data_7SX3
#
_model_server_result.job_id            Zu7Zc6DtsyxjzbJaVygSVA 
_model_server_result.datetime_utc      '2024-11-23 09:54:24' 
_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          7sx3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":2107}' 
#
_entry.id    7SX3 
#
_exptl.entry_id    7SX3 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          8 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' 
_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            7SX3 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7SX3 
_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 
_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
? 8 L N N 
? 8 M 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 207 A CYS 207 1_555 A SG CYS 239 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 229 A CYS 229 1_555 A SG CYS 245 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 A SG CYS 1046 A CYS 1046 1_555 A SG CYS 1057 A CYS 1057 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 1405 A CYS 1405 1_555 A SG CYS 1417 A CYS 1417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 B SG CYS 191 B CYS 191 1_555 B SG CYS 261 B CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 B SG CYS 226 B CYS 226 1_555 B SG CYS 313 B CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf7 B SG CYS 304 B CYS 304 1_555 B SG CYS 341 B CYS 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf8 B SG CYS 324 B CYS 324 1_555 B SG CYS 377 B CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? 
disulf ? disulf9 B SG CYS 330 B CYS 330 1_555 B SG CYS 376 B CYS 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf10 B SG CYS 334 B CYS 334 1_555 B SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? 
covale ? covale1 A C MET 286 A MET 286 1_555 A N TYS 287 A TYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 A C TYS 287 A TYS 287 1_555 A N ARG 288 A ARG 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 A ND2 ASN 1064 A ASN 1064 1_555 G C1 NAG . A NAG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_chem_comp.formula           'C40 H77 O10 P' 
_chem_comp.formula_weight    749.007 
_chem_comp.id                PGV 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     PHOSPHATIDYLGLYCEROL;2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL 
#
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
P O11 PGV sing 391 n n 
P O12 PGV sing 392 n n 
P O13 PGV doub 393 n n 
P O14 PGV sing 394 n n 
C01 C02 PGV sing 395 n n 
C01 O03 PGV sing 396 n n 
C01 H011 PGV sing 397 n n 
C01 H012 PGV sing 398 n n 
C02 C03 PGV sing 399 n n 
C02 O01 PGV sing 400 n n 
C02 H02 PGV sing 401 n n 
C03 O11 PGV sing 402 n n 
C03 H031 PGV sing 403 n n 
C03 H032 PGV sing 404 n n 
C04 C05 PGV sing 405 n n 
C04 O12 PGV sing 406 n n 
C04 H041 PGV sing 407 n n 
C04 H042 PGV sing 408 n n 
C05 C06 PGV sing 409 n n 
C05 O05 PGV sing 410 n n 
C05 H05 PGV sing 411 n n 
C06 O06 PGV sing 412 n n 
C06 H061 PGV sing 413 n n 
C06 H062 PGV sing 414 n n 
O01 C1 PGV sing 415 n n 
O02 C1 PGV doub 416 n n 
O03 C19 PGV sing 417 n n 
O04 C19 PGV doub 418 n n 
O05 H1 PGV sing 419 n n 
O06 H06 PGV sing 420 n n 
O14 H14 PGV sing 421 n n 
C1 C2 PGV sing 422 n n 
C2 C3 PGV sing 423 n n 
C2 H21 PGV sing 424 n n 
C2 H22 PGV sing 425 n n 
C3 C4 PGV sing 426 n n 
C3 H31 PGV sing 427 n n 
C3 H32 PGV sing 428 n n 
C4 C5 PGV sing 429 n n 
C4 H41 PGV sing 430 n n 
C4 H42 PGV sing 431 n n 
C5 C6 PGV sing 432 n n 
C5 H51 PGV sing 433 n n 
C5 H52 PGV sing 434 n n 
C6 C7 PGV sing 435 n n 
C6 H61 PGV sing 436 n n 
C6 H62 PGV sing 437 n n 
C7 C8 PGV sing 438 n n 
C7 H71 PGV sing 439 n n 
C7 H72 PGV sing 440 n n 
C8 C9 PGV sing 441 n n 
C8 H81 PGV sing 442 n n 
C8 H82 PGV sing 443 n n 
C9 C10 PGV sing 444 n n 
C9 H91 PGV sing 445 n n 
C9 H92 PGV sing 446 n n 
C10 C11 PGV sing 447 n n 
C10 H101 PGV sing 448 n n 
C10 H102 PGV sing 449 n n 
C11 C12 PGV doub 450 z n 
C11 H11 PGV sing 451 n n 
C12 C13 PGV sing 452 n n 
C12 H12 PGV sing 453 n n 
C13 C14 PGV sing 454 n n 
C13 H131 PGV sing 455 n n 
C13 H132 PGV sing 456 n n 
C14 C15 PGV sing 457 n n 
C14 H141 PGV sing 458 n n 
C14 H142 PGV sing 459 n n 
C15 C16 PGV sing 460 n n 
C15 H151 PGV sing 461 n n 
C15 H152 PGV sing 462 n n 
C16 C17 PGV sing 463 n n 
C16 H161 PGV sing 464 n n 
C16 H162 PGV sing 465 n n 
C17 C18 PGV sing 466 n n 
C17 H171 PGV sing 467 n n 
C17 H172 PGV sing 468 n n 
C18 H181 PGV sing 469 n n 
C18 H182 PGV sing 470 n n 
C18 H183 PGV sing 471 n n 
C19 C20 PGV sing 472 n n 
C20 C21 PGV sing 473 n n 
C20 H201 PGV sing 474 n n 
C20 H202 PGV sing 475 n n 
C21 C22 PGV sing 476 n n 
C21 H211 PGV sing 477 n n 
C21 H212 PGV sing 478 n n 
C22 C23 PGV sing 479 n n 
C22 H221 PGV sing 480 n n 
C22 H222 PGV sing 481 n n 
C23 C24 PGV sing 482 n n 
C23 H231 PGV sing 483 n n 
C23 H232 PGV sing 484 n n 
C24 C25 PGV sing 485 n n 
C24 H241 PGV sing 486 n n 
C24 H242 PGV sing 487 n n 
C25 C26 PGV sing 488 n n 
C25 H251 PGV sing 489 n n 
C25 H252 PGV sing 490 n n 
C26 C27 PGV sing 491 n n 
C26 H261 PGV sing 492 n n 
C26 H262 PGV sing 493 n n 
C27 C28 PGV sing 494 n n 
C27 H271 PGV sing 495 n n 
C27 H272 PGV sing 496 n n 
C28 C29 PGV sing 497 n n 
C28 H281 PGV sing 498 n n 
C28 H282 PGV sing 499 n n 
C29 C30 PGV sing 500 n n 
C29 H291 PGV sing 501 n n 
C29 H292 PGV sing 502 n n 
C30 C31 PGV sing 503 n n 
C30 H301 PGV sing 504 n n 
C30 H302 PGV sing 505 n n 
C31 C32 PGV sing 506 n n 
C31 H311 PGV sing 507 n n 
C31 H312 PGV sing 508 n n 
C32 C33 PGV sing 509 n n 
C32 H321 PGV sing 510 n n 
C32 H322 PGV sing 511 n n 
C33 C34 PGV sing 512 n n 
C33 H331 PGV sing 513 n n 
C33 H332 PGV sing 514 n n 
C34 H341 PGV sing 515 n n 
C34 H342 PGV sing 516 n n 
C34 H343 PGV sing 517 n n 
#
_atom_sites.entry_id                     7SX3 
_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 6 NAG A 1 2101 1801 NAG NAG . 
G 6 NAG A 1 2102 1802 NAG NAG . 
H 7 PEV A 1 2103 1803 PEV PEV . 
I 7 PEV A 1 2104 1804 PEV PEV . 
J 7 PEV A 1 2105 1805 PEV PEV . 
K 7 PEV A 1 2106 1807 PEV PEV . 
L 8 PGV A 1 2107 1808 PGV PGV . 
M 8 PGV A 1 2108 1809 PGV PGV . 
N 9 Y01 A 1 2109 1901 Y01 Y01 . 
O 9 Y01 A 1 2110 2001 Y01 Y01 . 
P 9 Y01 A 1 2111 2101 Y01 Y01 . 
#
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 PGV . . . L 8 181.411 211.994 226.07 1 77.18 ? P PGV 2107 A 1 
HETATM 2 C C01 PGV . . . L 8 183.616 216.164 227.867 1 77.18 ? C01 PGV 2107 A 1 
HETATM 3 C C02 PGV . . . L 8 182.516 215.688 226.919 1 77.18 ? C02 PGV 2107 A 1 
HETATM 4 C C03 PGV . . . L 8 182.71 214.207 226.607 1 77.18 ? C03 PGV 2107 A 1 
HETATM 5 C C04 PGV . . . L 8 179.595 210.14 226.414 1 77.18 ? C04 PGV 2107 A 1 
HETATM 6 C C05 PGV . . . L 8 178.449 209.617 225.551 1 77.18 ? C05 PGV 2107 A 1 
HETATM 7 C C06 PGV . . . L 8 178.725 209.937 224.083 1 77.18 ? C06 PGV 2107 A 1 
HETATM 8 O O01 PGV . . . L 8 182.578 216.424 225.731 1 77.18 ? O01 PGV 2107 A 1 
HETATM 9 O O02 PGV . . . L 8 180.728 217.621 226.157 1 77.18 ? O02 PGV 2107 A 1 
HETATM 10 O O05 PGV . . . L 8 177.255 210.227 225.944 1 77.18 ? O05 PGV 2107 A 1 
HETATM 11 O O06 PGV . . . L 8 180.106 210.003 223.868 1 77.18 ? O06 PGV 2107 A 1 
HETATM 12 O O11 PGV . . . L 8 181.464 213.612 226.385 1 77.18 ? O11 PGV 2107 A 1 
HETATM 13 O O12 PGV . . . L 8 179.848 211.476 226.096 1 77.18 ? O12 PGV 2107 A 1 
HETATM 14 O O13 PGV . . . L 8 182.202 211.255 227.123 1 77.18 ? O13 PGV 2107 A 1 
HETATM 15 O O14 PGV . . . L 8 182.011 211.722 224.712 1 77.18 ? O14 PGV 2107 A 1 
HETATM 16 C C1 PGV . . . L 8 181.833 217.612 225.736 1 77.18 ? C1 PGV 2107 A 1 
HETATM 17 C C2 PGV . . . L 8 182.442 218.902 225.185 1 77.18 ? C2 PGV 2107 A 1 
HETATM 18 C C3 PGV . . . L 8 183.427 219.48 226.203 1 77.18 ? C3 PGV 2107 A 1 
HETATM 19 C C4 PGV . . . L 8 184.233 220.599 225.541 1 77.18 ? C4 PGV 2107 A 1 
HETATM 20 C C5 PGV . . . L 8 185.135 221.263 226.589 1 77.18 ? C5 PGV 2107 A 1 
HETATM 21 C C6 PGV . . . L 8 186.312 221.963 225.901 1 77.18 ? C6 PGV 2107 A 1 
HETATM 22 C C7 PGV . . . L 8 186.428 223.393 226.437 1 77.18 ? C7 PGV 2107 A 1 
HETATM 23 C C8 PGV . . . L 8 187.746 224.02 225.968 1 77.18 ? C8 PGV 2107 A 1 
HETATM 24 C C9 PGV . . . L 8 187.484 224.899 224.741 1 77.18 ? C9 PGV 2107 A 1 
HETATM 25 C C10 PGV . . . L 8 188.799 225.539 224.292 1 77.18 ? C10 PGV 2107 A 1 
HETATM 26 C C11 PGV . . . L 8 188.621 226.151 222.9 1 77.18 ? C11 PGV 2107 A 1 
HETATM 27 C C12 PGV . . . L 8 189.667 226.558 222.2 1 77.18 ? C12 PGV 2107 A 1 
HETATM 28 C C13 PGV . . . L 8 191.092 226.433 222.759 1 77.18 ? C13 PGV 2107 A 1 
HETATM 29 C C14 PGV . . . L 8 192.017 227.406 222.019 1 77.18 ? C14 PGV 2107 A 1 
HETATM 30 C C15 PGV . . . L 8 193.405 227.375 222.669 1 77.18 ? C15 PGV 2107 A 1 
HETATM 31 C C16 PGV . . . L 8 194.479 227.422 221.578 1 77.18 ? C16 PGV 2107 A 1 
#
_model_server_stats.io_time_ms              127 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           368 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           31 
#