data_5BKJ
#
_model_server_result.job_id            1jFgavMac1uXTkaFWjy_cg 
_model_server_result.datetime_utc      '2024-11-21 14:24:17' 
_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          5bkj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":401}' 
#
_entry.id    5BKJ 
#
_exptl.entry_id    5BKJ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              749.007 
_entity.id                          2 
_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    4 
_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            5BKJ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BKJ 
_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    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 2 I N N 
? 2 M N N 
? 2 N N N 
? 2 O 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
metalc ? metalc1 A O THR 59 A THR 59 1_555 J K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? 
metalc ? metalc2 A OG1 THR 59 A THR 59 1_555 J K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.344 ? 
metalc ? metalc3 J K K . A K 402 1_555 F O THR 59 C THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc4 J K K . A K 402 1_555 F OG1 THR 59 C THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.376 ? 
metalc ? metalc5 J K K . A K 402 1_555 G O THR 59 E THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? 
metalc ? metalc6 J K K . A K 402 1_555 G OG1 THR 59 E THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.367 ? 
metalc ? metalc7 J K K . A K 402 1_555 H O THR 59 G THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc8 J K K . A K 402 1_555 H OG1 THR 59 G THR 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.361 ? 
#
_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 237 n n 
CAD HAD PGW sing 238 n n 
CAD HADA PGW sing 239 n n 
OAE CAD PGW sing 240 n n 
OAE HOAE PGW sing 241 n n 
OAF C05 PGW sing 242 n n 
OAF HOAF PGW sing 243 n n 
P O13 PGW sing 244 n n 
P O11 PGW sing 245 n n 
C01 O03 PGW sing 246 n n 
C01 C02 PGW sing 247 n n 
C01 H01 PGW sing 248 n n 
C01 H01A PGW sing 249 n n 
C1 C2 PGW sing 250 n n 
O01 C1 PGW sing 251 n n 
C02 O01 PGW sing 252 n n 
C02 H02 PGW sing 253 n n 
C2 C3 PGW sing 254 n n 
C2 H2 PGW sing 255 n n 
C2 H2A PGW sing 256 n n 
O02 C1 PGW doub 257 n n 
C03 C02 PGW sing 258 n n 
C03 H03 PGW sing 259 n n 
C03 H03A PGW sing 260 n n 
C3 C4 PGW sing 261 n n 
C3 H3 PGW sing 262 n n 
C3 H3A PGW sing 263 n n 
C04 C05 PGW sing 264 n n 
C04 O12 PGW sing 265 n n 
C04 H04 PGW sing 266 n n 
C04 H04A PGW sing 267 n n 
C4 C5 PGW sing 268 n n 
C4 H4 PGW sing 269 n n 
C4 H4A PGW sing 270 n n 
O04 C19 PGW doub 271 n n 
C05 H05 PGW sing 272 n n 
C5 C6 PGW sing 273 n n 
C5 H5 PGW sing 274 n n 
C5 H5A PGW sing 275 n n 
C06 C07 PGW sing 276 n n 
C06 H06 PGW sing 277 n n 
C06 H06A PGW sing 278 n n 
C6 C7 PGW sing 279 n n 
C6 H6 PGW sing 280 n n 
C6 H6A PGW sing 281 n n 
C07 H07 PGW sing 282 n n 
C07 H07A PGW sing 283 n n 
C7 C8 PGW sing 284 n n 
C7 H7 PGW sing 285 n n 
C7 H7A PGW sing 286 n n 
C08 C07 PGW sing 287 n n 
C08 H08 PGW sing 288 n n 
C08 H08A PGW sing 289 n n 
C8 C9 PGW sing 290 n n 
C8 H8 PGW sing 291 n n 
C8 H8A PGW sing 292 n n 
C09 C08 PGW sing 293 n n 
C09 C11 PGW sing 294 n n 
C09 H09 PGW sing 295 n n 
C09 H09A PGW sing 296 n n 
C9 C10 PGW doub 297 z n 
C10 C06 PGW sing 298 n n 
C11 H11 PGW sing 299 n n 
C11 H11A PGW sing 300 n n 
O11 C03 PGW sing 301 n n 
C12 C11 PGW sing 302 n n 
C12 H12 PGW sing 303 n n 
C12 H12A PGW sing 304 n n 
O12 P PGW sing 305 n n 
C13 C12 PGW sing 306 n n 
C13 C14 PGW sing 307 n n 
C13 H13 PGW sing 308 n n 
C13 H13A PGW sing 309 n n 
O13 HO13 PGW sing 310 n n 
C14 H14 PGW sing 311 n n 
C14 H14A PGW sing 312 n n 
C14 H14B PGW sing 313 n n 
O14 P PGW doub 314 n n 
C15 C16 PGW sing 315 n n 
C15 H15 PGW sing 316 n n 
C15 H15A PGW sing 317 n n 
C16 H16 PGW sing 318 n n 
C16 H16A PGW sing 319 n n 
C17 C16 PGW sing 320 n n 
C17 C18 PGW sing 321 n n 
C17 H17 PGW sing 322 n n 
C17 H17A PGW sing 323 n n 
C18 C28 PGW sing 324 n n 
C18 H18 PGW sing 325 n n 
C18 H18A PGW sing 326 n n 
C19 O03 PGW sing 327 n n 
C19 C20 PGW sing 328 n n 
C20 C21 PGW sing 329 n n 
C20 H20 PGW sing 330 n n 
C20 H20A PGW sing 331 n n 
C21 C22 PGW sing 332 n n 
C21 H21 PGW sing 333 n n 
C21 H21A PGW sing 334 n n 
C22 C23 PGW sing 335 n n 
C22 H22 PGW sing 336 n n 
C22 H22A PGW sing 337 n n 
C23 C24 PGW sing 338 n n 
C23 H23 PGW sing 339 n n 
C23 H23A PGW sing 340 n n 
C24 C25 PGW sing 341 n n 
C24 H24 PGW sing 342 n n 
C24 H24A PGW sing 343 n n 
C25 C26 PGW sing 344 n n 
C25 H25 PGW sing 345 n n 
C25 H25A PGW sing 346 n n 
C26 C27 PGW sing 347 n n 
C26 H26 PGW sing 348 n n 
C26 H26A PGW sing 349 n n 
C27 C15 PGW sing 350 n n 
C27 H27 PGW sing 351 n n 
C27 H27A PGW sing 352 n n 
C28 H28 PGW sing 353 n n 
C28 H28A PGW sing 354 n n 
C29 H29 PGW sing 355 n n 
C29 H29A PGW sing 356 n n 
C29 H29B PGW sing 357 n n 
C30 C28 PGW sing 358 n n 
C30 C29 PGW sing 359 n n 
C30 H30 PGW sing 360 n n 
C30 H30A PGW sing 361 n n 
C9 H9 PGW sing 362 n n 
C10 H10 PGW sing 363 n n 
#
_atom_sites.entry_id                     5BKJ 
_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
I 2 PGW A 1 401 401 PGW PGW . 
J 3 K A 1 402 1 K K . 
K 3 K A 1 403 5 K K . 
L 4 YQ1 A 1 404 501 YQ1 TPA . 
M 2 PGW C 1 401 401 PGW PGW . 
N 2 PGW E 1 401 401 PGW PGW . 
O 2 PGW G 1 401 401 PGW PGW . 
P 5 HOH A 1 501 338 HOH HOH . 
Q 5 HOH C 1 501 338 HOH HOH . 
R 5 HOH E 1 501 338 HOH HOH . 
S 5 HOH G 1 501 338 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 P P PGW . . . M 2 125.814 146.666 118.184 1 74.88 ? P PGW 401 C 1 
HETATM 2 C C01 PGW . . . M 2 123.358 142.906 116.006 1 74.88 ? C01 PGW 401 C 1 
HETATM 3 C C1 PGW . . . M 2 126.465 142.72 114.794 1 74.88 ? C1 PGW 401 C 1 
HETATM 4 O O01 PGW . . . M 2 125.857 142.485 116.013 1 74.88 ? O01 PGW 401 C 1 
HETATM 5 C C02 PGW . . . M 2 124.76 143.288 116.583 1 74.88 ? C02 PGW 401 C 1 
HETATM 6 C C2 PGW . . . M 2 126.031 141.837 113.664 1 74.88 ? C2 PGW 401 C 1 
HETATM 7 O O02 PGW . . . M 2 127.327 143.583 114.641 1 74.88 ? O02 PGW 401 C 1 
HETATM 8 C C03 PGW . . . M 2 125.015 144.808 116.573 1 74.88 ? C03 PGW 401 C 1 
HETATM 9 C C3 PGW . . . M 2 127.01 142.026 112.518 1 74.88 ? C3 PGW 401 C 1 
HETATM 10 O O03 PGW . . . M 2 123.319 141.526 115.616 1 74.88 ? O03 PGW 401 C 1 
HETATM 11 C C04 PGW . . . M 2 123.645 147.041 119.617 1 74.88 ? C04 PGW 401 C 1 
HETATM 12 C C4 PGW . . . M 2 126.277 142.126 111.208 1 74.88 ? C4 PGW 401 C 1 
HETATM 13 O O04 PGW . . . M 2 121.716 140.165 114.875 1 74.88 ? O04 PGW 401 C 1 
HETATM 14 C C05 PGW . . . M 2 123.121 147.832 120.823 1 74.88 ? C05 PGW 401 C 1 
HETATM 15 C C5 PGW . . . M 2 126.946 141.263 110.178 1 74.88 ? C5 PGW 401 C 1 
HETATM 16 C C06 PGW . . . M 2 130.336 142.194 105.212 1 74.88 ? C06 PGW 401 C 1 
HETATM 17 C C6 PGW . . . M 2 126.731 141.873 108.819 1 74.88 ? C6 PGW 401 C 1 
HETATM 18 C C07 PGW . . . M 2 130.465 141.58 103.837 1 74.88 ? C07 PGW 401 C 1 
HETATM 19 C C7 PGW . . . M 2 127.823 141.441 107.869 1 74.88 ? C7 PGW 401 C 1 
HETATM 20 C C8 PGW . . . M 2 128.756 142.602 107.635 1 74.88 ? C8 PGW 401 C 1 
HETATM 21 C C9 PGW . . . M 2 128.434 143.266 106.356 1 74.88 ? C9 PGW 401 C 1 
HETATM 22 C C10 PGW . . . M 2 129.148 143.084 105.251 1 74.88 ? C10 PGW 401 C 1 
HETATM 23 O O11 PGW . . . M 2 124.859 145.349 117.813 1 74.88 ? O11 PGW 401 C 1 
HETATM 24 O O12 PGW . . . M 2 124.992 147.295 119.521 1 74.88 ? O12 PGW 401 C 1 
HETATM 25 O O13 PGW . . . M 2 125.662 147.655 117.057 1 74.88 ? O13 PGW 401 C 1 
HETATM 26 O O14 PGW . . . M 2 127.068 146.124 118.701 1 74.88 ? O14 PGW 401 C 1 
HETATM 27 C C15 PGW . . . M 2 124.334 144.057 104.826 1 74.88 ? C15 PGW 401 C 1 
HETATM 28 C C16 PGW . . . M 2 125.687 144.367 104.228 1 74.88 ? C16 PGW 401 C 1 
HETATM 29 C C17 PGW . . . M 2 125.764 143.801 102.822 1 74.88 ? C17 PGW 401 C 1 
HETATM 30 C C18 PGW . . . M 2 126.823 144.54 102.029 1 74.88 ? C18 PGW 401 C 1 
HETATM 31 C C19 PGW . . . M 2 122.408 141.148 114.665 1 74.88 ? C19 PGW 401 C 1 
HETATM 32 C C20 PGW . . . M 2 122.316 141.975 113.416 1 74.88 ? C20 PGW 401 C 1 
HETATM 33 C C21 PGW . . . M 2 121.853 141.104 112.264 1 74.88 ? C21 PGW 401 C 1 
HETATM 34 C C22 PGW . . . M 2 122.599 141.473 111.004 1 74.88 ? C22 PGW 401 C 1 
HETATM 35 C C23 PGW . . . M 2 121.66 142.027 109.961 1 74.88 ? C23 PGW 401 C 1 
HETATM 36 C C24 PGW . . . M 2 122.327 143.148 109.209 1 74.88 ? C24 PGW 401 C 1 
HETATM 37 C C25 PGW . . . M 2 123.123 142.604 108.053 1 74.88 ? C25 PGW 401 C 1 
HETATM 38 C C26 PGW . . . M 2 123.044 143.526 106.862 1 74.88 ? C26 PGW 401 C 1 
HETATM 39 C C27 PGW . . . M 2 124.428 143.807 106.315 1 74.88 ? C27 PGW 401 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           39 
#