data_6TP4
#
_model_server_result.job_id            eEgGYvwdd_fCe_S8SxelgQ 
_model_server_result.datetime_utc      '2024-11-05 04:59:31' 
_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          6tp4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":406}' 
#
_entry.id    6TP4 
#
_exptl.entry_id    6TP4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-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          108.29 
_cell.angle_gamma         90 
_cell.entry_id            6TP4 
_cell.length_a            61.719 
_cell.length_b            146.666 
_cell.length_c            73.748 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6TP4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,N 1 1 
B,I,J,K,L,M 2 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
? 5 H N N 
? 5 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 95 A CYS 119 1_555 A SG CYS 178 A CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 B SG CYS 95 B CYS 119 1_555 B SG CYS 178 B CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C40 H77 O10 P' 
_chem_comp.formula_weight    749.007 
_chem_comp.id                PGW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)];PHOSPHATIDYLGLYCEROL 
#
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
CAD C05 PGW sing 290 n n 
CAD HAD PGW sing 291 n n 
CAD HADA PGW sing 292 n n 
OAE CAD PGW sing 293 n n 
OAE HOAE PGW sing 294 n n 
OAF C05 PGW sing 295 n n 
OAF HOAF PGW sing 296 n n 
P O13 PGW sing 297 n n 
P O11 PGW sing 298 n n 
C01 O03 PGW sing 299 n n 
C01 C02 PGW sing 300 n n 
C01 H01 PGW sing 301 n n 
C01 H01A PGW sing 302 n n 
C1 C2 PGW sing 303 n n 
O01 C1 PGW sing 304 n n 
C02 O01 PGW sing 305 n n 
C02 H02 PGW sing 306 n n 
C2 C3 PGW sing 307 n n 
C2 H2 PGW sing 308 n n 
C2 H2A PGW sing 309 n n 
O02 C1 PGW doub 310 n n 
C03 C02 PGW sing 311 n n 
C03 H03 PGW sing 312 n n 
C03 H03A PGW sing 313 n n 
C3 C4 PGW sing 314 n n 
C3 H3 PGW sing 315 n n 
C3 H3A PGW sing 316 n n 
C04 C05 PGW sing 317 n n 
C04 O12 PGW sing 318 n n 
C04 H04 PGW sing 319 n n 
C04 H04A PGW sing 320 n n 
C4 C5 PGW sing 321 n n 
C4 H4 PGW sing 322 n n 
C4 H4A PGW sing 323 n n 
O04 C19 PGW doub 324 n n 
C05 H05 PGW sing 325 n n 
C5 C6 PGW sing 326 n n 
C5 H5 PGW sing 327 n n 
C5 H5A PGW sing 328 n n 
C06 C07 PGW sing 329 n n 
C06 H06 PGW sing 330 n n 
C06 H06A PGW sing 331 n n 
C6 C7 PGW sing 332 n n 
C6 H6 PGW sing 333 n n 
C6 H6A PGW sing 334 n n 
C07 H07 PGW sing 335 n n 
C07 H07A PGW sing 336 n n 
C7 C8 PGW sing 337 n n 
C7 H7 PGW sing 338 n n 
C7 H7A PGW sing 339 n n 
C08 C07 PGW sing 340 n n 
C08 H08 PGW sing 341 n n 
C08 H08A PGW sing 342 n n 
C8 C9 PGW sing 343 n n 
C8 H8 PGW sing 344 n n 
C8 H8A PGW sing 345 n n 
C09 C08 PGW sing 346 n n 
C09 C11 PGW sing 347 n n 
C09 H09 PGW sing 348 n n 
C09 H09A PGW sing 349 n n 
C9 C10 PGW doub 350 z n 
C10 C06 PGW sing 351 n n 
C11 H11 PGW sing 352 n n 
C11 H11A PGW sing 353 n n 
O11 C03 PGW sing 354 n n 
C12 C11 PGW sing 355 n n 
C12 H12 PGW sing 356 n n 
C12 H12A PGW sing 357 n n 
O12 P PGW sing 358 n n 
C13 C12 PGW sing 359 n n 
C13 C14 PGW sing 360 n n 
C13 H13 PGW sing 361 n n 
C13 H13A PGW sing 362 n n 
O13 HO13 PGW sing 363 n n 
C14 H14 PGW sing 364 n n 
C14 H14A PGW sing 365 n n 
C14 H14B PGW sing 366 n n 
O14 P PGW doub 367 n n 
C15 C16 PGW sing 368 n n 
C15 H15 PGW sing 369 n n 
C15 H15A PGW sing 370 n n 
C16 H16 PGW sing 371 n n 
C16 H16A PGW sing 372 n n 
C17 C16 PGW sing 373 n n 
C17 C18 PGW sing 374 n n 
C17 H17 PGW sing 375 n n 
C17 H17A PGW sing 376 n n 
C18 C28 PGW sing 377 n n 
C18 H18 PGW sing 378 n n 
C18 H18A PGW sing 379 n n 
C19 O03 PGW sing 380 n n 
C19 C20 PGW sing 381 n n 
C20 C21 PGW sing 382 n n 
C20 H20 PGW sing 383 n n 
C20 H20A PGW sing 384 n n 
C21 C22 PGW sing 385 n n 
C21 H21 PGW sing 386 n n 
C21 H21A PGW sing 387 n n 
C22 C23 PGW sing 388 n n 
C22 H22 PGW sing 389 n n 
C22 H22A PGW sing 390 n n 
C23 C24 PGW sing 391 n n 
C23 H23 PGW sing 392 n n 
C23 H23A PGW sing 393 n n 
C24 C25 PGW sing 394 n n 
C24 H24 PGW sing 395 n n 
C24 H24A PGW sing 396 n n 
C25 C26 PGW sing 397 n n 
C25 H25 PGW sing 398 n n 
C25 H25A PGW sing 399 n n 
C26 C27 PGW sing 400 n n 
C26 H26 PGW sing 401 n n 
C26 H26A PGW sing 402 n n 
C27 C15 PGW sing 403 n n 
C27 H27 PGW sing 404 n n 
C27 H27A PGW sing 405 n n 
C28 H28 PGW sing 406 n n 
C28 H28A PGW sing 407 n n 
C29 H29 PGW sing 408 n n 
C29 H29A PGW sing 409 n n 
C29 H29B PGW sing 410 n n 
C30 C28 PGW sing 411 n n 
C30 C29 PGW sing 412 n n 
C30 H30 PGW sing 413 n n 
C30 H30A PGW sing 414 n n 
C9 H9 PGW sing 415 n n 
C10 H10 PGW sing 416 n n 
#
_atom_sites.entry_id                     6TP4 
_atom_sites.fract_transf_matrix[1][1]    0.016202 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005356 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006818 
_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]    0.014281 
_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
C 2 NRZ A 1 401 401 NRZ UNL . 
D 3 SOG A 1 402 1 SOG SOG . 
E 3 SOG A 1 403 4 SOG SOG . 
F 3 SOG A 1 404 5 SOG SOG . 
G 4 SO4 A 1 405 3 SO4 SO4 . 
H 5 PGW A 1 406 2 PGW PGW . 
I 3 SOG B 1 401 2 SOG SOG . 
J 3 SOG B 1 402 3 SOG SOG . 
K 4 SO4 B 1 403 1 SO4 SO4 . 
L 4 SO4 B 1 404 2 SO4 SO4 . 
M 5 PGW B 1 405 1 PGW PGW . 
N 6 HOH A 1 501 3 HOH HOH . 
N 6 HOH A 2 502 2 HOH HOH . 
N 6 HOH A 3 503 4 HOH HOH . 
N 6 HOH A 4 504 1 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 CAD PGW . . . H 5 67.226 -36.515 30.464 1 106.74 ? CAD PGW 406 A 1 
HETATM 2 O OAE PGW . . . H 5 66.64 -36.809 29.198 1 89.57 ? OAE PGW 406 A 1 
HETATM 3 O OAF PGW . . . H 5 67.349 -34.156 29.951 1 103.1 ? OAF PGW 406 A 1 
HETATM 4 P P PGW . . . H 5 66.904 -32.971 34.197 1 170.37 ? P PGW 406 A 1 
HETATM 5 C C01 PGW . . . H 5 62.776 -30.445 34.249 1 111.94 ? C01 PGW 406 A 1 
HETATM 6 C C1 PGW . . . H 5 64.733 -30.244 31.166 1 90.56 ? C1 PGW 406 A 1 
HETATM 7 O O01 PGW . . . H 5 64.271 -29.978 32.403 1 111.84 ? O01 PGW 406 A 1 
HETATM 8 C C02 PGW . . . H 5 63.597 -31.045 33.131 1 125.7 ? C02 PGW 406 A 1 
HETATM 9 C C2 PGW . . . H 5 64.599 -29.075 30.227 1 74.46 ? C2 PGW 406 A 1 
HETATM 10 O O02 PGW . . . H 5 65.19 -31.31 30.858 1 85.95 ? O02 PGW 406 A 1 
HETATM 11 C C03 PGW . . . H 5 64.5 -32.183 33.553 1 154.27 ? C03 PGW 406 A 1 
HETATM 12 C C3 PGW . . . H 5 65.869 -28.313 30.017 1 55.32 ? C3 PGW 406 A 1 
HETATM 13 O O03 PGW . . . H 5 61.533 -30.017 33.65 1 109.86 ? O03 PGW 406 A 1 
HETATM 14 C C04 PGW . . . H 5 67.432 -34.76 32.289 1 140.91 ? C04 PGW 406 A 1 
HETATM 15 C C4 PGW . . . H 5 65.735 -27.278 28.912 1 52.26 ? C4 PGW 406 A 1 
HETATM 16 O O04 PGW . . . H 5 60.96 -32.152 33.299 1 108.11 ? O04 PGW 406 A 1 
HETATM 17 C C05 PGW . . . H 5 66.896 -35.108 30.915 1 117.62 ? C05 PGW 406 A 1 
HETATM 18 C C5 PGW . . . H 5 66.931 -26.373 28.745 1 58.89 ? C5 PGW 406 A 1 
HETATM 19 C C06 PGW . . . H 5 66.617 -20.421 25.856 1 69.28 ? C06 PGW 406 A 1 
HETATM 20 C C6 PGW . . . H 5 66.765 -25.314 27.683 1 49.36 ? C6 PGW 406 A 1 
HETATM 21 C C07 PGW . . . H 5 65.975 -19.089 25.624 1 81.19 ? C07 PGW 406 A 1 
HETATM 22 C C7 PGW . . . H 5 67.781 -24.185 27.791 1 47.15 ? C7 PGW 406 A 1 
HETATM 23 C C08 PGW . . . H 5 65.848 -18.727 24.151 1 89.14 ? C08 PGW 406 A 1 
HETATM 24 C C8 PGW . . . H 5 67.473 -23.004 26.931 1 55.62 ? C8 PGW 406 A 1 
HETATM 25 C C09 PGW . . . H 5 64.875 -17.607 23.864 1 89.3 ? C09 PGW 406 A 1 
HETATM 26 C C9 PGW . . . H 5 67.804 -21.698 27.588 1 50.53 ? C9 PGW 406 A 1 
HETATM 27 C C10 PGW . . . H 5 67.34 -20.554 27.161 1 53.57 ? C10 PGW 406 A 1 
HETATM 28 C C11 PGW . . . H 5 63.457 -18.069 23.608 1 78.69 ? C11 PGW 406 A 1 
HETATM 29 O O11 PGW . . . H 5 65.781 -31.821 34.143 1 170.15 ? O11 PGW 406 A 1 
HETATM 30 C C12 PGW . . . H 5 62.447 -16.954 23.479 1 69.18 ? C12 PGW 406 A 1 
HETATM 31 O O12 PGW . . . H 5 66.93 -33.441 32.655 1 160.88 ? O12 PGW 406 A 1 
HETATM 32 C C13 PGW . . . H 5 61.054 -17.452 23.199 1 67.4 ? C13 PGW 406 A 1 
HETATM 33 O O13 PGW . . . H 5 68.224 -32.378 34.611 1 167.63 ? O13 PGW 406 A 1 
HETATM 34 C C14 PGW . . . H 5 60.004 -16.417 23.515 1 74.84 ? C14 PGW 406 A 1 
HETATM 35 O O14 PGW . . . H 5 66.343 -34.112 34.999 1 170.01 ? O14 PGW 406 A 1 
HETATM 36 C C15 PGW . . . H 5 57.914 -22.687 30.954 1 42.76 ? C15 PGW 406 A 1 
HETATM 37 C C16 PGW . . . H 5 57.369 -22.503 29.566 1 41.07 ? C16 PGW 406 A 1 
HETATM 38 C C17 PGW . . . H 5 58.411 -22.56 28.477 1 38.21 ? C17 PGW 406 A 1 
HETATM 39 C C18 PGW . . . H 5 58.034 -23.488 27.344 1 24.73 ? C18 PGW 406 A 1 
HETATM 40 C C19 PGW . . . H 5 60.818 -30.978 33.063 1 106.57 ? C19 PGW 406 A 1 
HETATM 41 C C20 PGW . . . H 5 59.837 -30.431 32.061 1 94.24 ? C20 PGW 406 A 1 
HETATM 42 C C21 PGW . . . H 5 58.952 -29.349 32.602 1 76.65 ? C21 PGW 406 A 1 
HETATM 43 C C22 PGW . . . H 5 57.693 -29.164 31.768 1 62.43 ? C22 PGW 406 A 1 
HETATM 44 C C23 PGW . . . H 5 56.755 -28.078 32.251 1 49.38 ? C23 PGW 406 A 1 
HETATM 45 C C24 PGW . . . H 5 57.073 -26.689 31.752 1 35.15 ? C24 PGW 406 A 1 
HETATM 46 C C25 PGW . . . H 5 55.939 -25.708 31.952 1 49.69 ? C25 PGW 406 A 1 
HETATM 47 C C26 PGW . . . H 5 56.091 -24.402 31.202 1 54.49 ? C26 PGW 406 A 1 
HETATM 48 C C27 PGW . . . H 5 56.938 -23.348 31.885 1 52.5 ? C27 PGW 406 A 1 
HETATM 49 C C28 PGW . . . H 5 58.607 -23.104 25.999 1 23.11 ? C28 PGW 406 A 1 
HETATM 50 C C29 PGW . . . H 5 58.635 -23.52 23.512 1 38.08 ? C29 PGW 406 A 1 
HETATM 51 C C30 PGW . . . H 5 58.132 -23.974 24.861 1 33.16 ? C30 PGW 406 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           51 
#