data_8YHQ
#
_model_server_result.job_id            P2yy1eAr7IqsOvjCCkdgWQ 
_model_server_result.datetime_utc      '2024-12-26 13:22:55' 
_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          8yhq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":402}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              593.773 
_entity.id                          12 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate' 
_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            8YHQ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YHQ 
_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    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 
_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
? 12 V N N 
? 12 FA 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 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? 
disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? 
metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? 
metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? 
metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? 
metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
#
_chem_comp.formula           'C30 H60 N O8 P' 
_chem_comp.formula_weight    593.773 
_chem_comp.id                9PE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     3-SN-PHOSPHATIDYLETHANOLAMINE 
#
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
O12 P 9PE doub 315 n n 
P O11 9PE sing 316 n n 
P O14 9PE sing 317 n n 
P O13 9PE sing 318 n n 
C12 N 9PE sing 319 n n 
N HN 9PE sing 320 n n 
N HNA 9PE sing 321 n n 
O11 C1 9PE sing 322 n n 
O13 C11 9PE sing 323 n n 
O14 HO14 9PE sing 324 n n 
C11 C12 9PE sing 325 n n 
C11 H11 9PE sing 326 n n 
C11 H11A 9PE sing 327 n n 
C12 H12 9PE sing 328 n n 
C12 H12A 9PE sing 329 n n 
C2 C1 9PE sing 330 n n 
C1 H1 9PE sing 331 n n 
C1 H1A 9PE sing 332 n n 
O21 C2 9PE sing 333 n n 
C2 C3 9PE sing 334 n n 
C2 H2 9PE sing 335 n n 
O31 C3 9PE sing 336 n n 
C3 H3 9PE sing 337 n n 
C3 H3A 9PE sing 338 n n 
O31 C31 9PE sing 339 n n 
C31 O32 9PE doub 340 n n 
C32 C31 9PE sing 341 n n 
C33 C32 9PE sing 342 n n 
C32 H32 9PE sing 343 n n 
C32 H32A 9PE sing 344 n n 
C34 C33 9PE sing 345 n n 
C33 H33 9PE sing 346 n n 
C33 H33A 9PE sing 347 n n 
C35 C34 9PE sing 348 n n 
C34 H34 9PE sing 349 n n 
C34 H34A 9PE sing 350 n n 
C36 C35 9PE sing 351 n n 
C35 H35 9PE sing 352 n n 
C35 H35A 9PE sing 353 n n 
C37 C36 9PE sing 354 n n 
C36 H36 9PE sing 355 n n 
C36 H36A 9PE sing 356 n n 
C37 H37 9PE sing 357 n n 
C37 H37A 9PE sing 358 n n 
C37 H37B 9PE sing 359 n n 
C21 O21 9PE sing 360 n n 
O22 C21 9PE doub 361 n n 
C22 C21 9PE sing 362 n n 
C23 C22 9PE sing 363 n n 
C22 H22 9PE sing 364 n n 
C22 H22A 9PE sing 365 n n 
C23 C24 9PE sing 366 n n 
C23 H23 9PE sing 367 n n 
C23 H23A 9PE sing 368 n n 
C25 C24 9PE sing 369 n n 
C24 H24 9PE sing 370 n n 
C24 H24A 9PE sing 371 n n 
C26 C25 9PE sing 372 n n 
C25 H25 9PE sing 373 n n 
C25 H25A 9PE sing 374 n n 
C27 C26 9PE sing 375 n n 
C26 H26 9PE sing 376 n n 
C26 H26A 9PE sing 377 n n 
C28 C27 9PE sing 378 n n 
C27 H27 9PE sing 379 n n 
C27 H27A 9PE sing 380 n n 
C28 C29 9PE sing 381 n n 
C28 H28 9PE sing 382 n n 
C28 H28A 9PE sing 383 n n 
C2A C29 9PE sing 384 n n 
C29 H29 9PE sing 385 n n 
C29 H29A 9PE sing 386 n n 
C2A C2B 9PE sing 387 n n 
C2A H2A 9PE sing 388 n n 
C2A H2AA 9PE sing 389 n n 
C2C C2B 9PE sing 390 n n 
C2B H2B 9PE sing 391 n n 
C2B H2BA 9PE sing 392 n n 
C2C C2D 9PE sing 393 n n 
C2C H2C 9PE sing 394 n n 
C2C H2CA 9PE sing 395 n n 
C2E C2D 9PE sing 396 n n 
C2D H2D 9PE sing 397 n n 
C2D H2DA 9PE sing 398 n n 
C2E C2F 9PE sing 399 n n 
C2E H2E 9PE sing 400 n n 
C2E H2EA 9PE sing 401 n n 
C2G C2F 9PE sing 402 n n 
C2F H2F 9PE sing 403 n n 
C2F H2FA 9PE sing 404 n n 
C2H C2G 9PE sing 405 n n 
C2G H2G 9PE sing 406 n n 
C2G H2GA 9PE sing 407 n n 
C2I C2H 9PE sing 408 n n 
C2H H2H 9PE sing 409 n n 
C2H H2HA 9PE sing 410 n n 
C2I H2I 9PE sing 411 n n 
C2I H2IA 9PE sing 412 n n 
C2I H2IB 9PE sing 413 n n 
#
_atom_sites.entry_id                     8YHQ 
_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
U 11 6PH C 1 401 402 6PH 6PH . 
V 12 9PE C 1 402 403 9PE 9PE . 
W 13 HEM C 1 403 404 HEM HEM . 
X 13 HEM C 1 404 405 HEM HEM . 
Y 14 8PE C 1 405 406 8PE 8PE . 
Z 15 CN5 C 1 406 407 CN5 CN5 . 
AA 16 UQ6 C 1 407 408 UQ6 UQ6 . 
BA 17 A1D6K C 1 408 401 A1D6K A1D . 
CA 13 HEM D 1 401 402 HEM HEM . 
DA 18 7PH D 1 402 401 7PH 7PH . 
EA 16 UQ6 L 1 401 402 UQ6 UQ6 . 
FA 12 9PE L 1 402 403 9PE 9PE . 
GA 13 HEM L 1 403 404 HEM HEM . 
HA 19 CN3 L 1 404 405 CN3 CN3 . 
IA 13 HEM L 1 405 406 HEM HEM . 
JA 17 A1D6K L 1 406 401 A1D6K A1D . 
KA 13 HEM M 1 401 401 HEM HEM . 
LA 11 6PH N 1 401 401 6PH 6PH . 
MA 18 7PH N 1 402 402 7PH 7PH . 
NA 14 8PE Q 1 101 101 8PE 8PE . 
#
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 P P 9PE . . . V 12 148.349 124.84 136.517 1 23.42 ? P 9PE 402 C 1 
HETATM 2 N N 9PE . . . V 12 146.853 124.054 140.385 1 23.42 ? N 9PE 402 C 1 
HETATM 3 O O11 9PE . . . V 12 148.487 123.707 135.329 1 23.42 ? O11 9PE 402 C 1 
HETATM 4 O O12 9PE . . . V 12 149.366 124.566 137.595 1 23.42 ? O12 9PE 402 C 1 
HETATM 5 O O13 9PE . . . V 12 146.838 124.774 137.157 1 23.42 ? O13 9PE 402 C 1 
HETATM 6 O O14 9PE . . . V 12 148.572 126.218 135.953 1 23.42 ? O14 9PE 402 C 1 
HETATM 7 C C11 9PE . . . V 12 146.627 125.418 138.376 1 23.42 ? C11 9PE 402 C 1 
HETATM 8 C C12 9PE . . . V 12 145.93 124.471 139.352 1 23.42 ? C12 9PE 402 C 1 
HETATM 9 C C1 9PE . . . V 12 149.521 123.807 134.398 1 23.42 ? C1 9PE 402 C 1 
HETATM 10 C C2 9PE . . . V 12 149.066 124.656 133.211 1 23.42 ? C2 9PE 402 C 1 
HETATM 11 C C3 9PE . . . V 12 149.812 124.295 131.913 1 23.42 ? C3 9PE 402 C 1 
HETATM 12 O O31 9PE . . . V 12 150.009 125.446 131.147 1 23.42 ? O31 9PE 402 C 1 
HETATM 13 O O32 9PE . . . V 12 150.341 124.848 129.016 1 23.42 ? O32 9PE 402 C 1 
HETATM 14 C C31 9PE . . . V 12 149.613 125.326 129.812 1 23.42 ? C31 9PE 402 C 1 
HETATM 15 C C32 9PE . . . V 12 148.238 125.822 129.389 1 23.42 ? C32 9PE 402 C 1 
HETATM 16 C C33 9PE . . . V 12 147.866 125.353 127.99 1 23.42 ? C33 9PE 402 C 1 
HETATM 17 C C34 9PE . . . V 12 146.454 125.821 127.665 1 23.42 ? C34 9PE 402 C 1 
HETATM 18 C C35 9PE . . . V 12 145.839 124.981 126.546 1 23.42 ? C35 9PE 402 C 1 
HETATM 19 C C36 9PE . . . V 12 144.935 125.814 125.644 1 23.42 ? C36 9PE 402 C 1 
HETATM 20 C C37 9PE . . . V 12 143.719 124.995 125.217 1 23.42 ? C37 9PE 402 C 1 
HETATM 21 O O21 9PE . . . V 12 147.666 124.613 133.1 1 23.42 ? O21 9PE 402 C 1 
HETATM 22 O O22 9PE . . . V 12 147.39 122.365 133.017 1 23.42 ? O22 9PE 402 C 1 
HETATM 23 C C21 9PE . . . V 12 147.017 123.442 132.703 1 23.42 ? C21 9PE 402 C 1 
HETATM 24 C C22 9PE . . . V 12 145.808 123.612 131.809 1 23.42 ? C22 9PE 402 C 1 
HETATM 25 C C23 9PE . . . V 12 145.041 122.305 131.653 1 23.42 ? C23 9PE 402 C 1 
HETATM 26 C C24 9PE . . . V 12 143.709 122.537 130.942 1 23.42 ? C24 9PE 402 C 1 
HETATM 27 C C25 9PE . . . V 12 143.884 122.891 129.463 1 23.42 ? C25 9PE 402 C 1 
HETATM 28 C C26 9PE . . . V 12 142.62 123.47 128.823 1 23.42 ? C26 9PE 402 C 1 
HETATM 29 C C27 9PE . . . V 12 141.343 122.792 129.306 1 23.42 ? C27 9PE 402 C 1 
HETATM 30 C C28 9PE . . . V 12 140.194 123.057 128.339 1 23.42 ? C28 9PE 402 C 1 
HETATM 31 C C29 9PE . . . V 12 139.855 124.541 128.309 1 23.42 ? C29 9PE 402 C 1 
HETATM 32 C C2A 9PE . . . V 12 138.35 124.737 128.441 1 23.42 ? C2A 9PE 402 C 1 
HETATM 33 C C2B 9PE . . . V 12 138.062 126.205 128.144 1 23.42 ? C2B 9PE 402 C 1 
HETATM 34 C C2C 9PE . . . V 12 136.913 126.793 128.962 1 23.42 ? C2C 9PE 402 C 1 
HETATM 35 C C2D 9PE . . . V 12 137.225 128.251 129.292 1 23.42 ? C2D 9PE 402 C 1 
HETATM 36 C C2E 9PE . . . V 12 137.315 129.068 128.008 1 23.42 ? C2E 9PE 402 C 1 
HETATM 37 C C2F 9PE . . . V 12 137.233 130.56 128.306 1 23.42 ? C2F 9PE 402 C 1 
HETATM 38 C C2G 9PE . . . V 12 136.924 131.338 127.014 1 23.42 ? C2G 9PE 402 C 1 
HETATM 39 C C2H 9PE . . . V 12 135.459 131.582 126.625 1 23.42 ? C2H 9PE 402 C 1 
HETATM 40 C C2I 9PE . . . V 12 134.421 131.49 127.74 1 23.42 ? C2I 9PE 402 C 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    40 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          26 
_model_server_stats.element_count           40 
#