
V 3 PX4 D 1 605 901 PX4 PX4 . 
W 3 PX4 E 1 901 901 PX4 PX4 . 
X 3 PX4 E 1 902 601 PX4 PX4 . 
Y 4 PIO E 1 903 801 PIO PIO . 
#
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 O1 PIO . . . Y 4 130.538 157.15 120.227 1 132.08 ? O1 PIO 903 E 1 
HETATM 2 P P1 PIO . . . Y 4 130.963 158.259 121.37 1 132.08 ? P1 PIO 903 E 1 
HETATM 3 O O11 PIO . . . Y 4 130.343 159.594 121.032 1 132.08 ? O11 PIO 903 E 1 
HETATM 4 O O12 PIO . . . Y 4 130.47 157.804 122.722 1 132.08 ? O12 PIO 903 E 1 
HETATM 5 O O13 PIO . . . Y 4 132.604 158.41 121.407 1 132.08 ? O13 PIO 903 E 1 
HETATM 6 C C1A PIO . . . Y 4 133.891 159.387 124.888 1 132.08 ? C1A PIO 903 E 1 
HETATM 7 O O1A PIO . . . Y 4 133.112 159.299 125.777 1 132.08 ? O1A PIO 903 E 1 
HETATM 8 C C1B PIO . . . Y 4 132.396 163.569 123.095 1 132.08 ? C1B PIO 903 E 1 
HETATM 9 O O1B PIO . . . Y 4 131.739 163.655 122.112 1 132.08 ? O1B PIO 903 E 1 
HETATM 10 C C1C PIO . . . Y 4 133.159 159.689 121.297 1 132.08 ? C1C PIO 903 E 1 
HETATM 11 C C2A PIO . . . Y 4 135.327 159.825 125.171 1 132.08 ? C2A PIO 903 E 1 
HETATM 12 C C2B PIO . . . Y 4 132.368 164.687 124.134 1 132.08 ? C2B PIO 903 E 1 
HETATM 13 C C2C PIO . . . Y 4 133.525 160.17 122.699 1 132.08 ? C2C PIO 903 E 1 
HETATM 14 O O2C PIO . . . Y 4 133.493 159.084 123.581 1 132.08 ? O2C PIO 903 E 1 
HETATM 15 C C3A PIO . . . Y 4 135.918 159.118 126.388 1 132.08 ? C3A PIO 903 E 1 
HETATM 16 C C3B PIO . . . Y 4 131.658 164.266 125.418 1 132.08 ? C3B PIO 903 E 1 
HETATM 17 C C3C PIO . . . Y 4 132.519 161.229 123.146 1 132.08 ? C3C PIO 903 E 1 
HETATM 18 O O3C PIO . . . Y 4 133.197 162.441 123.305 1 132.08 ? O3C PIO 903 E 1 
HETATM 19 C C4A PIO . . . Y 4 135.768 159.938 127.667 1 132.08 ? C4A PIO 903 E 1 
HETATM 20 C C4B PIO . . . Y 4 132.237 164.955 126.651 1 132.08 ? C4B PIO 903 E 1 
HETATM 21 C C5A PIO . . . Y 4 134.841 159.263 128.676 1 132.08 ? C5A PIO 903 E 1 
HETATM 22 C C5B PIO . . . Y 4 132.801 163.958 127.661 1 132.08 ? C5B PIO 903 E 1 
HETATM 23 C C6A PIO . . . Y 4 135.254 159.536 130.12 1 132.08 ? C6A PIO 903 E 1 
HETATM 24 C C6B PIO . . . Y 4 133.527 164.648 128.814 1 132.08 ? C6B PIO 903 E 1 
HETATM 25 C C7A PIO . . . Y 4 135.265 158.263 130.964 1 132.08 ? C7A PIO 903 E 1 
HETATM 26 C C7B PIO . . . Y 4 133.282 163.952 130.151 1 132.08 ? C7B PIO 903 E 1 
HETATM 27 C C8A PIO . . . Y 4 134.901 158.531 132.423 1 132.08 ? C8A PIO 903 E 1 
HETATM 28 C C8B PIO . . . Y 4 134.181 164.496 131.259 1 132.08 ? C8B PIO 903 E 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           28 
#