data_7FDV
#
_model_server_result.job_id            dja1K5bxiTQJu3IekjTnlA 
_model_server_result.datetime_utc      '2024-11-22 22:11:26' 
_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          7fdv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":703}' 
#
_entry.id    7FDV 
#
_exptl.entry_id    7FDV 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              703.028 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(E,2S,3R)-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate' 
_entity.pdbx_number_of_molecules    2 
_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            7FDV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7FDV 
_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    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,G,H 
_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 H N N 
#
_chem_comp.formula           'C39 H79 N2 O6 P' 
_chem_comp.formula_weight    703.028 
_chem_comp.id                HWP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(E,2S,3R)-2-(hexadecanoylamino)-3-oxidanyl-octadec-4-enyl] 2-(trimethylazaniumyl)ethyl phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     N-Palmitoylsphingomyelin 
#
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
C30 N28 HWP sing 276 n n 
O24 P22 HWP doub 277 n n 
N28 C31 HWP sing 278 n n 
N28 C27 HWP sing 279 n n 
N28 C29 HWP sing 280 n n 
C26 C27 HWP sing 281 n n 
C26 O25 HWP sing 282 n n 
O17 C16 HWP doub 283 n n 
C20 O21 HWP sing 284 n n 
C20 C19 HWP sing 285 n n 
O25 P22 HWP sing 286 n n 
P22 O21 HWP sing 287 n n 
P22 O23 HWP sing 288 n n 
C16 C15 HWP sing 289 n n 
C16 N18 HWP sing 290 n n 
C19 N18 HWP sing 291 n n 
C19 C32 HWP sing 292 n n 
C15 C14 HWP sing 293 n n 
C32 O48 HWP sing 294 n n 
C32 C33 HWP sing 295 n n 
C14 C13 HWP sing 296 n n 
C13 C12 HWP sing 297 n n 
C33 C34 HWP doub 298 e n 
C12 C11 HWP sing 299 n n 
C34 C35 HWP sing 300 n n 
C11 C10 HWP sing 301 n n 
C10 C9 HWP sing 302 n n 
C35 C36 HWP sing 303 n n 
C8 C9 HWP sing 304 n n 
C8 C7 HWP sing 305 n n 
C36 C37 HWP sing 306 n n 
C6 C7 HWP sing 307 n n 
C6 C5 HWP sing 308 n n 
C37 C38 HWP sing 309 n n 
C5 C4 HWP sing 310 n n 
C38 C39 HWP sing 311 n n 
C4 C3 HWP sing 312 n n 
C39 C40 HWP sing 313 n n 
C1 C2 HWP sing 314 n n 
C3 C2 HWP sing 315 n n 
C40 C41 HWP sing 316 n n 
C41 C42 HWP sing 317 n n 
C42 C43 HWP sing 318 n n 
C43 C44 HWP sing 319 n n 
C44 C45 HWP sing 320 n n 
C45 C46 HWP sing 321 n n 
C46 C47 HWP sing 322 n n 
C10 H1 HWP sing 323 n n 
C10 H2 HWP sing 324 n n 
C13 H3 HWP sing 325 n n 
C13 H4 HWP sing 326 n n 
C15 H5 HWP sing 327 n n 
C15 H6 HWP sing 328 n n 
C20 H7 HWP sing 329 n n 
C20 H8 HWP sing 330 n n 
C26 H9 HWP sing 331 n n 
C26 H10 HWP sing 332 n n 
C1 H11 HWP sing 333 n n 
C1 H12 HWP sing 334 n n 
C1 H13 HWP sing 335 n n 
C2 H14 HWP sing 336 n n 
C2 H15 HWP sing 337 n n 
C3 H16 HWP sing 338 n n 
C3 H17 HWP sing 339 n n 
C4 H18 HWP sing 340 n n 
C4 H19 HWP sing 341 n n 
C5 H20 HWP sing 342 n n 
C5 H21 HWP sing 343 n n 
C6 H22 HWP sing 344 n n 
C6 H23 HWP sing 345 n n 
C7 H24 HWP sing 346 n n 
C7 H25 HWP sing 347 n n 
C8 H26 HWP sing 348 n n 
C8 H27 HWP sing 349 n n 
C9 H28 HWP sing 350 n n 
C9 H29 HWP sing 351 n n 
C11 H30 HWP sing 352 n n 
C11 H31 HWP sing 353 n n 
C12 H32 HWP sing 354 n n 
C12 H33 HWP sing 355 n n 
C14 H34 HWP sing 356 n n 
C14 H35 HWP sing 357 n n 
N18 H36 HWP sing 358 n n 
C19 H37 HWP sing 359 n n 
C27 H39 HWP sing 360 n n 
C27 H40 HWP sing 361 n n 
C29 H41 HWP sing 362 n n 
C29 H42 HWP sing 363 n n 
C29 H43 HWP sing 364 n n 
C30 H44 HWP sing 365 n n 
C30 H45 HWP sing 366 n n 
C30 H46 HWP sing 367 n n 
C31 H47 HWP sing 368 n n 
C31 H48 HWP sing 369 n n 
C31 H49 HWP sing 370 n n 
C32 H50 HWP sing 371 n n 
C33 H51 HWP sing 372 n n 
C34 H52 HWP sing 373 n n 
C35 H53 HWP sing 374 n n 
C35 H54 HWP sing 375 n n 
C36 H55 HWP sing 376 n n 
C36 H56 HWP sing 377 n n 
C37 H57 HWP sing 378 n n 
C37 H58 HWP sing 379 n n 
C38 H59 HWP sing 380 n n 
C38 H60 HWP sing 381 n n 
C39 H61 HWP sing 382 n n 
C39 H62 HWP sing 383 n n 
C40 H63 HWP sing 384 n n 
C40 H64 HWP sing 385 n n 
C41 H65 HWP sing 386 n n 
C41 H66 HWP sing 387 n n 
C42 H67 HWP sing 388 n n 
C42 H68 HWP sing 389 n n 
C43 H69 HWP sing 390 n n 
C43 H70 HWP sing 391 n n 
C44 H71 HWP sing 392 n n 
C44 H72 HWP sing 393 n n 
C45 H73 HWP sing 394 n n 
C45 H74 HWP sing 395 n n 
C46 H75 HWP sing 396 n n 
C46 H76 HWP sing 397 n n 
C47 H77 HWP sing 398 n n 
C47 H78 HWP sing 399 n n 
C47 H79 HWP sing 400 n n 
O48 H80 HWP sing 401 n n 
#
_atom_sites.entry_id                     7FDV 
_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 ATP A 1 701 702 ATP ATP . 
D 3 HWP A 1 702 703 HWP LIG . 
E 4 CLR A 1 703 701 CLR CLR . 
F 4 CLR D 1 701 701 CLR CLR . 
G 2 ATP D 1 702 702 ATP ATP . 
H 3 HWP D 1 703 703 HWP LIG . 
#
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 C10 HWP . . . H 3 132.241 124.037 124.512 1 20 ? C10 HWP 703 D 1 
HETATM 2 C C13 HWP . . . H 3 129.549 122.283 122.529 1 20 ? C13 HWP 703 D 1 
HETATM 3 C C15 HWP . . . H 3 128.658 120.609 120.812 1 20 ? C15 HWP 703 D 1 
HETATM 4 C C20 HWP . . . H 3 131.626 116.73 120.071 1 20 ? C20 HWP 703 D 1 
HETATM 5 C C26 HWP . . . H 3 135.687 113.842 119.131 1 20 ? C26 HWP 703 D 1 
HETATM 6 P P22 HWP . . . H 3 133.914 115.417 120.231 1 20 ? P22 HWP 703 D 1 
HETATM 7 C C1 HWP . . . H 3 136.419 132.13 130.012 1 20 ? C1 HWP 703 D 1 
HETATM 8 C C2 HWP . . . H 3 135.153 131.317 130.378 1 20 ? C2 HWP 703 D 1 
HETATM 9 C C3 HWP . . . H 3 135.33 129.775 130.284 1 20 ? C3 HWP 703 D 1 
HETATM 10 C C4 HWP . . . H 3 134.417 129.114 129.218 1 20 ? C4 HWP 703 D 1 
HETATM 11 C C5 HWP . . . H 3 135.173 128.084 128.353 1 20 ? C5 HWP 703 D 1 
HETATM 12 C C6 HWP . . . H 3 134.555 127.859 126.97 1 20 ? C6 HWP 703 D 1 
HETATM 13 C C7 HWP . . . H 3 133.463 126.786 126.977 1 20 ? C7 HWP 703 D 1 
HETATM 14 C C8 HWP . . . H 3 133.451 125.927 125.72 1 20 ? C8 HWP 703 D 1 
HETATM 15 C C9 HWP . . . H 3 132.355 124.871 125.784 1 20 ? C9 HWP 703 D 1 
HETATM 16 C C11 HWP . . . H 3 130.881 123.359 124.443 1 20 ? C11 HWP 703 D 1 
HETATM 17 C C12 HWP . . . H 3 130.781 122.166 123.454 1 20 ? C12 HWP 703 D 1 
HETATM 18 C C14 HWP . . . H 3 128.856 120.929 122.311 1 20 ? C14 HWP 703 D 1 
HETATM 19 C C16 HWP . . . H 3 128.912 119.111 120.469 1 20 ? C16 HWP 703 D 1 
HETATM 20 O O17 HWP . . . H 3 128.233 118.578 119.677 1 20 ? O17 HWP 703 D 1 
HETATM 21 N N18 HWP . . . H 3 130.005 118.347 121.115 1 20 ? N18 HWP 703 D 1 
HETATM 22 C C19 HWP . . . H 3 130.243 116.911 120.805 1 20 ? C19 HWP 703 D 1 
HETATM 23 O O21 HWP . . . H 3 132.259 115.48 120.368 1 20 ? O21 HWP 703 D 1 
HETATM 24 O O23 HWP . . . H 3 134.428 116.101 121.453 1 20 -1 O23 HWP 703 D 1 
HETATM 25 O O24 HWP . . . H 3 134.305 116.177 118.992 1 20 -1 O24 HWP 703 D 1 
HETATM 26 O O25 HWP . . . H 3 134.644 113.933 120.082 1 20 ? O25 HWP 703 D 1 
HETATM 27 C C27 HWP . . . H 3 136.784 112.849 119.584 1 20 ? C27 HWP 703 D 1 
HETATM 28 N N28 HWP . . . H 3 138.142 113.117 119.098 1 20 1 N28 HWP 703 D 1 
HETATM 29 C C29 HWP . . . H 3 139.078 112.347 119.886 1 20 ? C29 HWP 703 D 1 
HETATM 30 C C30 HWP . . . H 3 138.307 112.741 117.695 1 20 ? C30 HWP 703 D 1 
HETATM 31 C C31 HWP . . . H 3 138.488 114.523 119.192 1 20 ? C31 HWP 703 D 1 
HETATM 32 C C32 HWP . . . H 3 130.117 116.142 122.141 1 20 ? C32 HWP 703 D 1 
HETATM 33 C C33 HWP . . . H 3 130.559 116.969 123.372 1 20 ? C33 HWP 703 D 1 
HETATM 34 C C34 HWP . . . H 3 129.787 117.415 124.36 1 20 ? C34 HWP 703 D 1 
HETATM 35 C C35 HWP . . . H 3 130.48 118.22 125.49 1 20 ? C35 HWP 703 D 1 
HETATM 36 C C36 HWP . . . H 3 129.792 118.119 126.851 1 20 ? C36 HWP 703 D 1 
HETATM 37 C C37 HWP . . . H 3 130.454 117.179 127.895 1 20 ? C37 HWP 703 D 1 
HETATM 38 C C38 HWP . . . H 3 129.421 116.31 128.65 1 20 ? C38 HWP 703 D 1 
HETATM 39 C C39 HWP . . . H 3 129.968 115.758 129.991 1 20 ? C39 HWP 703 D 1 
HETATM 40 C C40 HWP . . . H 3 129.128 116.228 131.186 1 20 ? C40 HWP 703 D 1 
HETATM 41 C C41 HWP . . . H 3 129.409 115.48 132.477 1 20 ? C41 HWP 703 D 1 
HETATM 42 C C42 HWP . . . H 3 129.557 116.362 133.721 1 20 ? C42 HWP 703 D 1 
HETATM 43 C C43 HWP . . . H 3 128.291 116.67 134.533 1 20 ? C43 HWP 703 D 1 
HETATM 44 C C44 HWP . . . H 3 128.587 117.196 135.949 1 20 ? C44 HWP 703 D 1 
HETATM 45 C C45 HWP . . . H 3 127.356 117.364 136.84 1 20 ? C45 HWP 703 D 1 
HETATM 46 C C46 HWP . . . H 3 127.65 118.173 138.141 1 20 ? C46 HWP 703 D 1 
HETATM 47 C C47 HWP . . . H 3 126.454 118.349 139.126 1 20 ? C47 HWP 703 D 1 
HETATM 48 O O48 HWP . . . H 3 128.801 115.744 122.29 1 20 ? O48 HWP 703 D 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           48 
#