data_8SJY
#
_model_server_result.job_id            jCVBr8wwFdHZNEAvbaNi-Q 
_model_server_result.datetime_utc      '2024-11-17 22:20:10' 
_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          8sjy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":303}' 
#
_entry.id    8SJY 
#
_exptl.entry_id    8SJY 
_exptl.method      'ELECTRON CRYSTALLOGRAPHY' 
#
_entity.details                     ? 
_entity.formula_weight              703.028 
_entity.id                          2 
_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    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            8SJY 
_cell.length_a            65.5 
_cell.length_b            65.5 
_cell.length_c            200 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SJY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        89 
_symmetry.space_group_name_Hall    'P 4 2' 
_symmetry.space_group_name_H-M     'P 4 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K 1 1 
A,B,C,D,E,F,G,H,I,J,K 1 2 
A,B,C,D,E,F,G,H,I,J,K 1 3 
A,B,C,D,E,F,G,H,I,J,K 1 4 
A,B,C,D,E,F,G,H,I,J,K 1 5 
A,B,C,D,E,F,G,H,I,J,K 1 6 
A,B,C,D,E,F,G,H,I,J,K 1 7 
A,B,C,D,E,F,G,H,I,J,K 1 8 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 131 0 0 
3 'crystal symmetry operation' 3_645 -y+1,x-1,z 0 -1 0 1 0 0 0 0 1 65.5 -65.5 0 
4 'crystal symmetry operation' 4_665 y+1,-x+1,z 0 1 0 -1 0 0 0 0 1 65.5 65.5 0 
5 'crystal symmetry operation' 5_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 131 0 0 
6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
7 'crystal symmetry operation' 7_645 y+1,x-1,-z 0 1 0 1 0 0 0 0 -1 65.5 -65.5 0 
8 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 65.5 65.5 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F 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 229 n n 
O24 P22 HWP doub 230 n n 
N28 C31 HWP sing 231 n n 
N28 C27 HWP sing 232 n n 
N28 C29 HWP sing 233 n n 
C26 C27 HWP sing 234 n n 
C26 O25 HWP sing 235 n n 
O17 C16 HWP doub 236 n n 
C20 O21 HWP sing 237 n n 
C20 C19 HWP sing 238 n n 
O25 P22 HWP sing 239 n n 
P22 O21 HWP sing 240 n n 
P22 O23 HWP sing 241 n n 
C16 C15 HWP sing 242 n n 
C16 N18 HWP sing 243 n n 
C19 N18 HWP sing 244 n n 
C19 C32 HWP sing 245 n n 
C15 C14 HWP sing 246 n n 
C32 O48 HWP sing 247 n n 
C32 C33 HWP sing 248 n n 
C14 C13 HWP sing 249 n n 
C13 C12 HWP sing 250 n n 
C33 C34 HWP doub 251 e n 
C12 C11 HWP sing 252 n n 
C34 C35 HWP sing 253 n n 
C11 C10 HWP sing 254 n n 
C10 C9 HWP sing 255 n n 
C35 C36 HWP sing 256 n n 
C8 C9 HWP sing 257 n n 
C8 C7 HWP sing 258 n n 
C36 C37 HWP sing 259 n n 
C6 C7 HWP sing 260 n n 
C6 C5 HWP sing 261 n n 
C37 C38 HWP sing 262 n n 
C5 C4 HWP sing 263 n n 
C38 C39 HWP sing 264 n n 
C4 C3 HWP sing 265 n n 
C39 C40 HWP sing 266 n n 
C1 C2 HWP sing 267 n n 
C3 C2 HWP sing 268 n n 
C40 C41 HWP sing 269 n n 
C41 C42 HWP sing 270 n n 
C42 C43 HWP sing 271 n n 
C43 C44 HWP sing 272 n n 
C44 C45 HWP sing 273 n n 
C45 C46 HWP sing 274 n n 
C46 C47 HWP sing 275 n n 
C10 H1 HWP sing 276 n n 
C10 H2 HWP sing 277 n n 
C13 H3 HWP sing 278 n n 
C13 H4 HWP sing 279 n n 
C15 H5 HWP sing 280 n n 
C15 H6 HWP sing 281 n n 
C20 H7 HWP sing 282 n n 
C20 H8 HWP sing 283 n n 
C26 H9 HWP sing 284 n n 
C26 H10 HWP sing 285 n n 
C1 H11 HWP sing 286 n n 
C1 H12 HWP sing 287 n n 
C1 H13 HWP sing 288 n n 
C2 H14 HWP sing 289 n n 
C2 H15 HWP sing 290 n n 
C3 H16 HWP sing 291 n n 
C3 H17 HWP sing 292 n n 
C4 H18 HWP sing 293 n n 
C4 H19 HWP sing 294 n n 
C5 H20 HWP sing 295 n n 
C5 H21 HWP sing 296 n n 
C6 H22 HWP sing 297 n n 
C6 H23 HWP sing 298 n n 
C7 H24 HWP sing 299 n n 
C7 H25 HWP sing 300 n n 
C8 H26 HWP sing 301 n n 
C8 H27 HWP sing 302 n n 
C9 H28 HWP sing 303 n n 
C9 H29 HWP sing 304 n n 
C11 H30 HWP sing 305 n n 
C11 H31 HWP sing 306 n n 
C12 H32 HWP sing 307 n n 
C12 H33 HWP sing 308 n n 
C14 H34 HWP sing 309 n n 
C14 H35 HWP sing 310 n n 
N18 H36 HWP sing 311 n n 
C19 H37 HWP sing 312 n n 
C27 H39 HWP sing 313 n n 
C27 H40 HWP sing 314 n n 
C29 H41 HWP sing 315 n n 
C29 H42 HWP sing 316 n n 
C29 H43 HWP sing 317 n n 
C30 H44 HWP sing 318 n n 
C30 H45 HWP sing 319 n n 
C30 H46 HWP sing 320 n n 
C31 H47 HWP sing 321 n n 
C31 H48 HWP sing 322 n n 
C31 H49 HWP sing 323 n n 
C32 H50 HWP sing 324 n n 
C33 H51 HWP sing 325 n n 
C34 H52 HWP sing 326 n n 
C35 H53 HWP sing 327 n n 
C35 H54 HWP sing 328 n n 
C36 H55 HWP sing 329 n n 
C36 H56 HWP sing 330 n n 
C37 H57 HWP sing 331 n n 
C37 H58 HWP sing 332 n n 
C38 H59 HWP sing 333 n n 
C38 H60 HWP sing 334 n n 
C39 H61 HWP sing 335 n n 
C39 H62 HWP sing 336 n n 
C40 H63 HWP sing 337 n n 
C40 H64 HWP sing 338 n n 
C41 H65 HWP sing 339 n n 
C41 H66 HWP sing 340 n n 
C42 H67 HWP sing 341 n n 
C42 H68 HWP sing 342 n n 
C43 H69 HWP sing 343 n n 
C43 H70 HWP sing 344 n n 
C44 H71 HWP sing 345 n n 
C44 H72 HWP sing 346 n n 
C45 H73 HWP sing 347 n n 
C45 H74 HWP sing 348 n n 
C46 H75 HWP sing 349 n n 
C46 H76 HWP sing 350 n n 
C47 H77 HWP sing 351 n n 
C47 H78 HWP sing 352 n n 
C47 H79 HWP sing 353 n n 
O48 H80 HWP sing 354 n n 
#
_atom_sites.entry_id                     8SJY 
_atom_sites.fract_transf_matrix[1][1]    0.015267 
_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]    0.015267 
_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]    0.005 
_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
B 2 HWP A 1 301 302 HWP LSM . 
C 2 HWP A 1 302 303 HWP LSM . 
D 2 HWP A 1 303 305 HWP LSM . 
E 2 HWP A 1 304 306 HWP LSM . 
F 2 HWP A 1 305 307 HWP LSM . 
G 3 CLR A 1 306 401 CLR CLR . 
H 3 CLR A 1 307 402 CLR CLR . 
I 3 CLR A 1 308 403 CLR CLR . 
J 3 CLR A 1 309 404 CLR CLR . 
K 4 HOH A 1 401 912 HOH HOH . 
K 4 HOH A 2 402 993 HOH HOH . 
K 4 HOH A 3 403 930 HOH HOH . 
K 4 HOH A 4 404 925 HOH HOH . 
K 4 HOH A 5 405 983 HOH HOH . 
K 4 HOH A 6 406 984 HOH HOH . 
K 4 HOH A 7 407 981 HOH HOH . 
K 4 HOH A 8 408 964 HOH HOH . 
K 4 HOH A 9 409 949 HOH HOH . 
K 4 HOH A 10 410 982 HOH HOH . 
K 4 HOH A 11 411 980 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 C10 HWP . . . D 2 42.543 37.239 28.073 1 121.11 ? C10 HWP 303 A 1 
HETATM 2 C C13 HWP . . . D 2 40.445 35.301 30.569 1 125.02 ? C13 HWP 303 A 1 
HETATM 3 C C15 HWP . . . D 2 39.174 34.537 32.519 1 117.68 ? C15 HWP 303 A 1 
HETATM 4 C C20 HWP . . . D 2 38.221 32.211 36.075 1 126.5 ? C20 HWP 303 A 1 
HETATM 5 C C26 HWP . . . D 2 40.172 33.034 38.799 1 127.84 ? C26 HWP 303 A 1 
HETATM 6 P P22 HWP . . . D 2 40.94 32.731 36.104 1 104.95 ? P22 HWP 303 A 1 
HETATM 7 C C3 HWP . . . D 2 48.062 37.114 21.688 1 80.71 ? C3 HWP 303 A 1 
HETATM 8 C C4 HWP . . . D 2 47.762 37.865 22.977 1 98.97 ? C4 HWP 303 A 1 
HETATM 9 C C5 HWP . . . D 2 46.966 36.954 23.865 1 93.57 ? C5 HWP 303 A 1 
HETATM 10 C C6 HWP . . . D 2 46.284 37.789 24.927 1 92.32 ? C6 HWP 303 A 1 
HETATM 11 C C7 HWP . . . D 2 45.288 36.891 25.585 1 114.3 ? C7 HWP 303 A 1 
HETATM 12 C C8 HWP . . . D 2 44.431 37.643 26.543 1 127.46 ? C8 HWP 303 A 1 
HETATM 13 C C9 HWP . . . D 2 43.37 36.672 26.965 1 114.96 ? C9 HWP 303 A 1 
HETATM 14 C C11 HWP . . . D 2 41.731 36.075 28.63 1 117.06 ? C11 HWP 303 A 1 
HETATM 15 C C12 HWP . . . D 2 41.039 36.537 29.9 1 121.61 ? C12 HWP 303 A 1 
HETATM 16 C C14 HWP . . . D 2 39.703 35.76 31.799 1 117.19 ? C14 HWP 303 A 1 
HETATM 17 C C16 HWP . . . D 2 38.193 35.032 33.559 1 117.49 ? C16 HWP 303 A 1 
HETATM 18 O O17 HWP . . . D 2 37.609 36.108 33.421 1 118.24 ? O17 HWP 303 A 1 
HETATM 19 N N18 HWP . . . D 2 37.982 34.235 34.647 1 112.97 ? N18 HWP 303 A 1 
HETATM 20 C C19 HWP . . . D 2 37.979 32.772 34.611 1 131.97 ? C19 HWP 303 A 1 
HETATM 21 O O21 HWP . . . D 2 39.53 31.745 36.176 1 116.15 ? O21 HWP 303 A 1 
HETATM 22 O O23 HWP . . . D 2 42.059 31.948 35.543 1 102.19 ? O23 HWP 303 A 1 
HETATM 23 O O24 HWP . . . D 2 40.637 34.072 35.564 1 114.71 ? O24 HWP 303 A 1 
HETATM 24 O O25 HWP . . . D 2 41.115 32.83 37.856 1 114.68 ? O25 HWP 303 A 1 
HETATM 25 C C27 HWP . . . D 2 40.826 33.111 40.215 1 136.31 ? C27 HWP 303 A 1 
HETATM 26 N N28 HWP . . . D 2 41.594 31.842 40.657 1 120.86 ? N28 HWP 303 A 1 
HETATM 27 C C29 HWP . . . D 2 41.633 31.787 42.162 1 100.98 ? C29 HWP 303 A 1 
HETATM 28 C C30 HWP . . . D 2 43.012 31.901 40.137 1 114.93 ? C30 HWP 303 A 1 
HETATM 29 C C31 HWP . . . D 2 40.913 30.595 40.128 1 95 ? C31 HWP 303 A 1 
HETATM 30 C C32 HWP . . . D 2 36.632 32.264 34.018 1 135.32 ? C32 HWP 303 A 1 
HETATM 31 C C33 HWP . . . D 2 36.947 31.402 32.825 1 136.54 ? C33 HWP 303 A 1 
HETATM 32 C C34 HWP . . . D 2 38.016 30.648 32.999 1 134.94 ? C34 HWP 303 A 1 
HETATM 33 C C35 HWP . . . D 2 38.414 29.749 31.869 1 119.41 ? C35 HWP 303 A 1 
HETATM 34 C C36 HWP . . . D 2 37.701 30.12 30.587 1 125.42 ? C36 HWP 303 A 1 
HETATM 35 C C37 HWP . . . D 2 38.126 29.102 29.545 1 111.16 ? C37 HWP 303 A 1 
HETATM 36 C C38 HWP . . . D 2 37.388 29.354 28.249 1 118.4 ? C38 HWP 303 A 1 
HETATM 37 C C39 HWP . . . D 2 37.836 28.275 27.251 1 109.7 ? C39 HWP 303 A 1 
HETATM 38 C C40 HWP . . . D 2 36.999 28.44 25.993 1 102.56 ? C40 HWP 303 A 1 
HETATM 39 C C41 HWP . . . D 2 37.497 27.498 24.904 1 94.98 ? C41 HWP 303 A 1 
HETATM 40 C C42 HWP . . . D 2 36.858 27.981 23.615 1 91.6 ? C42 HWP 303 A 1 
HETATM 41 C C43 HWP . . . D 2 37.339 27.165 22.426 1 89.23 ? C43 HWP 303 A 1 
HETATM 42 C C44 HWP . . . D 2 36.899 27.933 21.188 1 83.99 ? C44 HWP 303 A 1 
HETATM 43 C C45 HWP . . . D 2 37.404 27.272 19.907 1 88.49 ? C45 HWP 303 A 1 
HETATM 44 C C46 HWP . . . D 2 36.943 28.165 18.744 1 77.25 ? C46 HWP 303 A 1 
HETATM 45 C C47 HWP . . . D 2 37.286 27.545 17.4 1 67.75 ? C47 HWP 303 A 1 
HETATM 46 O O48 HWP . . . D 2 35.909 31.592 34.999 1 120.75 ? O48 HWP 303 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           378 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           46 
#