data_8JNI
#
_model_server_result.job_id            -0VIJOAqynWPT13MpNrVqQ 
_model_server_result.datetime_utc      '2024-11-04 18:47:05' 
_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          8jni 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1402}' 
#
_entry.id    8JNI 
#
_exptl.entry_id    8JNI 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1047.088 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 3 D N N 
? 3 E N N 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             855 
_struct_conn.ptnr1_auth_asym_id             B 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              855 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             855 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              855 
_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                1.989 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C47 H85 O19 P3' 
_chem_comp.formula_weight    1047.088 
_chem_comp.id                PT5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Phosphatidylinositol 4,5-bisphosphate;PtdIns(4,5)P2' 
#
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
C23 C24 PT5 sing 275 n n 
C23 C22 PT5 sing 276 n n 
C22 C21 PT5 doub 277 e n 
C21 C20 PT5 sing 278 n n 
C20 C19 PT5 sing 279 n n 
C19 C18 PT5 doub 280 z n 
C16 C17 PT5 sing 281 n n 
C16 C15 PT5 doub 282 z n 
C18 C17 PT5 sing 283 n n 
C15 C14 PT5 sing 284 n n 
C14 C13 PT5 sing 285 n n 
C13 C12 PT5 sing 286 n n 
O17 C10 PT5 doub 287 n n 
O52 P5 PT5 doub 288 n n 
O6 C6 PT5 sing 289 n n 
C12 C10 PT5 sing 290 n n 
O53 P5 PT5 sing 291 n n 
C10 O16 PT5 sing 292 n n 
P5 O5 PT5 sing 293 n n 
P5 O51 PT5 sing 294 n n 
O5 C5 PT5 sing 295 n n 
C5 C6 PT5 sing 296 n n 
C5 C4 PT5 sing 297 n n 
C6 C1 PT5 sing 298 n n 
C1 C2 PT5 sing 299 n n 
C1 O1 PT5 sing 300 n n 
O16 C8 PT5 sing 301 n n 
C7 O13 PT5 sing 302 n n 
C7 C8 PT5 sing 303 n n 
C2 O2 PT5 sing 304 n n 
C2 C3 PT5 sing 305 n n 
O13 P1 PT5 sing 306 n n 
C8 C9 PT5 sing 307 n n 
O4 C4 PT5 sing 308 n n 
O4 P4 PT5 sing 309 n n 
C4 C3 PT5 sing 310 n n 
C3 O3 PT5 sing 311 n n 
O1 P1 PT5 sing 312 n n 
O42 P4 PT5 doub 313 n n 
P1 O11 PT5 doub 314 n n 
P1 O12 PT5 sing 315 n n 
P4 O41 PT5 sing 316 n n 
P4 O43 PT5 sing 317 n n 
C9 O18 PT5 sing 318 n n 
C31 C11 PT5 sing 319 n n 
C31 C32 PT5 sing 320 n n 
O18 C11 PT5 sing 321 n n 
C11 O19 PT5 doub 322 n n 
C32 C33 PT5 sing 323 n n 
C33 C34 PT5 sing 324 n n 
C34 C35 PT5 sing 325 n n 
C35 C36 PT5 sing 326 n n 
C36 C37 PT5 sing 327 n n 
C37 C38 PT5 sing 328 n n 
C40 C39 PT5 sing 329 n n 
C39 C38 PT5 sing 330 n n 
O12 H1 PT5 sing 331 n n 
O6 H2 PT5 sing 332 n n 
C1 H3 PT5 sing 333 n n 
C6 H4 PT5 sing 334 n n 
C2 H5 PT5 sing 335 n n 
O2 H6 PT5 sing 336 n n 
C3 H7 PT5 sing 337 n n 
O3 H8 PT5 sing 338 n n 
C4 H9 PT5 sing 339 n n 
O41 H10 PT5 sing 340 n n 
O43 H11 PT5 sing 341 n n 
C5 H12 PT5 sing 342 n n 
O51 H13 PT5 sing 343 n n 
O53 H14 PT5 sing 344 n n 
C7 H15 PT5 sing 345 n n 
C7 H16 PT5 sing 346 n n 
C8 H17 PT5 sing 347 n n 
C9 H18 PT5 sing 348 n n 
C9 H19 PT5 sing 349 n n 
C12 H20 PT5 sing 350 n n 
C12 H21 PT5 sing 351 n n 
C13 H22 PT5 sing 352 n n 
C13 H23 PT5 sing 353 n n 
C14 H24 PT5 sing 354 n n 
C14 H25 PT5 sing 355 n n 
C15 H26 PT5 sing 356 n n 
C16 H28 PT5 sing 357 n n 
C17 H30 PT5 sing 358 n n 
C17 H31 PT5 sing 359 n n 
C18 H32 PT5 sing 360 n n 
C19 H33 PT5 sing 361 n n 
C20 H34 PT5 sing 362 n n 
C20 H35 PT5 sing 363 n n 
C21 H36 PT5 sing 364 n n 
C22 H38 PT5 sing 365 n n 
C23 H40 PT5 sing 366 n n 
C23 H41 PT5 sing 367 n n 
C24 H42 PT5 sing 368 n n 
C31 H45 PT5 sing 369 n n 
C31 H46 PT5 sing 370 n n 
C32 H47 PT5 sing 371 n n 
C32 H48 PT5 sing 372 n n 
C33 H49 PT5 sing 373 n n 
C33 H50 PT5 sing 374 n n 
C34 H51 PT5 sing 375 n n 
C34 H52 PT5 sing 376 n n 
C35 H53 PT5 sing 377 n n 
C35 H54 PT5 sing 378 n n 
C36 H55 PT5 sing 379 n n 
C36 H56 PT5 sing 380 n n 
C37 H57 PT5 sing 381 n n 
C37 H58 PT5 sing 382 n n 
C38 H59 PT5 sing 383 n n 
C38 H60 PT5 sing 384 n n 
C39 H61 PT5 sing 385 n n 
C39 H62 PT5 sing 386 n n 
C40 H63 PT5 sing 387 n n 
C40 H64 PT5 sing 388 n n 
C24 C25 PT5 doub 389 n n 
C25 C26 PT5 sing 390 n n 
C26 C27 PT5 sing 391 n n 
C27 C28 PT5 sing 392 n n 
C28 C29 PT5 sing 393 n n 
C29 C30 PT5 sing 394 n n 
C40 C41 PT5 sing 395 n n 
C41 C42 PT5 sing 396 n n 
C42 C43 PT5 sing 397 n n 
C43 C44 PT5 sing 398 n n 
C44 C45 PT5 sing 399 n n 
C45 C46 PT5 sing 400 n n 
C46 C47 PT5 sing 401 n n 
C25 H27 PT5 sing 402 n n 
C26 H29 PT5 sing 403 n n 
C26 H37 PT5 sing 404 n n 
C27 H39 PT5 sing 405 n n 
C27 H43 PT5 sing 406 n n 
C28 H44 PT5 sing 407 n n 
C28 H65 PT5 sing 408 n n 
C29 H66 PT5 sing 409 n n 
C29 H67 PT5 sing 410 n n 
C30 H68 PT5 sing 411 n n 
C30 H69 PT5 sing 412 n n 
C30 H70 PT5 sing 413 n n 
C41 H71 PT5 sing 414 n n 
C41 H72 PT5 sing 415 n n 
C42 H73 PT5 sing 416 n n 
C42 H74 PT5 sing 417 n n 
C43 H75 PT5 sing 418 n n 
C43 H76 PT5 sing 419 n n 
C44 H77 PT5 sing 420 n n 
C44 H78 PT5 sing 421 n n 
C45 H79 PT5 sing 422 n n 
C45 H80 PT5 sing 423 n n 
C46 H81 PT5 sing 424 n n 
C46 H82 PT5 sing 425 n n 
C47 H83 PT5 sing 426 n n 
C47 H84 PT5 sing 427 n n 
C47 H85 PT5 sing 428 n n 
#
_atom_sites.entry_id                     8JNI 
_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
C 2 CL B 1 1401 1401 CL CL . 
D 3 PT5 B 1 1402 1301 PT5 PT5 . 
E 3 PT5 A 1 1301 1301 PT5 PT5 . 
F 2 CL A 1 1302 1401 CL CL . 
#
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 O12 PT5 . . . D 3 140.3 165.555 147.065 1 62.28 -1 O12 PT5 1402 B 1 
HETATM 2 P P1 PT5 . . . D 3 141.521 164.879 147.545 1 62.28 ? P1 PT5 1402 B 1 
HETATM 3 O O13 PT5 . . . D 3 141.295 164.007 148.857 1 62.28 ? O13 PT5 1402 B 1 
HETATM 4 O O11 PT5 . . . D 3 142.242 163.954 146.565 1 62.28 ? O11 PT5 1402 B 1 
HETATM 5 O O6 PT5 . . . D 3 142.504 168.21 146.491 1 62.28 ? O6 PT5 1402 B 1 
HETATM 6 O O1 PT5 . . . D 3 142.61 165.868 148.089 1 62.28 ? O1 PT5 1402 B 1 
HETATM 7 C C1 PT5 . . . D 3 143.806 166.527 147.628 1 62.28 ? C1 PT5 1402 B 1 
HETATM 8 C C6 PT5 . . . D 3 143.516 168.011 147.471 1 62.28 ? C6 PT5 1402 B 1 
HETATM 9 C C2 PT5 . . . D 3 144.876 166.291 148.679 1 62.28 ? C2 PT5 1402 B 1 
HETATM 10 O O2 PT5 . . . D 3 144.41 166.73 149.947 1 62.28 ? O2 PT5 1402 B 1 
HETATM 11 C C3 PT5 . . . D 3 146.173 166.994 148.31 1 62.28 ? C3 PT5 1402 B 1 
HETATM 12 O O3 PT5 . . . D 3 147.107 166.847 149.373 1 62.28 ? O3 PT5 1402 B 1 
HETATM 13 C C4 PT5 . . . D 3 145.94 168.471 148.026 1 62.28 ? C4 PT5 1402 B 1 
HETATM 14 O O4 PT5 . . . D 3 147.145 169.003 147.437 1 62.28 ? O4 PT5 1402 B 1 
HETATM 15 P P4 PT5 . . . D 3 148.386 169.742 148.151 1 62.28 ? P4 PT5 1402 B 1 
HETATM 16 O O41 PT5 . . . D 3 148.449 169.41 149.595 1 62.28 ? O41 PT5 1402 B 1 
HETATM 17 O O42 PT5 . . . D 3 149.632 169.284 147.386 1 62.28 -1 O42 PT5 1402 B 1 
HETATM 18 O O43 PT5 . . . D 3 148.189 171.238 147.891 1 62.28 ? O43 PT5 1402 B 1 
HETATM 19 C C5 PT5 . . . D 3 144.802 168.703 147.046 1 62.28 ? C5 PT5 1402 B 1 
HETATM 20 O O5 PT5 . . . D 3 145.193 168.213 145.746 1 62.28 ? O5 PT5 1402 B 1 
HETATM 21 P P5 PT5 . . . D 3 145.071 169.09 144.391 1 62.28 ? P5 PT5 1402 B 1 
HETATM 22 O O52 PT5 . . . D 3 146.354 169.085 143.642 1 62.28 ? O52 PT5 1402 B 1 
HETATM 23 O O51 PT5 . . . D 3 143.913 168.469 143.604 1 62.28 -1 O51 PT5 1402 B 1 
HETATM 24 O O53 PT5 . . . D 3 144.646 170.492 144.838 1 62.28 ? O53 PT5 1402 B 1 
HETATM 25 C C7 PT5 . . . D 3 140.392 162.901 149.052 1 62.28 ? C7 PT5 1402 B 1 
HETATM 26 C C8 PT5 . . . D 3 140.645 162.413 150.45 1 62.28 ? C8 PT5 1402 B 1 
HETATM 27 C C9 PT5 . . . D 3 139.401 161.868 151.099 1 62.28 ? C9 PT5 1402 B 1 
HETATM 28 O O16 PT5 . . . D 3 141.655 161.363 150.322 1 62.28 ? O16 PT5 1402 B 1 
HETATM 29 C C10 PT5 . . . D 3 142.12 160.794 151.442 1 62.28 ? C10 PT5 1402 B 1 
HETATM 30 O O17 PT5 . . . D 3 141.896 159.655 151.757 1 62.28 ? O17 PT5 1402 B 1 
HETATM 31 O O18 PT5 . . . D 3 139.555 161.978 152.533 1 62.28 ? O18 PT5 1402 B 1 
HETATM 32 C C11 PT5 . . . D 3 138.561 161.514 153.289 1 62.28 ? C11 PT5 1402 B 1 
HETATM 33 O O19 PT5 . . . D 3 137.728 160.741 152.898 1 62.28 ? O19 PT5 1402 B 1 
HETATM 34 C C12 PT5 . . . D 3 142.973 161.756 152.213 1 62.28 ? C12 PT5 1402 B 1 
HETATM 35 C C13 PT5 . . . D 3 143.529 161.175 153.501 1 62.28 ? C13 PT5 1402 B 1 
HETATM 36 C C14 PT5 . . . D 3 142.516 161.073 154.628 1 62.28 ? C14 PT5 1402 B 1 
HETATM 37 C C15 PT5 . . . D 3 143.094 160.491 155.907 1 62.28 ? C15 PT5 1402 B 1 
HETATM 38 C C16 PT5 . . . D 3 142.11 160.444 157.061 1 62.28 ? C16 PT5 1402 B 1 
HETATM 39 C C17 PT5 . . . D 3 141.563 161.806 157.456 1 62.28 ? C17 PT5 1402 B 1 
HETATM 40 C C31 PT5 . . . D 3 138.626 162.078 154.677 1 62.28 ? C31 PT5 1402 B 1 
HETATM 41 C C32 PT5 . . . D 3 137.511 161.57 155.581 1 62.28 ? C32 PT5 1402 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           41 
#