data_6GA1
#
_model_server_result.job_id            Qrs5kIQ4l6yIEXna70V8rg 
_model_server_result.datetime_utc      '2024-11-16 18:59:08' 
_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          6ga1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":311}' 
#
_entry.id    6GA1 
#
_exptl.entry_id    6GA1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              653.157 
_entity.id                          3 
_entity.src_method                  syn 
_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            6GA1 
_cell.length_a            61.7 
_cell.length_b            61.7 
_cell.length_c            109.2 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GA1 
_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 -61.7 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 -30.85 -53.433767 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 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            NZ 
_struct_conn.ptnr1_label_comp_id            LYS 
_struct_conn.ptnr1_label_seq_id             216 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              216 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            C15 
_struct_conn.ptnr2_label_comp_id            RET 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             RET 
_struct_conn.ptnr2_auth_seq_id              301 
_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                1.332 
_struct_conn.pdbx_value_order               ? 
#
_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                     6GA1 
_atom_sites.fract_transf_matrix[1][1]    0.016207 
_atom_sites.fract_transf_matrix[1][2]    0.009357 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018715 
_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]    0.009158 
_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 36 HOH HOH . 
Q 12 HOH A 2 402 11 HOH HOH . 
Q 12 HOH A 3 403 18 HOH HOH . 
Q 12 HOH A 4 404 10 HOH HOH . 
Q 12 HOH A 5 405 16 HOH HOH . 
Q 12 HOH A 6 406 13 HOH HOH . 
Q 12 HOH A 7 407 3 HOH HOH . 
Q 12 HOH A 8 408 35 HOH HOH . 
Q 12 HOH A 9 409 17 HOH HOH . 
Q 12 HOH A 10 410 27 HOH HOH . 
Q 12 HOH A 11 411 1 HOH HOH . 
Q 12 HOH A 12 412 30 HOH HOH . 
Q 12 HOH A 13 413 20 HOH HOH . 
Q 12 HOH A 14 414 40 HOH HOH . 
Q 12 HOH A 15 415 33 HOH HOH . 
Q 12 HOH A 16 416 2 HOH HOH . 
Q 12 HOH A 17 417 43 HOH HOH . 
Q 12 HOH A 18 418 12 HOH HOH . 
Q 12 HOH A 19 419 14 HOH HOH . 
Q 12 HOH A 20 420 8 HOH HOH . 
Q 12 HOH A 21 421 22 HOH HOH . 
Q 12 HOH A 22 422 4 HOH HOH . 
Q 12 HOH A 23 423 9 HOH HOH . 
Q 12 HOH A 24 424 26 HOH HOH . 
Q 12 HOH A 25 425 6 HOH HOH . 
Q 12 HOH A 26 426 29 HOH HOH . 
Q 12 HOH A 27 427 5 HOH HOH . 
Q 12 HOH A 28 428 32 HOH HOH . 
Q 12 HOH A 29 429 19 HOH HOH . 
Q 12 HOH A 30 430 21 HOH HOH . 
Q 12 HOH A 31 431 31 HOH HOH . 
Q 12 HOH A 32 432 42 HOH HOH . 
Q 12 HOH A 33 433 7 HOH HOH . 
Q 12 HOH A 34 434 15 HOH HOH . 
Q 12 HOH A 35 435 34 HOH HOH . 
Q 12 HOH A 36 436 41 HOH HOH . 
Q 12 HOH A 37 437 38 HOH HOH . 
Q 12 HOH A 38 438 24 HOH HOH . 
Q 12 HOH A 39 439 28 HOH HOH . 
Q 12 HOH A 40 440 23 HOH HOH . 
Q 12 HOH A 41 441 39 HOH HOH . 
Q 12 HOH A 42 442 37 HOH HOH . 
Q 12 HOH A 43 443 25 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 -26.395 -22.009 -13.695 1 49.48 ? C1 L2P 311 A 1 
HETATM 2 O O1 L2P . . . L 3 -27.233 -21.081 -12.977 1 53.88 ? O1 L2P 311 A 1 
HETATM 3 C C2 L2P . . . L 3 -26.171 -21.546 -15.137 1 48.21 ? C2 L2P 311 A 1 
HETATM 4 O O2 L2P . . . L 3 -26.566 -20.175 -15.258 1 53.56 ? O2 L2P 311 A 1 
HETATM 5 C C3 L2P . . . L 3 -26.984 -22.381 -16.068 1 51.53 ? C3 L2P 311 A 1 
HETATM 6 O O3 L2P . . . L 3 -26.74 -23.752 -15.843 1 49.13 ? O3 L2P 311 A 1 
HETATM 7 C C11 L2P . . . L 3 -28.295 -21.713 -12.225 1 53.06 ? C11 L2P 311 A 1 
HETATM 8 C C12 L2P . . . L 3 -28.123 -21.45 -10.73 1 53.31 ? C12 L2P 311 A 1 
HETATM 9 C C13 L2P . . . L 3 -26.96 -22.251 -10.186 1 52.5 ? C13 L2P 311 A 1 
HETATM 10 C C14 L2P . . . L 3 -27.129 -23.704 -10.557 1 48.29 ? C14 L2P 311 A 1 
HETATM 11 C C15 L2P . . . L 3 -26.924 -22.123 -8.667 1 50.5 ? C15 L2P 311 A 1 
HETATM 12 C C16 L2P . . . L 3 -25.57 -22.617 -8.143 1 51.01 ? C16 L2P 311 A 1 
HETATM 13 C C17 L2P . . . L 3 -25.666 -22.84 -6.614 1 55.4 ? C17 L2P 311 A 1 
HETATM 14 C C18 L2P . . . L 3 -24.357 -23.361 -6.084 1 46.72 ? C18 L2P 311 A 1 
HETATM 15 C C19 L2P . . . L 3 -23.93 -24.496 -6.943 1 52.27 ? C19 L2P 311 A 1 
HETATM 16 C C20 L2P . . . L 3 -24.527 -23.887 -4.637 1 49.16 ? C20 L2P 311 A 1 
HETATM 17 C C21 L2P . . . L 3 -23.354 -24.83 -4.305 1 44.22 ? C21 L2P 311 A 1 
HETATM 18 C C22 L2P . . . L 3 -23.476 -25.393 -2.881 1 38.41 ? C22 L2P 311 A 1 
HETATM 19 C C23 L2P . . . L 3 -23.594 -24.252 -1.904 1 41.61 ? C23 L2P 311 A 1 
HETATM 20 C C24 L2P . . . L 3 -22.381 -23.379 -2.006 1 49.28 ? C24 L2P 311 A 1 
HETATM 21 C C25 L2P . . . L 3 -23.69 -24.792 -0.468 1 38.8 ? C25 L2P 311 A 1 
HETATM 22 C C26 L2P . . . L 3 -24.579 -23.825 0.353 1 35.65 ? C26 L2P 311 A 1 
HETATM 23 C C27 L2P . . . L 3 -23.915 -23.538 1.712 1 34.71 ? C27 L2P 311 A 1 
HETATM 24 C C28 L2P . . . L 3 -24.987 -23.502 2.834 1 38.8 ? C28 L2P 311 A 1 
HETATM 25 C C29 L2P . . . L 3 -24.433 -22.744 4.03 1 40.56 ? C29 L2P 311 A 1 
HETATM 26 C C30 L2P . . . L 3 -26.238 -22.799 2.336 1 48.22 ? C30 L2P 311 A 1 
HETATM 27 C C41 L2P . . . L 3 -26.031 -19.505 -16.425 1 50.16 ? C41 L2P 311 A 1 
HETATM 28 C C42 L2P . . . L 3 -24.979 -18.466 -15.978 1 41.84 ? C42 L2P 311 A 1 
HETATM 29 C C43 L2P . . . L 3 -25.675 -17.31 -15.249 1 46.27 ? C43 L2P 311 A 1 
HETATM 30 C C44 L2P . . . L 3 -25.03 -16.011 -15.65 1 46.02 ? C44 L2P 311 A 1 
HETATM 31 C C45 L2P . . . L 3 -25.564 -17.544 -13.75 1 43.6 ? C45 L2P 311 A 1 
HETATM 32 C C46 L2P . . . L 3 -25.255 -16.25 -12.96 1 43.61 ? C46 L2P 311 A 1 
HETATM 33 C C47 L2P . . . L 3 -26.115 -16.184 -11.671 1 45.7 ? C47 L2P 311 A 1 
HETATM 34 C C48 L2P . . . L 3 -25.503 -17.037 -10.548 1 41.14 ? C48 L2P 311 A 1 
HETATM 35 C C49 L2P . . . L 3 -26.342 -18.246 -10.348 1 49.27 ? C49 L2P 311 A 1 
HETATM 36 C C50 L2P . . . L 3 -25.464 -16.228 -9.253 1 44.98 ? C50 L2P 311 A 1 
HETATM 37 C C51 L2P . . . L 3 -25.138 -17.14 -8.046 1 45.75 ? C51 L2P 311 A 1 
HETATM 38 C C52 L2P . . . L 3 -26.2 -16.946 -6.937 1 48.2 ? C52 L2P 311 A 1 
HETATM 39 C C53 L2P . . . L 3 -26.18 -18.086 -5.911 1 48.35 ? C53 L2P 311 A 1 
HETATM 40 C C54 L2P . . . L 3 -25.63 -19.33 -6.545 1 51.49 ? C54 L2P 311 A 1 
HETATM 41 C C55 L2P . . . L 3 -27.59 -18.355 -5.409 1 54.79 ? C55 L2P 311 A 1 
HETATM 42 C C56 L2P . . . L 3 -27.679 -19.75 -4.721 1 51.47 ? C56 L2P 311 A 1 
HETATM 43 C C57 L2P . . . L 3 -28.756 -20.61 -5.409 1 50.92 ? C57 L2P 311 A 1 
HETATM 44 C C58 L2P . . . L 3 -28.995 -21.939 -4.669 1 49.59 ? C58 L2P 311 A 1 
HETATM 45 C C59 L2P . . . L 3 -29.198 -23.05 -5.668 1 47.09 ? C59 L2P 311 A 1 
HETATM 46 C C60 L2P . . . L 3 -27.805 -22.31 -3.746 1 47.91 ? C60 L2P 311 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           333 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#