data_6BW5 # _model_server_result.job_id CRpDJR7hyUNaIPCgAkN-rw _model_server_result.datetime_utc '2024-11-27 02:59:49' _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 6bw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":502}' # _entry.id 6BW5 # _exptl.entry_id 6BW5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 749.007 _entity.id 3 _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 103.53 _cell.angle_gamma 90 _cell.entry_id 6BW5 _cell.length_a 212.272 _cell.length_b 105.512 _cell.length_c 149.389 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6BW5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H 1 1 C,D,I,J,K,L 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 ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L 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 106 A CYS 106 1_555 B SG CYS 106 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf2 C SG CYS 106 C CYS 106 1_555 D SG CYS 106 D CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? # _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 235 n n CAD HAD PGW sing 236 n n CAD HADA PGW sing 237 n n OAE CAD PGW sing 238 n n OAE HOAE PGW sing 239 n n OAF C05 PGW sing 240 n n OAF HOAF PGW sing 241 n n P O13 PGW sing 242 n n P O11 PGW sing 243 n n C01 O03 PGW sing 244 n n C01 C02 PGW sing 245 n n C01 H01 PGW sing 246 n n C01 H01A PGW sing 247 n n C1 C2 PGW sing 248 n n O01 C1 PGW sing 249 n n C02 O01 PGW sing 250 n n C02 H02 PGW sing 251 n n C2 C3 PGW sing 252 n n C2 H2 PGW sing 253 n n C2 H2A PGW sing 254 n n O02 C1 PGW doub 255 n n C03 C02 PGW sing 256 n n C03 H03 PGW sing 257 n n C03 H03A PGW sing 258 n n C3 C4 PGW sing 259 n n C3 H3 PGW sing 260 n n C3 H3A PGW sing 261 n n C04 C05 PGW sing 262 n n C04 O12 PGW sing 263 n n C04 H04 PGW sing 264 n n C04 H04A PGW sing 265 n n C4 C5 PGW sing 266 n n C4 H4 PGW sing 267 n n C4 H4A PGW sing 268 n n O04 C19 PGW doub 269 n n C05 H05 PGW sing 270 n n C5 C6 PGW sing 271 n n C5 H5 PGW sing 272 n n C5 H5A PGW sing 273 n n C06 C07 PGW sing 274 n n C06 H06 PGW sing 275 n n C06 H06A PGW sing 276 n n C6 C7 PGW sing 277 n n C6 H6 PGW sing 278 n n C6 H6A PGW sing 279 n n C07 H07 PGW sing 280 n n C07 H07A PGW sing 281 n n C7 C8 PGW sing 282 n n C7 H7 PGW sing 283 n n C7 H7A PGW sing 284 n n C08 C07 PGW sing 285 n n C08 H08 PGW sing 286 n n C08 H08A PGW sing 287 n n C8 C9 PGW sing 288 n n C8 H8 PGW sing 289 n n C8 H8A PGW sing 290 n n C09 C08 PGW sing 291 n n C09 C11 PGW sing 292 n n C09 H09 PGW sing 293 n n C09 H09A PGW sing 294 n n C9 C10 PGW doub 295 z n C10 C06 PGW sing 296 n n C11 H11 PGW sing 297 n n C11 H11A PGW sing 298 n n O11 C03 PGW sing 299 n n C12 C11 PGW sing 300 n n C12 H12 PGW sing 301 n n C12 H12A PGW sing 302 n n O12 P PGW sing 303 n n C13 C12 PGW sing 304 n n C13 C14 PGW sing 305 n n C13 H13 PGW sing 306 n n C13 H13A PGW sing 307 n n O13 HO13 PGW sing 308 n n C14 H14 PGW sing 309 n n C14 H14A PGW sing 310 n n C14 H14B PGW sing 311 n n O14 P PGW doub 312 n n C15 C16 PGW sing 313 n n C15 H15 PGW sing 314 n n C15 H15A PGW sing 315 n n C16 H16 PGW sing 316 n n C16 H16A PGW sing 317 n n C17 C16 PGW sing 318 n n C17 C18 PGW sing 319 n n C17 H17 PGW sing 320 n n C17 H17A PGW sing 321 n n C18 C28 PGW sing 322 n n C18 H18 PGW sing 323 n n C18 H18A PGW sing 324 n n C19 O03 PGW sing 325 n n C19 C20 PGW sing 326 n n C20 C21 PGW sing 327 n n C20 H20 PGW sing 328 n n C20 H20A PGW sing 329 n n C21 C22 PGW sing 330 n n C21 H21 PGW sing 331 n n C21 H21A PGW sing 332 n n C22 C23 PGW sing 333 n n C22 H22 PGW sing 334 n n C22 H22A PGW sing 335 n n C23 C24 PGW sing 336 n n C23 H23 PGW sing 337 n n C23 H23A PGW sing 338 n n C24 C25 PGW sing 339 n n C24 H24 PGW sing 340 n n C24 H24A PGW sing 341 n n C25 C26 PGW sing 342 n n C25 H25 PGW sing 343 n n C25 H25A PGW sing 344 n n C26 C27 PGW sing 345 n n C26 H26 PGW sing 346 n n C26 H26A PGW sing 347 n n C27 C15 PGW sing 348 n n C27 H27 PGW sing 349 n n C27 H27A PGW sing 350 n n C28 H28 PGW sing 351 n n C28 H28A PGW sing 352 n n C29 H29 PGW sing 353 n n C29 H29A PGW sing 354 n n C29 H29B PGW sing 355 n n C30 C28 PGW sing 356 n n C30 C29 PGW sing 357 n n C30 H30 PGW sing 358 n n C30 H30A PGW sing 359 n n C9 H9 PGW sing 360 n n C10 H10 PGW sing 361 n n # _atom_sites.entry_id 6BW5 _atom_sites.fract_transf_matrix[1][1] 0.004711 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001134 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009478 _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] 0.006885 _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 E 2 TUM A 1 501 409 TUM TUM . F 3 PGW A 1 502 410 PGW PGW . G 2 TUM B 1 501 409 TUM TUM . H 3 PGW B 1 502 410 PGW PGW . I 2 TUM C 1 501 409 TUM TUM . J 3 PGW C 1 502 410 PGW PGW . K 2 TUM D 1 501 409 TUM TUM . L 3 PGW D 1 502 410 PGW PGW . # 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 3 42.96 2.317 12.41 1 92.55 ? CAD PGW 502 B 1 HETATM 2 O OAE PGW . . . H 3 43.899 3.281 12.802 1 82.86 ? OAE PGW 502 B 1 HETATM 3 O OAF PGW . . . H 3 42.215 1.877 14.628 1 68.66 ? OAF PGW 502 B 1 HETATM 4 P P PGW . . . H 3 40.237 0.118 10.721 1 107.87 ? P PGW 502 B 1 HETATM 5 C C01 PGW . . . H 3 38.504 -0.309 6.745 1 99.13 ? C01 PGW 502 B 1 HETATM 6 C C1 PGW . . . H 3 36.143 1.588 8.839 1 75.85 ? C1 PGW 502 B 1 HETATM 7 O O01 PGW . . . H 3 36.815 0.543 8.19 1 92.51 ? O01 PGW 502 B 1 HETATM 8 C C02 PGW . . . H 3 38.032 0.882 7.578 1 106.9 ? C02 PGW 502 B 1 HETATM 9 C C2 PGW . . . H 3 34.617 1.595 8.91 1 60.35 ? C2 PGW 502 B 1 HETATM 10 O O02 PGW . . . H 3 36.748 2.476 9.335 1 73.23 ? O02 PGW 502 B 1 HETATM 11 C C03 PGW . . . H 3 39.097 1.219 8.625 1 101.41 ? C03 PGW 502 B 1 HETATM 12 C C3 PGW . . . H 3 34.073 2.882 9.536 1 61.14 ? C3 PGW 502 B 1 HETATM 13 O O03 PGW . . . H 3 38.351 0.007 5.391 1 80.49 ? O03 PGW 502 B 1 HETATM 14 C C04 PGW . . . H 3 40.595 1.557 12.895 1 85 ? C04 PGW 502 B 1 HETATM 15 C C4 PGW . . . H 3 32.921 2.636 10.507 1 64.32 ? C4 PGW 502 B 1 HETATM 16 C C05 PGW . . . H 3 41.788 2.381 13.391 1 76.94 ? C05 PGW 502 B 1 HETATM 17 C C5 PGW . . . H 3 33.002 3.544 11.731 1 41.68 ? C5 PGW 502 B 1 HETATM 18 C C06 PGW . . . H 3 32.532 7.232 15.884 1 19.84 ? C06 PGW 502 B 1 HETATM 19 C C6 PGW . . . H 3 32.062 3.083 12.839 1 34.2 ? C6 PGW 502 B 1 HETATM 20 C C07 PGW . . . H 3 31.025 7.274 16.133 1 21.28 ? C07 PGW 502 B 1 HETATM 21 C C7 PGW . . . H 3 32.699 3.239 14.215 1 30 ? C7 PGW 502 B 1 HETATM 22 C C08 PGW . . . H 3 30.304 8.143 15.101 1 23 ? C08 PGW 502 B 1 HETATM 23 C C8 PGW . . . H 3 33.108 4.686 14.473 1 26.72 ? C8 PGW 502 B 1 HETATM 24 C C09 PGW . . . H 3 29.008 7.525 14.583 1 26.1 ? C09 PGW 502 B 1 HETATM 25 C C9 PGW . . . H 3 33.368 4.877 15.966 1 40.78 ? C9 PGW 502 B 1 HETATM 26 C C10 PGW . . . H 3 33.11 6.011 16.594 1 27.28 ? C10 PGW 502 B 1 HETATM 27 C C11 PGW . . . H 3 28.861 7.691 13.075 1 26.03 ? C11 PGW 502 B 1 HETATM 28 O O11 PGW . . . H 3 38.978 0.301 9.674 1 99.38 ? O11 PGW 502 B 1 HETATM 29 C C12 PGW . . . H 3 27.421 7.495 12.61 1 22.19 ? C12 PGW 502 B 1 HETATM 30 O O12 PGW . . . H 3 40.565 1.539 11.495 1 97.86 ? O12 PGW 502 B 1 HETATM 31 C C13 PGW . . . H 3 27.308 7.593 11.092 1 27.79 ? C13 PGW 502 B 1 HETATM 32 O O13 PGW . . . H 3 41.46 -0.333 9.958 1 109.43 ? O13 PGW 502 B 1 HETATM 33 C C14 PGW . . . H 3 25.948 7.133 10.577 1 22.96 ? C14 PGW 502 B 1 HETATM 34 O O14 PGW . . . H 3 39.869 -0.943 11.73 1 124.53 ? O14 PGW 502 B 1 HETATM 35 H HAD PGW . . . H 3 43.364 1.435 12.438 1 111.06 ? HAD PGW 502 B 1 HETATM 36 H HADA PGW . . . H 3 42.649 2.507 11.512 1 111.06 ? HADA PGW 502 B 1 HETATM 37 H HOAE PGW . . . H 3 44.565 3.26 12.274 1 99.43 ? HOAE PGW 502 B 1 HETATM 38 H HOAF PGW . . . H 3 41.677 1.272 14.888 1 82.39 ? HOAF PGW 502 B 1 HETATM 39 H H01 PGW . . . H 3 39.438 -0.489 6.935 1 118.96 ? H01 PGW 502 B 1 HETATM 40 H H01A PGW . . . H 3 37.971 -1.09 6.96 1 118.96 ? H01A PGW 502 B 1 HETATM 41 H H02 PGW . . . H 3 37.897 1.648 6.998 1 128.28 ? H02 PGW 502 B 1 HETATM 42 H H2 PGW . . . H 3 34.323 0.838 9.441 1 72.42 ? H2 PGW 502 B 1 HETATM 43 H H2A PGW . . . H 3 34.26 1.506 8.012 1 72.42 ? H2A PGW 502 B 1 HETATM 44 H H03 PGW . . . H 3 39.981 1.154 8.23 1 121.7 ? H03 PGW 502 B 1 HETATM 45 H H03A PGW . . . H 3 38.954 2.118 8.96 1 121.7 ? H03A PGW 502 B 1 HETATM 46 H H3 PGW . . . H 3 33.763 3.466 8.826 1 73.37 ? H3 PGW 502 B 1 HETATM 47 H H3A PGW . . . H 3 34.792 3.325 10.012 1 73.37 ? H3A PGW 502 B 1 HETATM 48 H H04 PGW . . . H 3 40.674 0.649 13.226 1 102 ? H04 PGW 502 B 1 HETATM 49 H H04A PGW . . . H 3 39.774 1.95 13.229 1 102 ? H04A PGW 502 B 1 HETATM 50 H H4 PGW . . . H 3 32.946 1.711 10.798 1 77.19 ? H4 PGW 502 B 1 HETATM 51 H H4A PGW . . . H 3 32.082 2.8 10.048 1 77.19 ? H4A PGW 502 B 1 HETATM 52 H H05 PGW . . . H 3 41.514 3.305 13.5 1 92.32 ? H05 PGW 502 B 1 HETATM 53 H H5 PGW . . . H 3 32.764 4.448 11.471 1 50.02 ? H5 PGW 502 B 1 HETATM 54 H H5A PGW . . . H 3 33.912 3.541 12.067 1 50.02 ? H5A PGW 502 B 1 HETATM 55 H H06 PGW . . . H 3 32.703 7.167 14.932 1 23.81 ? H06 PGW 502 B 1 HETATM 56 H H06A PGW . . . H 3 32.942 8.038 16.235 1 23.81 ? H06A PGW 502 B 1 HETATM 57 H H6 PGW . . . H 3 31.838 2.15 12.698 1 41.04 ? H6 PGW 502 B 1 HETATM 58 H H6A PGW . . . H 3 31.249 3.612 12.805 1 41.04 ? H6A PGW 502 B 1 HETATM 59 H H07 PGW . . . H 3 30.861 7.633 17.018 1 25.54 ? H07 PGW 502 B 1 HETATM 60 H H07A PGW . . . H 3 30.672 6.371 16.087 1 25.54 ? H07A PGW 502 B 1 HETATM 61 H H7 PGW . . . H 3 33.485 2.673 14.267 1 36 ? H7 PGW 502 B 1 HETATM 62 H H7A PGW . . . H 3 32.063 2.963 14.893 1 36 ? H7A PGW 502 B 1 HETATM 63 H H08 PGW . . . H 3 30.899 8.291 14.35 1 27.6 ? H08 PGW 502 B 1 HETATM 64 H H08A PGW . . . H 3 30.098 9 15.507 1 27.6 ? H08A PGW 502 B 1 HETATM 65 H H8 PGW . . . H 3 32.395 5.28 14.19 1 32.06 ? H8 PGW 502 B 1 HETATM 66 H H8A PGW . . . H 3 33.915 4.889 13.975 1 32.06 ? H8A PGW 502 B 1 HETATM 67 H H09 PGW . . . H 3 28.256 7.953 15.022 1 31.31 ? H09 PGW 502 B 1 HETATM 68 H H09A PGW . . . H 3 29.002 6.579 14.798 1 31.31 ? H09A PGW 502 B 1 HETATM 69 H H11 PGW . . . H 3 29.426 7.04 12.631 1 31.24 ? H11 PGW 502 B 1 HETATM 70 H H11A PGW . . . H 3 29.152 8.583 12.828 1 31.24 ? H11A PGW 502 B 1 HETATM 71 H H12 PGW . . . H 3 26.861 8.176 13.015 1 26.63 ? H12 PGW 502 B 1 HETATM 72 H H12A PGW . . . H 3 27.112 6.62 12.895 1 26.63 ? H12A PGW 502 B 1 HETATM 73 H H13 PGW . . . H 3 27.999 7.043 10.69 1 33.35 ? H13 PGW 502 B 1 HETATM 74 H H13A PGW . . . H 3 27.448 8.516 10.826 1 33.35 ? H13A PGW 502 B 1 HETATM 75 H H14 PGW . . . H 3 25.911 7.247 9.614 1 27.56 ? H14 PGW 502 B 1 HETATM 76 H H14A PGW . . . H 3 25.249 7.661 10.992 1 27.56 ? H14A PGW 502 B 1 HETATM 77 H H14B PGW . . . H 3 25.819 6.197 10.796 1 27.56 ? H14B PGW 502 B 1 HETATM 78 H H9 PGW . . . H 3 33.721 4.167 16.453 1 48.93 ? H9 PGW 502 B 1 HETATM 79 H H10 PGW . . . H 3 33.29 6.068 17.505 1 32.73 ? H10 PGW 502 B 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 687 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 79 #