data_7VGJ
#
_model_server_result.job_id            VKJEa8visp2z03a1s3hXuA 
_model_server_result.datetime_utc      '2025-03-04 13:14:29' 
_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          7vgj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1301}' 
#
_entry.id    7VGJ 
#
_exptl.entry_id    7VGJ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              792.075 
_entity.id                          3 
_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    1 
_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            7VGJ 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7VGJ 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            B 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             97 
_struct_conn.ptnr1_auth_asym_id             B 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              97 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             105 
_struct_conn.ptnr2_auth_asym_id             B 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              105 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.027 
_struct_conn.pdbx_value_order               ? 
#
_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 235 n n 
O C P5S doub 236 n n 
C OXT P5S sing 237 n n 
CA N P5S sing 238 n n 
N HN P5S sing 239 n n 
N HNA P5S sing 240 n n 
O19 C1 P5S sing 241 n n 
C1 C2 P5S sing 242 n n 
C1 H1 P5S sing 243 n n 
C1 H1A P5S sing 244 n n 
C2 O37 P5S sing 245 n n 
C2 C3 P5S sing 246 n n 
C2 H2 P5S sing 247 n n 
O16 C3 P5S sing 248 n n 
C3 H3 P5S sing 249 n n 
C3 H3A P5S sing 250 n n 
CB CA P5S sing 251 n n 
CA HA P5S sing 252 n n 
CB OG P5S sing 253 n n 
CB HB P5S sing 254 n n 
CB HBA P5S sing 255 n n 
P12 OG P5S sing 256 n n 
O16 P12 P5S sing 257 n n 
O13 P12 P5S doub 258 n n 
P12 O15 P5S sing 259 n n 
O15 HO15 P5S sing 260 n n 
C20 C17 P5S sing 261 n n 
O19 C17 P5S sing 262 n n 
C17 O18 P5S doub 263 n n 
C21 C20 P5S sing 264 n n 
C20 H20 P5S sing 265 n n 
C20 H20A P5S sing 266 n n 
C21 C22 P5S sing 267 n n 
C21 H21 P5S sing 268 n n 
C21 H21A P5S sing 269 n n 
C23 C22 P5S sing 270 n n 
C22 H22 P5S sing 271 n n 
C22 H22A P5S sing 272 n n 
C24 C23 P5S sing 273 n n 
C23 H23 P5S sing 274 n n 
C23 H23A P5S sing 275 n n 
C25 C24 P5S sing 276 n n 
C24 H24 P5S sing 277 n n 
C24 H24A P5S sing 278 n n 
C26 C25 P5S sing 279 n n 
C25 H25 P5S sing 280 n n 
C25 H25A P5S sing 281 n n 
C26 C27 P5S sing 282 n n 
C26 H26 P5S sing 283 n n 
C26 H26A P5S sing 284 n n 
C27 C28 P5S sing 285 n n 
C27 H27 P5S sing 286 n n 
C27 H27A P5S sing 287 n n 
C29 C28 P5S sing 288 n n 
C28 H28 P5S sing 289 n n 
C28 H28A P5S sing 290 n n 
C30 C29 P5S sing 291 n n 
C29 H29 P5S sing 292 n n 
C29 H29A P5S sing 293 n n 
C31 C30 P5S sing 294 n n 
C30 H30 P5S sing 295 n n 
C30 H30A P5S sing 296 n n 
C31 C32 P5S sing 297 n n 
C31 H31 P5S sing 298 n n 
C31 H31A P5S sing 299 n n 
C33 C32 P5S sing 300 n n 
C32 H32 P5S sing 301 n n 
C32 H32A P5S sing 302 n n 
C33 C34 P5S sing 303 n n 
C33 H33 P5S sing 304 n n 
C33 H33A P5S sing 305 n n 
C35 C34 P5S sing 306 n n 
C34 H34 P5S sing 307 n n 
C34 H34A P5S sing 308 n n 
C36 C35 P5S sing 309 n n 
C35 H35 P5S sing 310 n n 
C35 H35A P5S sing 311 n n 
C36 H36 P5S sing 312 n n 
C36 H36A P5S sing 313 n n 
C36 H36B P5S sing 314 n n 
C38 O37 P5S sing 315 n n 
O47 C38 P5S doub 316 n n 
C38 C39 P5S sing 317 n n 
C40 C39 P5S sing 318 n n 
C39 H39 P5S sing 319 n n 
C39 H39A P5S sing 320 n n 
C41 C40 P5S sing 321 n n 
C40 H40 P5S sing 322 n n 
C40 H40A P5S sing 323 n n 
C42 C41 P5S sing 324 n n 
C41 H41 P5S sing 325 n n 
C41 H41A P5S sing 326 n n 
C43 C42 P5S sing 327 n n 
C42 H42 P5S sing 328 n n 
C42 H42A P5S sing 329 n n 
C43 C44 P5S sing 330 n n 
C43 H43 P5S sing 331 n n 
C43 H43A P5S sing 332 n n 
C44 C45 P5S sing 333 n n 
C44 H44 P5S sing 334 n n 
C44 H44A P5S sing 335 n n 
C45 C46 P5S sing 336 n n 
C45 H45 P5S sing 337 n n 
C45 H45A P5S sing 338 n n 
C46 C48 P5S sing 339 n n 
C46 H46 P5S sing 340 n n 
C46 H46A P5S sing 341 n n 
C48 C49 P5S sing 342 n n 
C48 H48 P5S sing 343 n n 
C48 H48A P5S sing 344 n n 
C49 C50 P5S sing 345 n n 
C49 H49 P5S sing 346 n n 
C49 H49A P5S sing 347 n n 
C50 C51 P5S sing 348 n n 
C50 H50 P5S sing 349 n n 
C50 H50A P5S sing 350 n n 
C51 C52 P5S sing 351 n n 
C51 H51 P5S sing 352 n n 
C51 H51A P5S sing 353 n n 
C53 C52 P5S sing 354 n n 
C52 H52 P5S sing 355 n n 
C52 H52A P5S sing 356 n n 
C53 C54 P5S sing 357 n n 
C53 H53 P5S sing 358 n n 
C53 H53A P5S sing 359 n n 
C55 C54 P5S sing 360 n n 
C54 H54 P5S sing 361 n n 
C54 H54A P5S sing 362 n n 
C55 C56 P5S sing 363 n n 
C55 H55 P5S sing 364 n n 
C55 H55A P5S sing 365 n n 
C56 H56 P5S sing 366 n n 
C56 H56A P5S sing 367 n n 
C56 H56B P5S sing 368 n n 
OXT HXT P5S sing 369 n n 
#
_atom_sites.entry_id                     7VGJ 
_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 
#
_pdbx_nonpoly_scheme.asym_id          C 
_pdbx_nonpoly_scheme.entity_id        3 
_pdbx_nonpoly_scheme.mon_id           P5S 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      1301 
_pdbx_nonpoly_scheme.auth_seq_num     1 
_pdbx_nonpoly_scheme.pdb_mon_id       P5S 
_pdbx_nonpoly_scheme.auth_mon_id      P5S 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 . . . C 3 109.467 111.109 128.363 1 63.02 ? C P5S 1301 A 1 
HETATM 2 N N P5S . . . C 3 111.881 110.909 128.406 1 63.02 ? N P5S 1301 A 1 
HETATM 3 O O P5S . . . C 3 109.348 109.921 128.756 1 63.02 ? O P5S 1301 A 1 
HETATM 4 C C1 P5S . . . C 3 107.189 114.173 121.417 1 63.02 ? C1 P5S 1301 A 1 
HETATM 5 C C2 P5S . . . C 3 107.255 113.466 122.77 1 63.02 ? C2 P5S 1301 A 1 
HETATM 6 C C3 P5S . . . C 3 108.681 113.438 123.322 1 63.02 ? C3 P5S 1301 A 1 
HETATM 7 C CA P5S . . . C 3 110.791 111.845 128.585 1 63.02 ? CA P5S 1301 A 1 
HETATM 8 C CB P5S . . . C 3 110.974 113.035 127.637 1 63.02 ? CB P5S 1301 A 1 
HETATM 9 O OG P5S . . . C 3 110.388 112.834 126.384 1 63.02 ? OG P5S 1301 A 1 
HETATM 10 P P12 P5S . . . C 3 110.052 114.166 125.478 1 63.02 ? P12 P5S 1301 A 1 
HETATM 11 O O13 P5S . . . C 3 109.908 115.342 126.406 1 63.02 ? O13 P5S 1301 A 1 
HETATM 12 O O15 P5S . . . C 3 111.175 114.47 124.522 1 63.02 ? O15 P5S 1301 A 1 
HETATM 13 O O16 P5S . . . C 3 108.653 113.908 124.642 1 63.02 ? O16 P5S 1301 A 1 
HETATM 14 C C17 P5S . . . C 3 105.659 114.29 119.605 1 63.02 ? C17 P5S 1301 A 1 
HETATM 15 O O18 P5S . . . C 3 105.854 115.449 119.534 1 63.02 ? O18 P5S 1301 A 1 
HETATM 16 O O19 P5S . . . C 3 106.285 113.507 120.584 1 63.02 ? O19 P5S 1301 A 1 
HETATM 17 C C20 P5S . . . C 3 104.698 113.643 118.618 1 63.02 ? C20 P5S 1301 A 1 
HETATM 18 C C21 P5S . . . C 3 104.009 114.713 117.775 1 63.02 ? C21 P5S 1301 A 1 
HETATM 19 C C22 P5S . . . C 3 102.657 114.205 117.248 1 63.02 ? C22 P5S 1301 A 1 
HETATM 20 C C23 P5S . . . C 3 102.728 112.737 116.81 1 63.02 ? C23 P5S 1301 A 1 
HETATM 21 C C24 P5S . . . C 3 102.299 112.549 115.35 1 63.02 ? C24 P5S 1301 A 1 
HETATM 22 C C25 P5S . . . C 3 101.189 113.526 114.966 1 63.02 ? C25 P5S 1301 A 1 
HETATM 23 C C26 P5S . . . C 3 101.178 113.759 113.456 1 63.02 ? C26 P5S 1301 A 1 
HETATM 24 C C27 P5S . . . C 3 100.075 114.761 113.114 1 63.02 ? C27 P5S 1301 A 1 
HETATM 25 C C28 P5S . . . C 3 100.212 115.225 111.662 1 63.02 ? C28 P5S 1301 A 1 
HETATM 26 C C29 P5S . . . C 3 99.048 116.144 111.285 1 63.02 ? C29 P5S 1301 A 1 
HETATM 27 C C30 P5S . . . C 3 99.439 117.049 110.118 1 63.02 ? C30 P5S 1301 A 1 
HETATM 28 C C31 P5S . . . C 3 98.261 117.165 109.149 1 63.02 ? C31 P5S 1301 A 1 
HETATM 29 C C32 P5S . . . C 3 98.261 118.529 108.459 1 63.02 ? C32 P5S 1301 A 1 
HETATM 30 C C33 P5S . . . C 3 97.245 118.523 107.32 1 63.02 ? C33 P5S 1301 A 1 
HETATM 31 C C34 P5S . . . C 3 96.629 119.914 107.177 1 63.02 ? C34 P5S 1301 A 1 
HETATM 32 C C35 P5S . . . C 3 95.561 119.896 106.083 1 63.02 ? C35 P5S 1301 A 1 
HETATM 33 C C36 P5S . . . C 3 94.673 121.135 106.191 1 63.02 ? C36 P5S 1301 A 1 
HETATM 34 O O37 P5S . . . C 3 106.754 112.172 122.623 1 63.02 ? O37 P5S 1301 A 1 
HETATM 35 C C38 P5S . . . C 3 106.111 111.683 123.762 1 63.02 ? C38 P5S 1301 A 1 
HETATM 36 C C39 P5S . . . C 3 105.134 110.512 123.665 1 63.02 ? C39 P5S 1301 A 1 
HETATM 37 C C40 P5S . . . C 3 104.601 110.396 122.242 1 63.02 ? C40 P5S 1301 A 1 
HETATM 38 C C41 P5S . . . C 3 103.168 110.923 122.177 1 63.02 ? C41 P5S 1301 A 1 
HETATM 39 C C42 P5S . . . C 3 102.538 110.633 120.814 1 63.02 ? C42 P5S 1301 A 1 
HETATM 40 C C43 P5S . . . C 3 103.607 110.417 119.742 1 63.02 ? C43 P5S 1301 A 1 
HETATM 41 C C44 P5S . . . C 3 103.052 109.528 118.635 1 63.02 ? C44 P5S 1301 A 1 
HETATM 42 C C45 P5S . . . C 3 104.034 109.473 117.468 1 63.02 ? C45 P5S 1301 A 1 
HETATM 43 C C46 P5S . . . C 3 103.512 108.484 116.427 1 63.02 ? C46 P5S 1301 A 1 
HETATM 44 O O47 P5S . . . C 3 106.326 112.172 124.816 1 63.02 ? O47 P5S 1301 A 1 
HETATM 45 C C48 P5S . . . C 3 103.516 109.118 115.036 1 63.02 ? C48 P5S 1301 A 1 
HETATM 46 C C49 P5S . . . C 3 103.259 108.041 113.985 1 63.02 ? C49 P5S 1301 A 1 
HETATM 47 C C50 P5S . . . C 3 102.327 108.587 112.908 1 63.02 ? C50 P5S 1301 A 1 
HETATM 48 C C51 P5S . . . C 3 103.09 108.712 111.591 1 63.02 ? C51 P5S 1301 A 1 
HETATM 49 C C52 P5S . . . C 3 102.403 107.882 110.506 1 63.02 ? C52 P5S 1301 A 1 
HETATM 50 C C53 P5S . . . C 3 102.829 108.391 109.132 1 63.02 ? C53 P5S 1301 A 1 
HETATM 51 C C54 P5S . . . C 3 102.313 107.439 108.059 1 63.02 ? C54 P5S 1301 A 1 
HETATM 52 C C55 P5S . . . C 3 103.237 106.23 107.972 1 63.02 ? C55 P5S 1301 A 1 
HETATM 53 C C56 P5S . . . C 3 102.807 105.352 106.8 1 63.02 ? C56 P5S 1301 A 1 
HETATM 54 O OXT P5S . . . C 3 108.486 111.665 127.81 1 63.02 ? OXT P5S 1301 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          27 
_model_server_stats.element_count           54 
#