data_6I3Y # _model_server_result.job_id yAb0oygMiVTUGio5XFaVcQ _model_server_result.datetime_utc '2024-12-03 14:36:55' _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 6i3y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 6I3Y # _exptl.entry_id 6I3Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 792.075 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _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 6I3Y _cell.length_a 126 _cell.length_b 126 _cell.length_c 178.32 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6I3Y _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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,D,E,F,H 1 1 B,C,G,I,J 1 2 # 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' 9_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N # 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 C SG CYS 22 A CYS 21 1_555 C SG CYS 61 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf2 C SG CYS 32 A CYS 31 1_555 C SG CYS 51 A CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf3 D SG CYS 22 H CYS 21 1_555 D SG CYS 61 H CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 D SG CYS 32 H CYS 31 1_555 D SG CYS 51 H CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? # _chem_comp.formula 'C42 H82 N O10 P' _chem_comp.formula_weight 792.075 _chem_comp.id P5S _chem_comp.mon_nstd_flag . _chem_comp.name O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'phosphatidyl serine' # 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 CA C P5S sing 319 n n O C P5S doub 320 n n C OXT P5S sing 321 n n CA N P5S sing 322 n n N HN P5S sing 323 n n N HNA P5S sing 324 n n O19 C1 P5S sing 325 n n C1 C2 P5S sing 326 n n C1 H1 P5S sing 327 n n C1 H1A P5S sing 328 n n C2 O37 P5S sing 329 n n C2 C3 P5S sing 330 n n C2 H2 P5S sing 331 n n O16 C3 P5S sing 332 n n C3 H3 P5S sing 333 n n C3 H3A P5S sing 334 n n CB CA P5S sing 335 n n CA HA P5S sing 336 n n CB OG P5S sing 337 n n CB HB P5S sing 338 n n CB HBA P5S sing 339 n n P12 OG P5S sing 340 n n O16 P12 P5S sing 341 n n O13 P12 P5S doub 342 n n P12 O15 P5S sing 343 n n O15 HO15 P5S sing 344 n n C20 C17 P5S sing 345 n n O19 C17 P5S sing 346 n n C17 O18 P5S doub 347 n n C21 C20 P5S sing 348 n n C20 H20 P5S sing 349 n n C20 H20A P5S sing 350 n n C21 C22 P5S sing 351 n n C21 H21 P5S sing 352 n n C21 H21A P5S sing 353 n n C23 C22 P5S sing 354 n n C22 H22 P5S sing 355 n n C22 H22A P5S sing 356 n n C24 C23 P5S sing 357 n n C23 H23 P5S sing 358 n n C23 H23A P5S sing 359 n n C25 C24 P5S sing 360 n n C24 H24 P5S sing 361 n n C24 H24A P5S sing 362 n n C26 C25 P5S sing 363 n n C25 H25 P5S sing 364 n n C25 H25A P5S sing 365 n n C26 C27 P5S sing 366 n n C26 H26 P5S sing 367 n n C26 H26A P5S sing 368 n n C27 C28 P5S sing 369 n n C27 H27 P5S sing 370 n n C27 H27A P5S sing 371 n n C29 C28 P5S sing 372 n n C28 H28 P5S sing 373 n n C28 H28A P5S sing 374 n n C30 C29 P5S sing 375 n n C29 H29 P5S sing 376 n n C29 H29A P5S sing 377 n n C31 C30 P5S sing 378 n n C30 H30 P5S sing 379 n n C30 H30A P5S sing 380 n n C31 C32 P5S sing 381 n n C31 H31 P5S sing 382 n n C31 H31A P5S sing 383 n n C33 C32 P5S sing 384 n n C32 H32 P5S sing 385 n n C32 H32A P5S sing 386 n n C33 C34 P5S sing 387 n n C33 H33 P5S sing 388 n n C33 H33A P5S sing 389 n n C35 C34 P5S sing 390 n n C34 H34 P5S sing 391 n n C34 H34A P5S sing 392 n n C36 C35 P5S sing 393 n n C35 H35 P5S sing 394 n n C35 H35A P5S sing 395 n n C36 H36 P5S sing 396 n n C36 H36A P5S sing 397 n n C36 H36B P5S sing 398 n n C38 O37 P5S sing 399 n n O47 C38 P5S doub 400 n n C38 C39 P5S sing 401 n n C40 C39 P5S sing 402 n n C39 H39 P5S sing 403 n n C39 H39A P5S sing 404 n n C41 C40 P5S sing 405 n n C40 H40 P5S sing 406 n n C40 H40A P5S sing 407 n n C42 C41 P5S sing 408 n n C41 H41 P5S sing 409 n n C41 H41A P5S sing 410 n n C43 C42 P5S sing 411 n n C42 H42 P5S sing 412 n n C42 H42A P5S sing 413 n n C43 C44 P5S sing 414 n n C43 H43 P5S sing 415 n n C43 H43A P5S sing 416 n n C44 C45 P5S sing 417 n n C44 H44 P5S sing 418 n n C44 H44A P5S sing 419 n n C45 C46 P5S sing 420 n n C45 H45 P5S sing 421 n n C45 H45A P5S sing 422 n n C46 C48 P5S sing 423 n n C46 H46 P5S sing 424 n n C46 H46A P5S sing 425 n n C48 C49 P5S sing 426 n n C48 H48 P5S sing 427 n n C48 H48A P5S sing 428 n n C49 C50 P5S sing 429 n n C49 H49 P5S sing 430 n n C49 H49A P5S sing 431 n n C50 C51 P5S sing 432 n n C50 H50 P5S sing 433 n n C50 H50A P5S sing 434 n n C51 C52 P5S sing 435 n n C51 H51 P5S sing 436 n n C51 H51A P5S sing 437 n n C53 C52 P5S sing 438 n n C52 H52 P5S sing 439 n n C52 H52A P5S sing 440 n n C53 C54 P5S sing 441 n n C53 H53 P5S sing 442 n n C53 H53A P5S sing 443 n n C55 C54 P5S sing 444 n n C54 H54 P5S sing 445 n n C54 H54A P5S sing 446 n n C55 C56 P5S sing 447 n n C55 H55 P5S sing 448 n n C55 H55A P5S sing 449 n n C56 H56 P5S sing 450 n n C56 H56A P5S sing 451 n n C56 H56B P5S sing 452 n n OXT HXT P5S sing 453 n n # _atom_sites.entry_id 6I3Y _atom_sites.fract_transf_matrix[1][1] 0.007937 _atom_sites.fract_transf_matrix[1][2] 0.004582 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009164 _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] 0.005608 _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 E 3 LMT C 1 201 1 LMT LMT . F 4 P5S C 1 202 3 P5S P5S . G 4 P5S F 1 201 4 P5S P5S . H 5 HOH C 1 301 8 HOH HOH . H 5 HOH C 2 302 5 HOH HOH . H 5 HOH C 3 303 6 HOH HOH . H 5 HOH C 4 304 7 HOH HOH . I 5 HOH F 1 301 3 HOH HOH . I 5 HOH F 2 302 15 HOH HOH . I 5 HOH F 3 303 4 HOH HOH . I 5 HOH F 4 304 16 HOH HOH . I 5 HOH F 5 305 22 HOH HOH . I 5 HOH F 6 306 10 HOH HOH . I 5 HOH F 7 307 2 HOH HOH . I 5 HOH F 8 308 9 HOH HOH . I 5 HOH F 9 309 1 HOH HOH . I 5 HOH F 10 310 12 HOH HOH . I 5 HOH F 11 311 14 HOH HOH . I 5 HOH F 12 312 13 HOH HOH . I 5 HOH F 13 313 18 HOH HOH . I 5 HOH F 14 314 17 HOH HOH . I 5 HOH F 15 315 21 HOH HOH . I 5 HOH F 16 316 20 HOH HOH . J 5 HOH A 1 101 19 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 C P5S . . . G 4 -16.312 58.244 -31.774 0.3 66.7 ? C P5S 201 F 1 HETATM 2 N N P5S . . . G 4 -16.959 56.299 -30.604 0.3 71.09 ? N P5S 201 F 1 HETATM 3 O O P5S . . . G 4 -16.242 59.422 -32.085 0.3 63.96 ? O P5S 201 F 1 HETATM 4 C C1 P5S . . . G 4 -16.72 55.296 -24.012 0.3 47.68 ? C1 P5S 201 F 1 HETATM 5 C C2 P5S . . . G 4 -15.942 56.65 -23.918 0.3 52.24 ? C2 P5S 201 F 1 HETATM 6 C C3 P5S . . . G 4 -14.597 56.643 -24.68 0.3 52.66 ? C3 P5S 201 F 1 HETATM 7 C CA P5S . . . G 4 -16.929 57.754 -30.479 0.3 69.11 ? CA P5S 201 F 1 HETATM 8 C CB P5S . . . G 4 -16.145 58.03 -29.194 0.3 66.9 ? CB P5S 201 F 1 HETATM 9 O OG P5S . . . G 4 -16.097 56.866 -28.328 0.3 68.45 ? OG P5S 201 F 1 HETATM 10 P P12 P5S . . . G 4 -16.165 56.845 -26.696 0.3 67.73 ? P12 P5S 201 F 1 HETATM 11 O O13 P5S . . . G 4 -16.532 58.183 -26.141 0.3 68.49 ? O13 P5S 201 F 1 HETATM 12 O O15 P5S . . . G 4 -17.261 55.758 -26.183 0.3 65.46 ? O15 P5S 201 F 1 HETATM 13 O O16 P5S . . . G 4 -14.743 56.415 -26.086 0.3 55.41 ? O16 P5S 201 F 1 HETATM 14 C C17 P5S . . . G 4 -16.996 54.983 -21.567 0.3 34.93 ? C17 P5S 201 F 1 HETATM 15 O O18 P5S . . . G 4 -17.651 54.844 -20.567 0.3 37.48 ? O18 P5S 201 F 1 HETATM 16 O O19 P5S . . . G 4 -17.585 54.973 -22.904 0.3 39.48 ? O19 P5S 201 F 1 HETATM 17 C C20 P5S . . . G 4 -15.529 55.127 -21.378 0.3 31.71 ? C20 P5S 201 F 1 HETATM 18 C C21 P5S . . . G 4 -15.162 56.012 -20.201 0.3 29.11 ? C21 P5S 201 F 1 HETATM 19 C C22 P5S . . . G 4 -15.943 57.302 -20.005 0.3 26.2 ? C22 P5S 201 F 1 HETATM 20 C C23 P5S . . . G 4 -15.784 57.509 -18.499 0.3 24.52 ? C23 P5S 201 F 1 HETATM 21 C C24 P5S . . . G 4 -15.442 58.904 -18.075 0.3 22.58 ? C24 P5S 201 F 1 HETATM 22 C C25 P5S . . . G 4 -14.411 59.018 -16.969 0.3 21.8 ? C25 P5S 201 F 1 HETATM 23 C C26 P5S . . . G 4 -14.839 60.022 -15.901 0.3 21.66 ? C26 P5S 201 F 1 HETATM 24 C C27 P5S . . . G 4 -13.765 61.055 -15.561 0.3 21.25 ? C27 P5S 201 F 1 HETATM 25 C C28 P5S . . . G 4 -14.29 62.439 -15.906 0.3 21.04 ? C28 P5S 201 F 1 HETATM 26 C C29 P5S . . . G 4 -13.878 63.488 -14.891 0.3 20.6 ? C29 P5S 201 F 1 HETATM 27 O O37 P5S . . . G 4 -15.638 57.054 -22.568 0.3 55.72 ? O37 P5S 201 F 1 HETATM 28 C C38 P5S . . . G 4 -15.375 58.493 -22.498 0.3 58.59 ? C38 P5S 201 F 1 HETATM 29 C C39 P5S . . . G 4 -15.584 59.194 -21.171 0.3 56.56 ? C39 P5S 201 F 1 HETATM 30 C C40 P5S . . . G 4 -14.588 60.33 -20.979 0.3 55.22 ? C40 P5S 201 F 1 HETATM 31 C C41 P5S . . . G 4 -14.848 61.455 -21.954 0.3 55.64 ? C41 P5S 201 F 1 HETATM 32 C C42 P5S . . . G 4 -14.063 62.701 -21.567 0.3 59.59 ? C42 P5S 201 F 1 HETATM 33 C C43 P5S . . . G 4 -14.285 63.317 -20.186 0.3 59.84 ? C43 P5S 201 F 1 HETATM 34 O O47 P5S . . . G 4 -15.021 59.114 -23.504 0.3 58.43 ? O47 P5S 201 F 1 HETATM 35 O OXT P5S . . . G 4 -15.849 57.353 -32.646 0.3 60.78 ? OXT P5S 201 F 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #