data_6GA9
#
_model_server_result.job_id            0shZWZYiJbSQVCrR8kIM7A 
_model_server_result.datetime_utc      '2024-11-05 04:12:25' 
_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          6ga9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":311}' 
#
_entry.id    6GA9 
#
_exptl.entry_id    6GA9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              653.157 
_entity.id                          3 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            2,3-DI-PHYTANYL-GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_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         120 
_cell.entry_id            6GA9 
_cell.length_a            62.1 
_cell.length_b            62.1 
_cell.length_c            110.5 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GA9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -62.1 0 0 
3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -31.05 -53.780178 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 K 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
covale ? covale1 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.343 ? 
covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.304 ? 
#
_chem_comp.formula           'C43 H88 O3' 
_chem_comp.formula_weight    653.157 
_chem_comp.id                L2P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2,3-DI-PHYTANYL-GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL 
#
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
C1 O1 L2P sing 263 n n 
C1 C2 L2P sing 264 n n 
C1 H12 L2P sing 265 n n 
C1 H11 L2P sing 266 n n 
O1 C11 L2P sing 267 n n 
C2 O2 L2P sing 268 n n 
C2 C3 L2P sing 269 n n 
C2 H2 L2P sing 270 n n 
O2 C41 L2P sing 271 n n 
C3 O3 L2P sing 272 n n 
C3 H32 L2P sing 273 n n 
C3 H31 L2P sing 274 n n 
O3 H3O L2P sing 275 n n 
C11 C12 L2P sing 276 n n 
C11 H112 L2P sing 277 n n 
C11 H111 L2P sing 278 n n 
C12 C13 L2P sing 279 n n 
C12 H122 L2P sing 280 n n 
C12 H121 L2P sing 281 n n 
C13 C14 L2P sing 282 n n 
C13 C15 L2P sing 283 n n 
C13 H13 L2P sing 284 n n 
C14 H143 L2P sing 285 n n 
C14 H142 L2P sing 286 n n 
C14 H141 L2P sing 287 n n 
C15 C16 L2P sing 288 n n 
C15 H152 L2P sing 289 n n 
C15 H151 L2P sing 290 n n 
C16 C17 L2P sing 291 n n 
C16 H162 L2P sing 292 n n 
C16 H161 L2P sing 293 n n 
C17 C18 L2P sing 294 n n 
C17 H172 L2P sing 295 n n 
C17 H171 L2P sing 296 n n 
C18 C19 L2P sing 297 n n 
C18 C20 L2P sing 298 n n 
C18 H18 L2P sing 299 n n 
C19 H193 L2P sing 300 n n 
C19 H192 L2P sing 301 n n 
C19 H191 L2P sing 302 n n 
C20 C21 L2P sing 303 n n 
C20 H202 L2P sing 304 n n 
C20 H201 L2P sing 305 n n 
C21 C22 L2P sing 306 n n 
C21 H212 L2P sing 307 n n 
C21 H211 L2P sing 308 n n 
C22 C23 L2P sing 309 n n 
C22 H222 L2P sing 310 n n 
C22 H221 L2P sing 311 n n 
C23 C24 L2P sing 312 n n 
C23 C25 L2P sing 313 n n 
C23 H23 L2P sing 314 n n 
C24 H243 L2P sing 315 n n 
C24 H242 L2P sing 316 n n 
C24 H241 L2P sing 317 n n 
C25 C26 L2P sing 318 n n 
C25 H252 L2P sing 319 n n 
C25 H251 L2P sing 320 n n 
C26 C27 L2P sing 321 n n 
C26 H262 L2P sing 322 n n 
C26 H261 L2P sing 323 n n 
C27 C28 L2P sing 324 n n 
C27 H272 L2P sing 325 n n 
C27 H271 L2P sing 326 n n 
C28 C29 L2P sing 327 n n 
C28 C30 L2P sing 328 n n 
C28 H28 L2P sing 329 n n 
C29 H293 L2P sing 330 n n 
C29 H292 L2P sing 331 n n 
C29 H291 L2P sing 332 n n 
C30 H303 L2P sing 333 n n 
C30 H302 L2P sing 334 n n 
C30 H301 L2P sing 335 n n 
C41 C42 L2P sing 336 n n 
C41 H412 L2P sing 337 n n 
C41 H411 L2P sing 338 n n 
C42 C43 L2P sing 339 n n 
C42 H422 L2P sing 340 n n 
C42 H421 L2P sing 341 n n 
C43 C44 L2P sing 342 n n 
C43 C45 L2P sing 343 n n 
C43 H43 L2P sing 344 n n 
C44 H443 L2P sing 345 n n 
C44 H442 L2P sing 346 n n 
C44 H441 L2P sing 347 n n 
C45 C46 L2P sing 348 n n 
C45 H452 L2P sing 349 n n 
C45 H451 L2P sing 350 n n 
C46 C47 L2P sing 351 n n 
C46 H462 L2P sing 352 n n 
C46 H461 L2P sing 353 n n 
C47 C48 L2P sing 354 n n 
C47 H472 L2P sing 355 n n 
C47 H471 L2P sing 356 n n 
C48 C49 L2P sing 357 n n 
C48 C50 L2P sing 358 n n 
C48 H48 L2P sing 359 n n 
C49 H493 L2P sing 360 n n 
C49 H492 L2P sing 361 n n 
C49 H491 L2P sing 362 n n 
C50 C51 L2P sing 363 n n 
C50 H502 L2P sing 364 n n 
C50 H501 L2P sing 365 n n 
C51 C52 L2P sing 366 n n 
C51 H512 L2P sing 367 n n 
C51 H511 L2P sing 368 n n 
C52 C53 L2P sing 369 n n 
C52 H522 L2P sing 370 n n 
C52 H521 L2P sing 371 n n 
C53 C54 L2P sing 372 n n 
C53 C55 L2P sing 373 n n 
C53 H53 L2P sing 374 n n 
C54 H543 L2P sing 375 n n 
C54 H542 L2P sing 376 n n 
C54 H541 L2P sing 377 n n 
C55 C56 L2P sing 378 n n 
C55 H552 L2P sing 379 n n 
C55 H551 L2P sing 380 n n 
C56 C57 L2P sing 381 n n 
C56 H562 L2P sing 382 n n 
C56 H561 L2P sing 383 n n 
C57 C58 L2P sing 384 n n 
C57 H572 L2P sing 385 n n 
C57 H571 L2P sing 386 n n 
C58 C59 L2P sing 387 n n 
C58 C60 L2P sing 388 n n 
C58 H58 L2P sing 389 n n 
C59 H593 L2P sing 390 n n 
C59 H592 L2P sing 391 n n 
C59 H591 L2P sing 392 n n 
C60 H603 L2P sing 393 n n 
C60 H602 L2P sing 394 n n 
C60 H601 L2P sing 395 n n 
#
_atom_sites.entry_id                     6GA9 
_atom_sites.fract_transf_matrix[1][1]    0.016103 
_atom_sites.fract_transf_matrix[1][2]    0.009297 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018594 
_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]    0.00905 
_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
B 2 RET A 1 301 300 RET RET . 
C 3 L2P A 1 302 600 L2P L2P . 
D 4 TRD A 1 303 601 TRD TRD . 
E 5 D10 A 1 304 602 D10 D10 . 
F 6 HP6 A 1 305 603 HP6 HP6 . 
G 7 OCT A 1 306 604 OCT OCT . 
H 7 OCT A 1 307 605 OCT OCT . 
I 8 MYS A 1 308 606 MYS MYS . 
J 9 UND A 1 309 607 UND UND . 
K 3 L2P A 1 310 608 L2P L2P . 
L 3 L2P A 1 311 609 L2P L2P . 
M 10 DD9 A 1 312 611 DD9 DD9 . 
N 11 C14 A 1 313 612 C14 C14 . 
O 7 OCT A 1 314 613 OCT OCT . 
P 9 UND A 1 315 614 UND UND . 
Q 12 HOH A 1 401 636 HOH HOH . 
Q 12 HOH A 2 402 611 HOH HOH . 
Q 12 HOH A 3 403 627 HOH HOH . 
Q 12 HOH A 4 404 618 HOH HOH . 
Q 12 HOH A 5 405 613 HOH HOH . 
Q 12 HOH A 6 406 616 HOH HOH . 
Q 12 HOH A 7 407 610 HOH HOH . 
Q 12 HOH A 8 408 402 HOH HOH . 
Q 12 HOH A 9 409 631 HOH HOH . 
Q 12 HOH A 10 410 617 HOH HOH . 
Q 12 HOH A 11 411 406 HOH HOH . 
Q 12 HOH A 12 412 403 HOH HOH . 
Q 12 HOH A 13 413 401 HOH HOH . 
Q 12 HOH A 14 414 620 HOH HOH . 
Q 12 HOH A 15 415 630 HOH HOH . 
Q 12 HOH A 16 416 633 HOH HOH . 
Q 12 HOH A 17 417 614 HOH HOH . 
Q 12 HOH A 18 418 609 HOH HOH . 
Q 12 HOH A 19 419 606 HOH HOH . 
Q 12 HOH A 20 420 635 HOH HOH . 
Q 12 HOH A 21 421 407 HOH HOH . 
Q 12 HOH A 22 422 612 HOH HOH . 
Q 12 HOH A 23 423 626 HOH HOH . 
Q 12 HOH A 24 424 404 HOH HOH . 
Q 12 HOH A 25 425 501 HOH HOH . 
Q 12 HOH A 26 426 619 HOH HOH . 
Q 12 HOH A 27 427 622 HOH HOH . 
Q 12 HOH A 28 428 615 HOH HOH . 
Q 12 HOH A 29 429 628 HOH HOH . 
Q 12 HOH A 30 430 624 HOH HOH . 
Q 12 HOH A 31 431 621 HOH HOH . 
Q 12 HOH A 32 432 629 HOH HOH . 
Q 12 HOH A 33 433 623 HOH HOH . 
Q 12 HOH A 34 434 638 HOH HOH . 
Q 12 HOH A 35 435 634 HOH HOH . 
Q 12 HOH A 36 436 637 HOH HOH . 
Q 12 HOH A 37 437 632 HOH HOH . 
Q 12 HOH A 38 438 625 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 C1 L2P . . . L 3 -26.438 -22.124 -13.63 1 48.95 ? C1 L2P 311 A 1 
HETATM 2 O O1 L2P . . . L 3 -27.313 -21.201 -12.948 1 52.43 ? O1 L2P 311 A 1 
HETATM 3 C C2 L2P . . . L 3 -26.217 -21.681 -15.077 1 45.92 ? C2 L2P 311 A 1 
HETATM 4 O O2 L2P . . . L 3 -26.559 -20.294 -15.201 1 54.4 ? O2 L2P 311 A 1 
HETATM 5 C C3 L2P . . . L 3 -27.081 -22.506 -15.971 1 51.96 ? C3 L2P 311 A 1 
HETATM 6 O O3 L2P . . . L 3 -26.87 -23.878 -15.716 1 50.75 ? O3 L2P 311 A 1 
HETATM 7 C C11 L2P . . . L 3 -28.386 -21.829 -12.208 1 49.8 ? C11 L2P 311 A 1 
HETATM 8 C C12 L2P . . . L 3 -28.219 -21.565 -10.714 1 51.73 ? C12 L2P 311 A 1 
HETATM 9 C C13 L2P . . . L 3 -27.043 -22.356 -10.183 1 52.82 ? C13 L2P 311 A 1 
HETATM 10 C C14 L2P . . . L 3 -27.184 -23.805 -10.581 1 46.93 ? C14 L2P 311 A 1 
HETATM 11 C C15 L2P . . . L 3 -27.006 -22.266 -8.665 1 47.4 ? C15 L2P 311 A 1 
HETATM 12 C C16 L2P . . . L 3 -25.651 -22.789 -8.169 1 50.84 ? C16 L2P 311 A 1 
HETATM 13 C C17 L2P . . . L 3 -25.69 -22.931 -6.627 1 52.31 ? C17 L2P 311 A 1 
HETATM 14 C C18 L2P . . . L 3 -24.422 -23.573 -6.136 1 45.63 ? C18 L2P 311 A 1 
HETATM 15 C C19 L2P . . . L 3 -24.124 -24.754 -6.994 1 49.96 ? C19 L2P 311 A 1 
HETATM 16 C C20 L2P . . . L 3 -24.597 -24.077 -4.681 1 47.52 ? C20 L2P 311 A 1 
HETATM 17 C C21 L2P . . . L 3 -23.448 -25.043 -4.337 1 42.27 ? C21 L2P 311 A 1 
HETATM 18 C C22 L2P . . . L 3 -23.556 -25.556 -2.89 1 39.07 ? C22 L2P 311 A 1 
HETATM 19 C C23 L2P . . . L 3 -23.7 -24.383 -1.953 1 40.12 ? C23 L2P 311 A 1 
HETATM 20 C C24 L2P . . . L 3 -22.471 -23.533 -2.047 1 41.77 ? C24 L2P 311 A 1 
HETATM 21 C C25 L2P . . . L 3 -23.86 -24.868 -0.5 1 35.93 ? C25 L2P 311 A 1 
HETATM 22 C C26 L2P . . . L 3 -24.624 -23.791 0.313 1 37.28 ? C26 L2P 311 A 1 
HETATM 23 C C27 L2P . . . L 3 -24.07 -23.721 1.752 1 36.39 ? C27 L2P 311 A 1 
HETATM 24 C C28 L2P . . . L 3 -25.223 -23.572 2.783 1 37.23 ? C28 L2P 311 A 1 
HETATM 25 C C29 L2P . . . L 3 -24.733 -22.777 3.984 1 42.56 ? C29 L2P 311 A 1 
HETATM 26 C C30 L2P . . . L 3 -26.383 -22.817 2.155 1 49.79 ? C30 L2P 311 A 1 
HETATM 27 C C41 L2P . . . L 3 -26.059 -19.663 -16.408 1 49.89 ? C41 L2P 311 A 1 
HETATM 28 C C42 L2P . . . L 3 -25.076 -18.531 -16.033 1 43.1 ? C42 L2P 311 A 1 
HETATM 29 C C43 L2P . . . L 3 -25.819 -17.419 -15.281 1 45.83 ? C43 L2P 311 A 1 
HETATM 30 C C44 L2P . . . L 3 -25.298 -16.085 -15.74 1 45.5 ? C44 L2P 311 A 1 
HETATM 31 C C45 L2P . . . L 3 -25.609 -17.617 -13.788 1 45.38 ? C45 L2P 311 A 1 
HETATM 32 C C46 L2P . . . L 3 -25.412 -16.29 -13.017 1 43.09 ? C46 L2P 311 A 1 
HETATM 33 C C47 L2P . . . L 3 -26.304 -16.263 -11.748 1 44.95 ? C47 L2P 311 A 1 
HETATM 34 C C48 L2P . . . L 3 -25.702 -17.118 -10.62 1 42 ? C48 L2P 311 A 1 
HETATM 35 C C49 L2P . . . L 3 -26.539 -18.331 -10.44 1 48.89 ? C49 L2P 311 A 1 
HETATM 36 C C50 L2P . . . L 3 -25.704 -16.323 -9.317 1 44.53 ? C50 L2P 311 A 1 
HETATM 37 C C51 L2P . . . L 3 -25.343 -17.251 -8.133 1 44.87 ? C51 L2P 311 A 1 
HETATM 38 C C52 L2P . . . L 3 -26.334 -17.025 -6.964 1 50.32 ? C52 L2P 311 A 1 
HETATM 39 C C53 L2P . . . L 3 -26.265 -18.151 -5.924 1 48.85 ? C53 L2P 311 A 1 
HETATM 40 C C54 L2P . . . L 3 -25.743 -19.403 -6.563 1 47.68 ? C54 L2P 311 A 1 
HETATM 41 C C55 L2P . . . L 3 -27.649 -18.424 -5.358 1 50.76 ? C55 L2P 311 A 1 
HETATM 42 C C56 L2P . . . L 3 -27.724 -19.858 -4.753 1 51.74 ? C56 L2P 311 A 1 
HETATM 43 C C57 L2P . . . L 3 -28.906 -20.63 -5.37 1 49.99 ? C57 L2P 311 A 1 
HETATM 44 C C58 L2P . . . L 3 -29.136 -21.986 -4.677 1 49.72 ? C58 L2P 311 A 1 
HETATM 45 C C59 L2P . . . L 3 -29.347 -23.061 -5.718 1 48.86 ? C59 L2P 311 A 1 
HETATM 46 C C60 L2P . . . L 3 -27.939 -22.388 -3.776 1 47.19 ? C60 L2P 311 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           46 
#