data_5GYD
#
_model_server_result.job_id            J02dckGQ4kE2VmtVIZZS7w 
_model_server_result.datetime_utc      '2024-11-24 07:55:28' 
_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          5gyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":301}' 
#
_entry.id    5GYD 
#
_exptl.entry_id    5GYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              744.034 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,2-dioleoyl-sn-glycero-3-phosphoethanolamine 
_entity.pdbx_number_of_molecules    5 
_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            5GYD 
_cell.length_a            142.592 
_cell.length_b            219.073 
_cell.length_c            73.097 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
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 1 1 
C,D,G,H,I 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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
#
_chem_comp.formula           'C41 H78 N O8 P' 
_chem_comp.formula_weight    744.034 
_chem_comp.id                PEE 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              1,2-dioleoyl-sn-glycero-3-phosphoethanolamine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DOPE 
#
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
N C5 PEE sing 235 n n 
C5 C4 PEE sing 236 n n 
C4 O4P PEE sing 237 n n 
O4P P PEE sing 238 n n 
O1P P PEE doub 239 n n 
C1 O3P PEE sing 240 n n 
C1 C2 PEE sing 241 n n 
O3P P PEE sing 242 n n 
P O2P PEE sing 243 n n 
C2 C3 PEE sing 244 n n 
C2 O2 PEE sing 245 n n 
C3 O3 PEE sing 246 n n 
O2 C10 PEE sing 247 n n 
C31 C30 PEE sing 248 n n 
C31 C32 PEE sing 249 n n 
C33 C32 PEE sing 250 n n 
C33 C34 PEE sing 251 n n 
C30 O3 PEE sing 252 n n 
C30 O5 PEE doub 253 n n 
C10 O4 PEE doub 254 n n 
C10 C11 PEE sing 255 n n 
C34 C35 PEE sing 256 n n 
C11 C12 PEE sing 257 n n 
C35 C36 PEE sing 258 n n 
C36 C37 PEE sing 259 n n 
C37 C38 PEE sing 260 n n 
C38 C39 PEE doub 261 z n 
C12 C13 PEE sing 262 n n 
C39 C40 PEE sing 263 n n 
C13 C14 PEE sing 264 n n 
C14 C15 PEE sing 265 n n 
C40 C41 PEE sing 266 n n 
C15 C16 PEE sing 267 n n 
C41 C42 PEE sing 268 n n 
C16 C17 PEE sing 269 n n 
C42 C43 PEE sing 270 n n 
C17 C18 PEE sing 271 n n 
C43 C44 PEE sing 272 n n 
C18 C19 PEE doub 273 z n 
C46 C47 PEE sing 274 n n 
C46 C45 PEE sing 275 n n 
C44 C45 PEE sing 276 n n 
C19 C20 PEE sing 277 n n 
C20 C21 PEE sing 278 n n 
C21 C22 PEE sing 279 n n 
C22 C23 PEE sing 280 n n 
C23 C24 PEE sing 281 n n 
C24 C25 PEE sing 282 n n 
C26 C25 PEE sing 283 n n 
C26 C27 PEE sing 284 n n 
C27 H7 PEE sing 285 n n 
C27 H8 PEE sing 286 n n 
C27 H82 PEE sing 287 n n 
C26 H5 PEE sing 288 n n 
C26 H6 PEE sing 289 n n 
C25 H12 PEE sing 290 n n 
C25 H4 PEE sing 291 n n 
C24 H10 PEE sing 292 n n 
C24 H11 PEE sing 293 n n 
C23 H83 PEE sing 294 n n 
C23 H9 PEE sing 295 n n 
C22 H2 PEE sing 296 n n 
C22 H3 PEE sing 297 n n 
C21 H14 PEE sing 298 n n 
C21 H1 PEE sing 299 n n 
C20 H16 PEE sing 300 n n 
C20 H13 PEE sing 301 n n 
C19 H18 PEE sing 302 n n 
C18 H20 PEE sing 303 n n 
C17 H22 PEE sing 304 n n 
C17 H19 PEE sing 305 n n 
C16 H21 PEE sing 306 n n 
C16 H28 PEE sing 307 n n 
C15 H23 PEE sing 308 n n 
C15 H24 PEE sing 309 n n 
C14 H25 PEE sing 310 n n 
C14 H26 PEE sing 311 n n 
C13 H17 PEE sing 312 n n 
C13 H27 PEE sing 313 n n 
C12 H15 PEE sing 314 n n 
C12 H29 PEE sing 315 n n 
C11 H30 PEE sing 316 n n 
C11 H31 PEE sing 317 n n 
C2 H32 PEE sing 318 n n 
C1 H33 PEE sing 319 n n 
C1 H34 PEE sing 320 n n 
O2P H35 PEE sing 321 n n 
C4 H36 PEE sing 322 n n 
C4 H37 PEE sing 323 n n 
C5 H38 PEE sing 324 n n 
C5 H39 PEE sing 325 n n 
N H40 PEE sing 326 n n 
N H41 PEE sing 327 n n 
C3 H43 PEE sing 328 n n 
C3 H44 PEE sing 329 n n 
C31 H45 PEE sing 330 n n 
C31 H46 PEE sing 331 n n 
C32 H47 PEE sing 332 n n 
C32 H48 PEE sing 333 n n 
C33 H49 PEE sing 334 n n 
C33 H50 PEE sing 335 n n 
C34 H51 PEE sing 336 n n 
C34 H52 PEE sing 337 n n 
C35 H53 PEE sing 338 n n 
C35 H54 PEE sing 339 n n 
C36 H55 PEE sing 340 n n 
C36 H56 PEE sing 341 n n 
C37 H57 PEE sing 342 n n 
C37 H58 PEE sing 343 n n 
C38 H59 PEE sing 344 n n 
C39 H60 PEE sing 345 n n 
C40 H81 PEE sing 346 n n 
C40 H61 PEE sing 347 n n 
C41 H80 PEE sing 348 n n 
C41 H62 PEE sing 349 n n 
C42 H63 PEE sing 350 n n 
C42 H64 PEE sing 351 n n 
C43 H65 PEE sing 352 n n 
C43 H66 PEE sing 353 n n 
C44 H67 PEE sing 354 n n 
C44 H68 PEE sing 355 n n 
C45 H69 PEE sing 356 n n 
C45 H70 PEE sing 357 n n 
C46 H71 PEE sing 358 n n 
C46 H72 PEE sing 359 n n 
C47 H73 PEE sing 360 n n 
C47 H74 PEE sing 361 n n 
C47 H75 PEE sing 362 n n 
#
_atom_sites.entry_id                     5GYD 
_atom_sites.fract_transf_matrix[1][1]    0.007013 
_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]    0.004565 
_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]    0.01368 
_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 PEE A 1 301 1 PEE PEE . 
F 2 PEE B 1 301 1 PEE PEE . 
G 2 PEE C 1 301 1 PEE PEE . 
H 2 PEE D 1 301 1 PEE PEE . 
I 2 PEE D 1 302 1 PEE PEE . 
#
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 C27 PEE . . . G 2 46.7 57.657 -30.315 1 94.47 ? C27 PEE 301 C 1 
HETATM 2 C C26 PEE . . . G 2 47.132 58.71 -31.332 1 100.14 ? C26 PEE 301 C 1 
HETATM 3 C C25 PEE . . . G 2 45.901 59.442 -31.861 1 95.82 ? C25 PEE 301 C 1 
HETATM 4 C C24 PEE . . . G 2 46.238 60.916 -32.076 1 99.12 ? C24 PEE 301 C 1 
HETATM 5 C C23 PEE . . . G 2 45.241 61.783 -31.309 1 97.84 ? C23 PEE 301 C 1 
HETATM 6 C C22 PEE . . . G 2 45.554 63.257 -31.555 1 105.18 ? C22 PEE 301 C 1 
HETATM 7 C C21 PEE . . . G 2 45.204 64.066 -30.309 1 110.03 ? C21 PEE 301 C 1 
HETATM 8 C C20 PEE . . . G 2 46.101 63.633 -29.151 1 119.34 ? C20 PEE 301 C 1 
HETATM 9 C C19 PEE . . . G 2 45.272 63.536 -27.873 1 138.07 ? C19 PEE 301 C 1 
HETATM 10 C C18 PEE . . . G 2 45.825 62.417 -26.991 1 149.89 ? C18 PEE 301 C 1 
HETATM 11 C C17 PEE . . . G 2 44.934 62.251 -25.761 1 150.12 ? C17 PEE 301 C 1 
HETATM 12 C C16 PEE . . . G 2 45.47 61.113 -24.895 1 143.34 ? C16 PEE 301 C 1 
HETATM 13 C C15 PEE . . . G 2 44.453 59.974 -24.865 1 140.24 ? C15 PEE 301 C 1 
HETATM 14 C C14 PEE . . . G 2 45.188 58.636 -24.86 1 143.58 ? C14 PEE 301 C 1 
HETATM 15 C C13 PEE . . . G 2 45.787 58.39 -23.477 1 143.82 ? C13 PEE 301 C 1 
HETATM 16 C C12 PEE . . . G 2 46.143 56.912 -23.333 1 150.34 ? C12 PEE 301 C 1 
HETATM 17 C C11 PEE . . . G 2 46.722 56.661 -21.944 1 159.46 ? C11 PEE 301 C 1 
HETATM 18 C C10 PEE . . . G 2 47.233 55.225 -21.857 1 163.39 ? C10 PEE 301 C 1 
HETATM 19 O O4 PEE . . . G 2 46.808 54.371 -22.559 1 161.82 ? O4 PEE 301 C 1 
HETATM 20 O O2 PEE . . . G 2 48.183 55.059 -20.926 1 171.25 ? O2 PEE 301 C 1 
HETATM 21 C C2 PEE . . . G 2 47.729 55.326 -19.564 1 178.18 ? C2 PEE 301 C 1 
HETATM 22 C C1 PEE . . . G 2 47.551 54.005 -18.82 1 191.07 ? C1 PEE 301 C 1 
HETATM 23 O O3P PEE . . . G 2 47.943 54.164 -17.486 1 204.56 ? O3P PEE 301 C 1 
HETATM 24 P P PEE . . . G 2 49.195 53.251 -16.921 1 231.65 ? P PEE 301 C 1 
HETATM 25 O O2P PEE . . . G 2 49.362 53.489 -15.439 1 232.64 ? O2P PEE 301 C 1 
HETATM 26 O O1P PEE . . . G 2 48.902 51.79 -17.166 1 230.37 ? O1P PEE 301 C 1 
HETATM 27 O O4P PEE . . . G 2 50.582 53.673 -17.706 1 205.12 ? O4P PEE 301 C 1 
HETATM 28 C C4 PEE . . . G 2 51.368 54.697 -17.167 1 177.44 ? C4 PEE 301 C 1 
HETATM 29 C C5 PEE . . . G 2 51.663 55.736 -18.248 1 158.34 ? C5 PEE 301 C 1 
HETATM 30 N N PEE . . . G 2 52.396 56.846 -17.666 1 145.1 ? N PEE 301 C 1 
HETATM 31 C C3 PEE . . . G 2 48.765 56.182 -18.841 1 168.48 ? C3 PEE 301 C 1 
HETATM 32 O O3 PEE . . . G 2 48.11 57.325 -18.235 1 153.66 ? O3 PEE 301 C 1 
HETATM 33 C C30 PEE . . . G 2 47.396 58.052 -19.089 1 135.87 ? C30 PEE 301 C 1 
HETATM 34 O O5 PEE . . . G 2 46.595 57.576 -19.821 1 141.11 ? O5 PEE 301 C 1 
HETATM 35 C C31 PEE . . . G 2 47.692 59.548 -19.051 1 117 ? C31 PEE 301 C 1 
HETATM 36 C C32 PEE . . . G 2 46.393 60.318 -18.824 1 102.58 ? C32 PEE 301 C 1 
HETATM 37 C C33 PEE . . . G 2 46.341 61.516 -19.767 1 99.79 ? C33 PEE 301 C 1 
HETATM 38 C C34 PEE . . . G 2 44.903 61.738 -20.228 1 98.69 ? C34 PEE 301 C 1 
HETATM 39 C C35 PEE . . . G 2 44.752 63.163 -20.754 1 102.99 ? C35 PEE 301 C 1 
HETATM 40 C C36 PEE . . . G 2 43.612 63.212 -21.767 1 104.61 ? C36 PEE 301 C 1 
HETATM 41 C C37 PEE . . . G 2 43.217 64.665 -22.017 1 107.97 ? C37 PEE 301 C 1 
HETATM 42 C C38 PEE . . . G 2 43.346 64.978 -23.505 1 116.29 ? C38 PEE 301 C 1 
HETATM 43 C C39 PEE . . . G 2 43.243 66.486 -23.718 1 121.45 ? C39 PEE 301 C 1 
HETATM 44 C C40 PEE . . . G 2 42.009 66.798 -24.56 1 130.5 ? C40 PEE 301 C 1 
HETATM 45 C C41 PEE . . . G 2 42.42 66.972 -26.02 1 133.61 ? C41 PEE 301 C 1 
HETATM 46 C C42 PEE . . . G 2 41.458 66.194 -26.915 1 121.14 ? C42 PEE 301 C 1 
HETATM 47 C C43 PEE . . . G 2 42.214 65.068 -27.616 1 114 ? C43 PEE 301 C 1 
HETATM 48 C C44 PEE . . . G 2 41.326 63.828 -27.689 1 103.72 ? C44 PEE 301 C 1 
HETATM 49 C C45 PEE . . . G 2 41.993 62.777 -28.574 1 103.08 ? C45 PEE 301 C 1 
HETATM 50 C C46 PEE . . . G 2 41.357 61.412 -28.31 1 102.06 ? C46 PEE 301 C 1 
HETATM 51 C C47 PEE . . . G 2 42.256 60.314 -28.876 1 91.44 ? C47 PEE 301 C 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           51 
#