data_7U24
#
_model_server_result.job_id            mZgMF6_vKR0SbgblSwHa4A 
_model_server_result.datetime_utc      '2024-11-27 07:44:14' 
_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          7u24 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":401}' 
#
_entry.id    7U24 
#
_exptl.entry_id    7U24 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          6 
_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    9 
_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            7U24 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7U24 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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 
_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
? 6 I N N 
? 6 J N N 
? 6 M N N 
? 6 N N N 
? 6 Q N N 
? 6 R N N 
? 6 U N N 
? 6 V N N 
? 6 DA 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 A SG CYS 110 A CYS 110 1_555 A SG CYS 142 A CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 B SG CYS 110 B CYS 110 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 C SG CYS 110 C CYS 110 1_555 C SG CYS 142 C CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 D SG CYS 110 D CYS 110 1_555 D SG CYS 142 D CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf5 E SG CYS 6 E CYS 6 1_555 E SG CYS 26 E CYS 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 E ND2 ASN 10 E ASN 10 1_555 Y C1 NAG . E NAG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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 377 n n 
O C P5S doub 378 n n 
C OXT P5S sing 379 n n 
CA N P5S sing 380 n n 
N HN P5S sing 381 n n 
N HNA P5S sing 382 n n 
O19 C1 P5S sing 383 n n 
C1 C2 P5S sing 384 n n 
C1 H1 P5S sing 385 n n 
C1 H1A P5S sing 386 n n 
C2 O37 P5S sing 387 n n 
C2 C3 P5S sing 388 n n 
C2 H2 P5S sing 389 n n 
O16 C3 P5S sing 390 n n 
C3 H3 P5S sing 391 n n 
C3 H3A P5S sing 392 n n 
CB CA P5S sing 393 n n 
CA HA P5S sing 394 n n 
CB OG P5S sing 395 n n 
CB HB P5S sing 396 n n 
CB HBA P5S sing 397 n n 
P12 OG P5S sing 398 n n 
O16 P12 P5S sing 399 n n 
O13 P12 P5S doub 400 n n 
P12 O15 P5S sing 401 n n 
O15 HO15 P5S sing 402 n n 
C20 C17 P5S sing 403 n n 
O19 C17 P5S sing 404 n n 
C17 O18 P5S doub 405 n n 
C21 C20 P5S sing 406 n n 
C20 H20 P5S sing 407 n n 
C20 H20A P5S sing 408 n n 
C21 C22 P5S sing 409 n n 
C21 H21 P5S sing 410 n n 
C21 H21A P5S sing 411 n n 
C23 C22 P5S sing 412 n n 
C22 H22 P5S sing 413 n n 
C22 H22A P5S sing 414 n n 
C24 C23 P5S sing 415 n n 
C23 H23 P5S sing 416 n n 
C23 H23A P5S sing 417 n n 
C25 C24 P5S sing 418 n n 
C24 H24 P5S sing 419 n n 
C24 H24A P5S sing 420 n n 
C26 C25 P5S sing 421 n n 
C25 H25 P5S sing 422 n n 
C25 H25A P5S sing 423 n n 
C26 C27 P5S sing 424 n n 
C26 H26 P5S sing 425 n n 
C26 H26A P5S sing 426 n n 
C27 C28 P5S sing 427 n n 
C27 H27 P5S sing 428 n n 
C27 H27A P5S sing 429 n n 
C29 C28 P5S sing 430 n n 
C28 H28 P5S sing 431 n n 
C28 H28A P5S sing 432 n n 
C30 C29 P5S sing 433 n n 
C29 H29 P5S sing 434 n n 
C29 H29A P5S sing 435 n n 
C31 C30 P5S sing 436 n n 
C30 H30 P5S sing 437 n n 
C30 H30A P5S sing 438 n n 
C31 C32 P5S sing 439 n n 
C31 H31 P5S sing 440 n n 
C31 H31A P5S sing 441 n n 
C33 C32 P5S sing 442 n n 
C32 H32 P5S sing 443 n n 
C32 H32A P5S sing 444 n n 
C33 C34 P5S sing 445 n n 
C33 H33 P5S sing 446 n n 
C33 H33A P5S sing 447 n n 
C35 C34 P5S sing 448 n n 
C34 H34 P5S sing 449 n n 
C34 H34A P5S sing 450 n n 
C36 C35 P5S sing 451 n n 
C35 H35 P5S sing 452 n n 
C35 H35A P5S sing 453 n n 
C36 H36 P5S sing 454 n n 
C36 H36A P5S sing 455 n n 
C36 H36B P5S sing 456 n n 
C38 O37 P5S sing 457 n n 
O47 C38 P5S doub 458 n n 
C38 C39 P5S sing 459 n n 
C40 C39 P5S sing 460 n n 
C39 H39 P5S sing 461 n n 
C39 H39A P5S sing 462 n n 
C41 C40 P5S sing 463 n n 
C40 H40 P5S sing 464 n n 
C40 H40A P5S sing 465 n n 
C42 C41 P5S sing 466 n n 
C41 H41 P5S sing 467 n n 
C41 H41A P5S sing 468 n n 
C43 C42 P5S sing 469 n n 
C42 H42 P5S sing 470 n n 
C42 H42A P5S sing 471 n n 
C43 C44 P5S sing 472 n n 
C43 H43 P5S sing 473 n n 
C43 H43A P5S sing 474 n n 
C44 C45 P5S sing 475 n n 
C44 H44 P5S sing 476 n n 
C44 H44A P5S sing 477 n n 
C45 C46 P5S sing 478 n n 
C45 H45 P5S sing 479 n n 
C45 H45A P5S sing 480 n n 
C46 C48 P5S sing 481 n n 
C46 H46 P5S sing 482 n n 
C46 H46A P5S sing 483 n n 
C48 C49 P5S sing 484 n n 
C48 H48 P5S sing 485 n n 
C48 H48A P5S sing 486 n n 
C49 C50 P5S sing 487 n n 
C49 H49 P5S sing 488 n n 
C49 H49A P5S sing 489 n n 
C50 C51 P5S sing 490 n n 
C50 H50 P5S sing 491 n n 
C50 H50A P5S sing 492 n n 
C51 C52 P5S sing 493 n n 
C51 H51 P5S sing 494 n n 
C51 H51A P5S sing 495 n n 
C53 C52 P5S sing 496 n n 
C52 H52 P5S sing 497 n n 
C52 H52A P5S sing 498 n n 
C53 C54 P5S sing 499 n n 
C53 H53 P5S sing 500 n n 
C53 H53A P5S sing 501 n n 
C55 C54 P5S sing 502 n n 
C54 H54 P5S sing 503 n n 
C54 H54A P5S sing 504 n n 
C55 C56 P5S sing 505 n n 
C55 H55 P5S sing 506 n n 
C55 H55A P5S sing 507 n n 
C56 H56 P5S sing 508 n n 
C56 H56A P5S sing 509 n n 
C56 H56B P5S sing 510 n n 
OXT HXT P5S sing 511 n n 
#
_atom_sites.entry_id                     7U24 
_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
F 3 ATP A 1 401 401 ATP ATP . 
G 4 PTY A 1 402 506 PTY PTY . 
H 5 POV A 1 403 505 POV POV . 
I 6 P5S A 1 404 508 P5S P5S . 
J 6 P5S A 1 405 507 P5S P5S . 
K 3 ATP B 1 401 401 ATP ATP . 
L 5 POV B 1 402 505 POV POV . 
M 6 P5S B 1 403 506 P5S P5S . 
N 6 P5S B 1 404 507 P5S P5S . 
O 3 ATP C 1 401 401 ATP ATP . 
P 5 POV C 1 402 505 POV POV . 
Q 6 P5S C 1 403 506 P5S P5S . 
R 6 P5S D 1 401 507 P5S P5S . 
S 3 ATP D 1 402 401 ATP ATP . 
T 5 POV D 1 403 506 POV POV . 
U 6 P5S D 1 404 505 P5S P5S . 
V 6 P5S D 1 405 507 P5S P5S . 
W 7 GBM E 1 2001 2001 GBM GBM . 
X 3 ATP E 1 2002 2002 ATP ATP . 
Y 8 NAG E 1 2003 2101 NAG NAG . 
Z 4 PTY E 1 2004 2009 PTY PTY . 
AA 4 PTY E 1 2005 2003 PTY PTY . 
BA 4 PTY E 1 2006 2004 PTY PTY . 
CA 4 PTY E 1 2007 2008 PTY PTY . 
DA 6 P5S E 1 2008 2006 P5S P5S . 
#
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 . . . R 6 177.694 143.908 153.346 1 54.01 ? C P5S 401 D 1 
HETATM 2 N N P5S . . . R 6 178.405 142.945 155.581 1 54.01 ? N P5S 401 D 1 
HETATM 3 O O P5S . . . R 6 177.543 145.006 153.917 1 54.01 ? O P5S 401 D 1 
HETATM 4 C C1 P5S . . . R 6 173.497 138.184 155.854 1 54.01 ? C1 P5S 401 D 1 
HETATM 5 C C2 P5S . . . R 6 172.454 138.907 155.028 1 54.01 ? C2 P5S 401 D 1 
HETATM 6 C C3 P5S . . . R 6 172.995 139.928 154.039 1 54.01 ? C3 P5S 401 D 1 
HETATM 7 C CA P5S . . . R 6 177.935 142.663 154.239 1 54.01 ? CA P5S 401 D 1 
HETATM 8 C CB P5S . . . R 6 176.636 141.867 154.3 1 54.01 ? CB P5S 401 D 1 
HETATM 9 O OG P5S . . . R 6 176.579 140.882 153.288 1 54.01 ? OG P5S 401 D 1 
HETATM 10 P P12 P5S . . . R 6 175.179 140.405 152.59 1 54.01 ? P12 P5S 401 D 1 
HETATM 11 O O13 P5S . . . R 6 174.359 141.566 152.127 1 54.01 ? O13 P5S 401 D 1 
HETATM 12 O O15 P5S . . . R 6 175.482 139.268 151.658 1 54.01 ? O15 P5S 401 D 1 
HETATM 13 O O16 P5S . . . R 6 174.395 139.856 153.926 1 54.01 ? O16 P5S 401 D 1 
HETATM 14 C C17 P5S . . . R 6 174.462 139.618 157.45 1 54.01 ? C17 P5S 401 D 1 
HETATM 15 O O18 P5S . . . R 6 174.877 140.386 156.617 1 54.01 ? O18 P5S 401 D 1 
HETATM 16 O O19 P5S . . . R 6 173.559 138.68 157.187 1 54.01 ? O19 P5S 401 D 1 
HETATM 17 C C20 P5S . . . R 6 174.9 139.624 158.886 1 54.01 ? C20 P5S 401 D 1 
HETATM 18 C C21 P5S . . . R 6 174.076 138.753 159.822 1 54.01 ? C21 P5S 401 D 1 
HETATM 19 C C22 P5S . . . R 6 174.852 138.229 161.031 1 54.01 ? C22 P5S 401 D 1 
HETATM 20 C C23 P5S . . . R 6 175.125 139.276 162.112 1 54.01 ? C23 P5S 401 D 1 
HETATM 21 C C24 P5S . . . R 6 176.336 140.177 161.889 1 54.01 ? C24 P5S 401 D 1 
HETATM 22 C C25 P5S . . . R 6 176.203 141.519 162.598 1 54.01 ? C25 P5S 401 D 1 
HETATM 23 C C26 P5S . . . R 6 177.511 142.283 162.748 1 54.01 ? C26 P5S 401 D 1 
HETATM 24 C C27 P5S . . . R 6 178.554 141.546 163.58 1 54.01 ? C27 P5S 401 D 1 
HETATM 25 C C28 P5S . . . R 6 179.856 142.285 163.889 1 54.01 ? C28 P5S 401 D 1 
HETATM 26 C C29 P5S . . . R 6 180.322 143.277 162.823 1 54.01 ? C29 P5S 401 D 1 
HETATM 27 C C30 P5S . . . R 6 179.851 144.72 162.982 1 54.01 ? C30 P5S 401 D 1 
HETATM 28 C C31 P5S . . . R 6 180.254 145.599 161.804 1 54.01 ? C31 P5S 401 D 1 
HETATM 29 C C32 P5S . . . R 6 179.985 147.083 162.017 1 54.01 ? C32 P5S 401 D 1 
HETATM 30 C C33 P5S . . . R 6 180.703 147.966 161.003 1 54.01 ? C33 P5S 401 D 1 
HETATM 31 C C34 P5S . . . R 6 180.317 147.663 159.561 1 54.01 ? C34 P5S 401 D 1 
HETATM 32 C C35 P5S . . . R 6 180.888 148.658 158.559 1 54.01 ? C35 P5S 401 D 1 
HETATM 33 C C36 P5S . . . R 6 180.287 148.506 157.169 1 54.01 ? C36 P5S 401 D 1 
HETATM 34 O O37 P5S . . . R 6 171.495 139.489 155.923 1 54.01 ? O37 P5S 401 D 1 
HETATM 35 C C38 P5S . . . R 6 170.53 138.718 156.421 1 54.01 ? C38 P5S 401 D 1 
HETATM 36 C C39 P5S . . . R 6 170.248 139.032 157.865 1 54.01 ? C39 P5S 401 D 1 
HETATM 37 C C40 P5S . . . R 6 168.814 138.729 158.274 1 54.01 ? C40 P5S 401 D 1 
HETATM 38 C C41 P5S . . . R 6 168.331 139.613 159.417 1 54.01 ? C41 P5S 401 D 1 
HETATM 39 C C42 P5S . . . R 6 169.221 139.504 160.649 1 54.01 ? C42 P5S 401 D 1 
HETATM 40 C C43 P5S . . . R 6 168.528 139.864 161.957 1 54.01 ? C43 P5S 401 D 1 
HETATM 41 C C44 P5S . . . R 6 169.205 139.235 163.17 1 54.01 ? C44 P5S 401 D 1 
HETATM 42 C C45 P5S . . . R 6 168.533 139.568 164.496 1 54.01 ? C45 P5S 401 D 1 
HETATM 43 C C46 P5S . . . R 6 169.134 140.8 165.162 1 54.01 ? C46 P5S 401 D 1 
HETATM 44 O O47 P5S . . . R 6 169.951 137.879 155.777 1 54.01 ? O47 P5S 401 D 1 
HETATM 45 C C48 P5S . . . R 6 168.889 140.876 166.664 1 54.01 ? C48 P5S 401 D 1 
HETATM 46 C C49 P5S . . . R 6 169.787 141.893 167.357 1 54.01 ? C49 P5S 401 D 1 
HETATM 47 C C50 P5S . . . R 6 170.406 141.385 168.653 1 54.01 ? C50 P5S 401 D 1 
HETATM 48 C C51 P5S . . . R 6 170.866 142.507 169.577 1 54.01 ? C51 P5S 401 D 1 
HETATM 49 C C52 P5S . . . R 6 170.936 142.098 171.043 1 54.01 ? C52 P5S 401 D 1 
HETATM 50 C C53 P5S . . . R 6 171.202 143.269 171.981 1 54.01 ? C53 P5S 401 D 1 
HETATM 51 C C54 P5S . . . R 6 171.019 142.918 173.452 1 54.01 ? C54 P5S 401 D 1 
HETATM 52 C C55 P5S . . . R 6 172.255 142.295 174.088 1 54.01 ? C55 P5S 401 D 1 
HETATM 53 C C56 P5S . . . R 6 173.261 143.332 174.567 1 54.01 ? C56 P5S 401 D 1 
HETATM 54 O OXT P5S . . . R 6 177.672 143.704 152.114 1 54.01 ? OXT P5S 401 D 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           54 
#