data_9BU3
#
_model_server_result.job_id            GwkdGmSohbzVU3cl2TdZiA 
_model_server_result.datetime_utc      '2024-12-04 06:57:04' 
_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          9bu3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"SA","auth_seq_id":504}' 
#
_entry.id    9BU3 
#
_exptl.entry_id    9BU3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              746.566 
_entity.id                          4 
_entity.src_method                  syn 
_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    25 
_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            9BU3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9BU3 
_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_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB 
_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
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P N N 
? 4 R N N 
? 4 W N N 
? 4 X N N 
? 4 Y N N 
? 4 Z N N 
? 4 BA N N 
? 4 GA N N 
? 4 HA N N 
? 4 IA N N 
? 4 JA N N 
? 4 LA N N 
? 4 QA N N 
? 4 RA N N 
? 4 SA N N 
? 4 TA N N 
? 4 VA N N 
? 4 ZA N N 
? 4 DB N N 
? 4 EB N N 
? 4 FB N N 
? 4 GB 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 502 NAG 
2 n F NAG 2 F 2 NAG A 503 NAG 
2 n G NAG 1 G 1 NAG B 502 NAG 
2 n G NAG 2 G 2 NAG B 503 NAG 
2 n H NAG 1 H 1 NAG C 502 NAG 
2 n H NAG 2 H 2 NAG C 503 NAG 
2 n I NAG 1 I 1 NAG D 502 NAG 
2 n I NAG 2 I 2 NAG D 503 NAG 
2 n J NAG 1 J 1 NAG E 502 NAG 
2 n J NAG 2 J 2 NAG E 503 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
disulf ? disulf1 A SG CYS 231 A CYS 198 1_555 A SG CYS 242 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 B SG CYS 231 B CYS 198 1_555 B SG CYS 242 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 C SG CYS 231 C CYS 198 1_555 C SG CYS 242 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 D SG CYS 231 D CYS 198 1_555 D SG CYS 242 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf5 E SG CYS 231 E CYS 198 1_555 E SG CYS 242 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 A ND2 ASN 71 A ASN 38 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale2 B ND2 ASN 71 B ASN 38 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale3 C ND2 ASN 71 C ASN 38 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale4 D ND2 ASN 71 D ASN 38 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale5 E ND2 ASN 71 E ASN 38 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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 290 n n 
C1 C2 PIO sing 291 n n 
C1 C6 PIO sing 292 n n 
C1 H1 PIO sing 293 n n 
O1 P1 PIO sing 294 n n 
P1 O11 PIO sing 295 n n 
O11 H11 PIO sing 296 n n 
P1 O12 PIO doub 297 n n 
P1 O13 PIO sing 298 n n 
C2 O2 PIO sing 299 n n 
C2 C3 PIO sing 300 n n 
C2 H2 PIO sing 301 n n 
O2 HO2 PIO sing 302 n n 
C3 O3 PIO sing 303 n n 
C3 C4 PIO sing 304 n n 
C3 H3 PIO sing 305 n n 
O3 HO3 PIO sing 306 n n 
C4 O4 PIO sing 307 n n 
C4 C5 PIO sing 308 n n 
C4 H4 PIO sing 309 n n 
O4 P4 PIO sing 310 n n 
P4 O41 PIO sing 311 n n 
O41 H41 PIO sing 312 n n 
P4 O42 PIO doub 313 n n 
P4 O43 PIO sing 314 n n 
O43 H43 PIO sing 315 n n 
C5 O5 PIO sing 316 n n 
C5 C6 PIO sing 317 n n 
C5 H5 PIO sing 318 n n 
O5 P5 PIO sing 319 n n 
P5 O51 PIO sing 320 n n 
O51 H51 PIO sing 321 n n 
P5 O52 PIO sing 322 n n 
O52 H52 PIO sing 323 n n 
P5 O53 PIO doub 324 n n 
C6 O6 PIO sing 325 n n 
C6 H6 PIO sing 326 n n 
O6 HO6 PIO sing 327 n n 
O13 C1C PIO sing 328 n n 
C1A O1A PIO doub 329 n n 
C1A C2A PIO sing 330 n n 
C1A O2C PIO sing 331 n n 
C1B O1B PIO doub 332 n n 
C1B C2B PIO sing 333 n n 
C1B O3C PIO sing 334 n n 
C1C C2C PIO sing 335 n n 
C1C H1C PIO sing 336 n n 
C1C H1CA PIO sing 337 n n 
C2A C3A PIO sing 338 n n 
C2A H2A PIO sing 339 n n 
C2A H2AA PIO sing 340 n n 
C2B C3B PIO sing 341 n n 
C2B H2B PIO sing 342 n n 
C2B H2BA PIO sing 343 n n 
C2C O2C PIO sing 344 n n 
C2C C3C PIO sing 345 n n 
C2C H2C PIO sing 346 n n 
C3A C4A PIO sing 347 n n 
C3A H3A PIO sing 348 n n 
C3A H3AA PIO sing 349 n n 
C3B C4B PIO sing 350 n n 
C3B H3B PIO sing 351 n n 
C3B H3BA PIO sing 352 n n 
C3C O3C PIO sing 353 n n 
C3C H3C PIO sing 354 n n 
C3C H3CA PIO sing 355 n n 
C4A C5A PIO sing 356 n n 
C4A H4A PIO sing 357 n n 
C4A H4AA PIO sing 358 n n 
C4B C5B PIO sing 359 n n 
C4B H4B PIO sing 360 n n 
C4B H4BA PIO sing 361 n n 
C5A C6A PIO sing 362 n n 
C5A H5A PIO sing 363 n n 
C5A H5AA PIO sing 364 n n 
C5B C6B PIO sing 365 n n 
C5B H5B PIO sing 366 n n 
C5B H5BA PIO sing 367 n n 
C6A C7A PIO sing 368 n n 
C6A H6A PIO sing 369 n n 
C6A H6AA PIO sing 370 n n 
C6B C7B PIO sing 371 n n 
C6B H6B PIO sing 372 n n 
C6B H6BA PIO sing 373 n n 
C7A C8A PIO sing 374 n n 
C7A H7A PIO sing 375 n n 
C7A H7AA PIO sing 376 n n 
C7B C8B PIO sing 377 n n 
C7B H7B PIO sing 378 n n 
C7B H7BA PIO sing 379 n n 
C8A H8A PIO sing 380 n n 
C8A H8AA PIO sing 381 n n 
C8A H8AB PIO sing 382 n n 
C8B H8B PIO sing 383 n n 
C8B H8BA PIO sing 384 n n 
C8B H8BB PIO sing 385 n n 
#
_atom_sites.entry_id                     9BU3 
_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 GLY A 1 501 501 GLY GLY . 
L 3 GLY A 1 502 501 GLY GLY . 
M 4 PIO A 1 503 504 PIO PIO . 
N 4 PIO A 1 504 506 PIO PIO . 
O 4 PIO A 1 505 507 PIO PIO . 
P 4 PIO A 1 506 508 PIO PIO . 
Q 5 PX4 A 1 507 509 PX4 PX4 . 
R 4 PIO A 1 508 505 PIO PIO . 
S 5 PX4 A 1 509 513 PX4 PX4 . 
T 5 PX4 A 1 510 514 PX4 PX4 . 
U 5 PX4 A 1 511 515 PX4 PX4 . 
V 3 GLY B 1 501 501 GLY GLY . 
W 4 PIO B 1 502 504 PIO PIO . 
X 4 PIO B 1 503 506 PIO PIO . 
Y 4 PIO B 1 504 507 PIO PIO . 
Z 4 PIO B 1 505 508 PIO PIO . 
AA 5 PX4 B 1 506 509 PX4 PX4 . 
BA 4 PIO B 1 507 505 PIO PIO . 
CA 5 PX4 B 1 508 513 PX4 PX4 . 
DA 5 PX4 B 1 509 514 PX4 PX4 . 
EA 5 PX4 B 1 510 515 PX4 PX4 . 
FA 3 GLY C 1 501 501 GLY GLY . 
GA 4 PIO C 1 502 504 PIO PIO . 
HA 4 PIO C 1 503 506 PIO PIO . 
IA 4 PIO C 1 504 507 PIO PIO . 
JA 4 PIO C 1 505 508 PIO PIO . 
KA 5 PX4 C 1 506 509 PX4 PX4 . 
LA 4 PIO C 1 507 505 PIO PIO . 
MA 5 PX4 C 1 508 513 PX4 PX4 . 
NA 5 PX4 C 1 509 514 PX4 PX4 . 
OA 5 PX4 C 1 510 515 PX4 PX4 . 
PA 3 GLY D 1 501 501 GLY GLY . 
QA 4 PIO D 1 502 504 PIO PIO . 
RA 4 PIO D 1 503 506 PIO PIO . 
SA 4 PIO D 1 504 507 PIO PIO . 
TA 4 PIO D 1 505 508 PIO PIO . 
UA 5 PX4 D 1 506 509 PX4 PX4 . 
VA 4 PIO D 1 507 505 PIO PIO . 
WA 5 PX4 D 1 508 513 PX4 PX4 . 
XA 5 PX4 D 1 509 514 PX4 PX4 . 
YA 5 PX4 D 1 510 515 PX4 PX4 . 
ZA 4 PIO E 1 501 505 PIO PIO . 
AB 5 PX4 E 1 502 513 PX4 PX4 . 
BB 5 PX4 E 1 503 514 PX4 PX4 . 
CB 5 PX4 E 1 504 515 PX4 PX4 . 
DB 4 PIO E 1 505 504 PIO PIO . 
EB 4 PIO E 1 506 506 PIO PIO . 
FB 4 PIO E 1 507 507 PIO PIO . 
GB 4 PIO E 1 508 508 PIO PIO . 
HB 5 PX4 E 1 509 509 PX4 PX4 . 
IB 6 HOH A 1 601 504 HOH HOH . 
IB 6 HOH A 2 602 505 HOH HOH . 
IB 6 HOH A 3 603 506 HOH HOH . 
JB 6 HOH B 1 601 504 HOH HOH . 
JB 6 HOH B 2 602 506 HOH HOH . 
JB 6 HOH B 3 603 505 HOH HOH . 
KB 6 HOH C 1 601 504 HOH HOH . 
KB 6 HOH C 2 602 505 HOH HOH . 
KB 6 HOH C 3 603 506 HOH HOH . 
LB 6 HOH D 1 601 504 HOH HOH . 
LB 6 HOH D 2 602 506 HOH HOH . 
LB 6 HOH D 3 603 505 HOH HOH . 
MB 6 HOH E 1 601 504 HOH HOH . 
MB 6 HOH E 2 602 506 HOH HOH . 
MB 6 HOH E 3 603 505 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 C1A PIO . . . SA 4 139.301 180.687 155.774 1 85.11 ? C1A PIO 504 D 1 
HETATM 2 O O1A PIO . . . SA 4 139.456 181.38 156.749 1 85.11 ? O1A PIO 504 D 1 
HETATM 3 C C2A PIO . . . SA 4 140.389 179.993 154.991 1 85.11 ? C2A PIO 504 D 1 
HETATM 4 O O2C PIO . . . SA 4 138.072 180.465 155.275 1 85.11 ? O2C PIO 504 D 1 
HETATM 5 C C3A PIO . . . SA 4 140.387 180.293 153.519 1 85.11 ? C3A PIO 504 D 1 
HETATM 6 C C4A PIO . . . SA 4 141.439 179.497 152.764 1 85.11 ? C4A PIO 504 D 1 
HETATM 7 C C5A PIO . . . SA 4 141.309 179.559 151.26 1 85.11 ? C5A PIO 504 D 1 
HETATM 8 C C6A PIO . . . SA 4 142.355 178.764 150.515 1 85.11 ? C6A PIO 504 D 1 
#
_model_server_stats.io_time_ms              36 
_model_server_stats.parse_time_ms           32 
_model_server_stats.create_model_time_ms    97 
_model_server_stats.query_time_ms           1093 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           8 
#