data_4NT2
#
_model_server_result.job_id            3vkz_McITXf1FuTGfAh0RA 
_model_server_result.datetime_utc      '2024-11-04 22:56:08' 
_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          4nt2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    4NT2 
#
_exptl.entry_id    4NT2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              465.627 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium 
_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         120 
_cell.entry_id            4NT2 
_cell.length_a            108.827 
_cell.length_b            108.827 
_cell.length_c            105.007 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4NT2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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
? 2 B N N 
? 2 C N N 
#
_chem_comp.formula           'C23 H50 N2 O5 P 1' 
_chem_comp.formula_weight    465.627 
_chem_comp.id                SPU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'sphingosylphosphorylcholine, sphingosine phosphorylcholine' 
#
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
C11 C14 SPU sing 303 n n 
C11 C21 SPU sing 304 n n 
C14 C17 SPU sing 305 n n 
C17 C20 SPU sing 306 n n 
C20 C23 SPU sing 307 n n 
C23 C26 SPU sing 308 n n 
C26 C29 SPU sing 309 n n 
C29 C32 SPU sing 310 n n 
C32 C35 SPU sing 311 n n 
C35 C38 SPU sing 312 n n 
C38 C41 SPU sing 313 n n 
C41 C43 SPU doub 314 n n 
C43 C45 SPU sing 315 n n 
C45 O47 SPU sing 316 n n 
C45 C49 SPU sing 317 n n 
C49 N51 SPU sing 318 n n 
C49 C54 SPU sing 319 n n 
C54 O57 SPU sing 320 n n 
O57 P58 SPU sing 321 n n 
P58 O59 SPU sing 322 n n 
P58 O60 SPU doub 323 n n 
P58 O61 SPU sing 324 n n 
O61 C62 SPU sing 325 n n 
C62 C65 SPU sing 326 n n 
C65 N68 SPU sing 327 n n 
N68 C70 SPU sing 328 n n 
N68 C74 SPU sing 329 n n 
N68 C78 SPU sing 330 n n 
C21 C22 SPU sing 331 n n 
C22 C231 SPU sing 332 n n 
C11 H11 SPU sing 333 n n 
C11 H11A SPU sing 334 e n 
C14 H14 SPU sing 335 n n 
C14 H14A SPU sing 336 n n 
C17 H17 SPU sing 337 n n 
C17 H17A SPU sing 338 n n 
C20 H20 SPU sing 339 n n 
C20 H20A SPU sing 340 n n 
C23 H23 SPU sing 341 n n 
C23 H23A SPU sing 342 n n 
C26 H26 SPU sing 343 n n 
C26 H26A SPU sing 344 n n 
C29 H29 SPU sing 345 n n 
C29 H29A SPU sing 346 n n 
C32 H32 SPU sing 347 n n 
C32 H32A SPU sing 348 n n 
C35 H35 SPU sing 349 n n 
C35 H35A SPU sing 350 n n 
C38 H38 SPU sing 351 n n 
C38 H38A SPU sing 352 n n 
C41 H41 SPU sing 353 n n 
C43 H43 SPU sing 354 n n 
C45 H45 SPU sing 355 n n 
O47 HO47 SPU sing 356 n n 
C49 H49 SPU sing 357 n n 
N51 HN51 SPU sing 358 n n 
N51 HN5A SPU sing 359 n n 
C54 H54 SPU sing 360 n n 
C54 H54A SPU sing 361 n n 
O59 H59 SPU sing 362 n n 
C62 H62 SPU sing 363 n n 
C62 H62A SPU sing 364 n n 
C65 H65 SPU sing 365 n n 
C65 H65A SPU sing 366 n n 
C70 H70 SPU sing 367 n n 
C70 H70A SPU sing 368 n n 
C70 H70B SPU sing 369 n n 
C74 H74 SPU sing 370 n n 
C74 H74A SPU sing 371 n n 
C74 H74B SPU sing 372 n n 
C78 H78 SPU sing 373 n n 
C78 H78A SPU sing 374 n n 
C78 H78B SPU sing 375 n n 
C21 H44 SPU sing 376 n n 
C21 H451 SPU sing 377 n n 
C22 H46 SPU sing 378 n n 
C22 H47 SPU sing 379 n n 
C231 H48 SPU sing 380 n n 
C231 H491 SPU sing 381 n n 
C231 H50 SPU sing 382 n n 
#
_atom_sites.entry_id                     4NT2 
_atom_sites.fract_transf_matrix[1][1]    0.009189 
_atom_sites.fract_transf_matrix[1][2]    0.005305 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01061 
_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]    0.009523 
_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 SPU A 1 301 2 SPU DRG . 
C 2 SPU A 1 302 3 SPU DRG . 
D 3 SO4 A 1 303 1 SO4 SO4 . 
E 3 SO4 A 1 304 2 SO4 SO4 . 
F 3 SO4 A 1 305 3 SO4 SO4 . 
G 3 SO4 A 1 306 4 SO4 SO4 . 
H 3 SO4 A 1 307 5 SO4 SO4 . 
I 4 EDO A 1 308 1 EDO EDO . 
J 4 EDO A 1 309 2 EDO EDO . 
K 5 HOH A 1 401 1 HOH HOH . 
K 5 HOH A 2 402 2 HOH HOH . 
K 5 HOH A 3 403 3 HOH HOH . 
K 5 HOH A 4 404 4 HOH HOH . 
K 5 HOH A 5 405 5 HOH HOH . 
K 5 HOH A 6 406 6 HOH HOH . 
K 5 HOH A 7 407 7 HOH HOH . 
K 5 HOH A 8 408 8 HOH HOH . 
K 5 HOH A 9 409 9 HOH HOH . 
K 5 HOH A 10 410 10 HOH HOH . 
K 5 HOH A 11 411 11 HOH HOH . 
K 5 HOH A 12 412 12 HOH HOH . 
K 5 HOH A 13 413 13 HOH HOH . 
K 5 HOH A 14 414 14 HOH HOH . 
K 5 HOH A 15 415 15 HOH HOH . 
K 5 HOH A 16 416 16 HOH HOH . 
K 5 HOH A 17 417 17 HOH HOH . 
K 5 HOH A 18 418 18 HOH HOH . 
K 5 HOH A 19 419 19 HOH HOH . 
K 5 HOH A 20 420 20 HOH HOH . 
K 5 HOH A 21 421 21 HOH HOH . 
K 5 HOH A 22 422 22 HOH HOH . 
K 5 HOH A 23 423 23 HOH HOH . 
K 5 HOH A 24 424 24 HOH HOH . 
K 5 HOH A 25 425 25 HOH HOH . 
K 5 HOH A 26 426 26 HOH HOH . 
K 5 HOH A 27 427 27 HOH HOH . 
K 5 HOH A 28 428 28 HOH HOH . 
K 5 HOH A 29 429 29 HOH HOH . 
K 5 HOH A 30 430 30 HOH HOH . 
K 5 HOH A 31 431 31 HOH HOH . 
K 5 HOH A 32 432 32 HOH HOH . 
K 5 HOH A 33 433 33 HOH HOH . 
K 5 HOH A 34 434 34 HOH HOH . 
K 5 HOH A 35 435 35 HOH HOH . 
K 5 HOH A 36 436 36 HOH HOH . 
K 5 HOH A 37 437 37 HOH HOH . 
K 5 HOH A 38 438 38 HOH HOH . 
K 5 HOH A 39 439 39 HOH HOH . 
K 5 HOH A 40 440 40 HOH HOH . 
K 5 HOH A 41 441 41 HOH HOH . 
K 5 HOH A 42 442 42 HOH HOH . 
K 5 HOH A 43 443 43 HOH HOH . 
K 5 HOH A 44 444 44 HOH HOH . 
K 5 HOH A 45 445 45 HOH HOH . 
K 5 HOH A 46 446 46 HOH HOH . 
K 5 HOH A 47 447 47 HOH HOH . 
K 5 HOH A 48 448 48 HOH HOH . 
K 5 HOH A 49 449 49 HOH HOH . 
K 5 HOH A 50 450 50 HOH HOH . 
K 5 HOH A 51 451 51 HOH HOH . 
K 5 HOH A 52 452 52 HOH HOH . 
K 5 HOH A 53 453 53 HOH HOH . 
K 5 HOH A 54 454 54 HOH HOH . 
K 5 HOH A 55 455 55 HOH HOH . 
K 5 HOH A 56 456 56 HOH HOH . 
K 5 HOH A 57 457 57 HOH HOH . 
K 5 HOH A 58 458 58 HOH HOH . 
K 5 HOH A 59 459 59 HOH HOH . 
K 5 HOH A 60 460 60 HOH HOH . 
K 5 HOH A 61 461 61 HOH HOH . 
K 5 HOH A 62 462 62 HOH HOH . 
K 5 HOH A 63 463 63 HOH HOH . 
K 5 HOH A 64 464 64 HOH HOH . 
K 5 HOH A 65 465 65 HOH HOH . 
K 5 HOH A 66 466 66 HOH HOH . 
K 5 HOH A 67 467 67 HOH HOH . 
K 5 HOH A 68 468 68 HOH HOH . 
K 5 HOH A 69 469 69 HOH HOH . 
K 5 HOH A 70 470 70 HOH HOH . 
K 5 HOH A 71 471 71 HOH HOH . 
K 5 HOH A 72 472 72 HOH HOH . 
K 5 HOH A 73 473 73 HOH HOH . 
K 5 HOH A 74 474 74 HOH HOH . 
K 5 HOH A 75 475 75 HOH HOH . 
K 5 HOH A 76 476 76 HOH HOH . 
K 5 HOH A 77 477 77 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 C23 SPU . . . C 2 -50.793 -28.048 20.569 1 45.36 ? C23 SPU 302 A 1 
HETATM 2 C C26 SPU . . . C 2 -49.533 -27.524 21.335 1 59.74 ? C26 SPU 302 A 1 
HETATM 3 C C29 SPU . . . C 2 -48.636 -26.681 20.357 1 51.1 ? C29 SPU 302 A 1 
HETATM 4 C C32 SPU . . . C 2 -47.821 -25.638 21.169 1 64.16 ? C32 SPU 302 A 1 
HETATM 5 C C35 SPU . . . C 2 -47.132 -24.634 20.188 1 49.86 ? C35 SPU 302 A 1 
HETATM 6 C C38 SPU . . . C 2 -47.076 -23.239 20.835 1 51.3 ? C38 SPU 302 A 1 
HETATM 7 C C41 SPU . . . C 2 -45.846 -22.481 20.313 1 52.78 ? C41 SPU 302 A 1 
HETATM 8 C C43 SPU . . . C 2 -44.957 -21.929 21.195 1 59.68 ? C43 SPU 302 A 1 
HETATM 9 C C45 SPU . . . C 2 -43.709 -21.18 20.711 1 65.92 ? C45 SPU 302 A 1 
HETATM 10 O O47 SPU . . . C 2 -43.968 -20.599 19.473 1 68.46 ? O47 SPU 302 A 1 
HETATM 11 C C49 SPU . . . C 2 -43.347 -20.097 21.715 1 69.55 ? C49 SPU 302 A 1 
HETATM 12 N N51 SPU . . . C 2 -42.284 -19.325 21.211 1 71 ? N51 SPU 302 A 1 
HETATM 13 C C54 SPU . . . C 2 -44.563 -19.196 21.957 1 73.29 ? C54 SPU 302 A 1 
HETATM 14 O O57 SPU . . . C 2 -44.573 -18.103 20.969 1 75.98 ? O57 SPU 302 A 1 
HETATM 15 P P58 SPU . . . C 2 -45.357 -16.737 21.288 1 97.16 ? P58 SPU 302 A 1 
HETATM 16 O O59 SPU . . . C 2 -45.597 -16.088 19.973 1 97.02 ? O59 SPU 302 A 1 
HETATM 17 O O60 SPU . . . C 2 -44.63 -15.868 22.23 1 98.67 ? O60 SPU 302 A 1 
HETATM 18 O O61 SPU . . . C 2 -46.776 -17.168 21.826 1 125.28 ? O61 SPU 302 A 1 
HETATM 19 C C62 SPU . . . C 2 -47.713 -16.162 22.309 1 127.07 ? C62 SPU 302 A 1 
HETATM 20 C C65 SPU . . . C 2 -48.657 -16.793 23.369 1 108.08 ? C65 SPU 302 A 1 
HETATM 21 N N68 SPU . . . C 2 -49.995 -16.181 23.304 1 110.33 ? N68 SPU 302 A 1 
HETATM 22 C C70 SPU . . . C 2 -49.886 -14.753 23.512 1 112.24 ? C70 SPU 302 A 1 
HETATM 23 C C74 SPU . . . C 2 -50.573 -16.433 22.028 1 109.17 ? C74 SPU 302 A 1 
HETATM 24 C C78 SPU . . . C 2 -50.817 -16.742 24.315 1 110.78 ? C78 SPU 302 A 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           24 
#