data_1X0I
#
_model_server_result.job_id            cvsGVAp3-EcUZZBD05Yg0Q 
_model_server_result.datetime_utc      '2024-11-02 21:22:50' 
_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          1x0i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":280}' 
#
_entry.id    1X0I 
#
_exptl.entry_id    1X0I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              885.179 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" 
_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            1X0I 
_cell.length_a            102.64 
_cell.length_b            102.64 
_cell.length_c            109.04 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1X0I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        177 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 6 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.64 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.32 88.888847 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 F N N 
? 4 G 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             1 
_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            C 
_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             1 
_struct_conn.ptnr2_auth_comp_id             RET 
_struct_conn.ptnr2_auth_seq_id              250 
_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                1.356 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C46 H94 O11 P2 -2' 
_chem_comp.formula_weight    885.179 
_chem_comp.id                L3P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 L3P sing 272 n n 
C1 O1 L3P sing 273 n n 
C1 H12 L3P sing 274 n n 
C1 H11 L3P sing 275 n n 
C2 C3 L3P sing 276 n n 
C2 O2 L3P sing 277 n n 
C2 H2 L3P sing 278 n n 
C3 O3 L3P sing 279 n n 
C3 H32 L3P sing 280 n n 
C3 H31 L3P sing 281 n n 
C4 C5 L3P sing 282 n n 
C4 O4 L3P sing 283 n n 
C4 H42 L3P sing 284 n n 
C4 H41 L3P sing 285 n n 
C5 C6 L3P sing 286 n n 
C5 O5 L3P sing 287 n n 
C5 H5 L3P sing 288 n n 
C6 O6 L3P sing 289 n n 
C6 H62 L3P sing 290 n n 
C6 H61 L3P sing 291 n n 
O1 C11 L3P sing 292 n n 
O2 C41 L3P sing 293 n n 
O3 P1 L3P sing 294 n n 
O4 P1 L3P sing 295 n n 
O5 H5O L3P sing 296 n n 
O6 P2 L3P sing 297 n n 
O1P P1 L3P doub 298 n n 
O2P P1 L3P sing 299 n n 
O4P P2 L3P doub 300 n n 
O5P P2 L3P sing 301 n n 
O6P P2 L3P sing 302 n n 
O6P HOP6 L3P sing 303 n n 
C11 C12 L3P sing 304 n n 
C11 H112 L3P sing 305 n n 
C11 H111 L3P sing 306 n n 
C12 C13 L3P sing 307 n n 
C12 H122 L3P sing 308 n n 
C12 H121 L3P sing 309 n n 
C13 C14 L3P sing 310 n n 
C13 C15 L3P sing 311 n n 
C13 H13 L3P sing 312 n n 
C14 H143 L3P sing 313 n n 
C14 H142 L3P sing 314 n n 
C14 H141 L3P sing 315 n n 
C15 C16 L3P sing 316 n n 
C15 H152 L3P sing 317 n n 
C15 H151 L3P sing 318 n n 
C16 C17 L3P sing 319 n n 
C16 H162 L3P sing 320 n n 
C16 H161 L3P sing 321 n n 
C17 C18 L3P sing 322 n n 
C17 H172 L3P sing 323 n n 
C17 H171 L3P sing 324 n n 
C18 C19 L3P sing 325 n n 
C18 C20 L3P sing 326 n n 
C18 H18 L3P sing 327 n n 
C19 H193 L3P sing 328 n n 
C19 H192 L3P sing 329 n n 
C19 H191 L3P sing 330 n n 
C20 C21 L3P sing 331 n n 
C20 H202 L3P sing 332 n n 
C20 H201 L3P sing 333 n n 
C21 C22 L3P sing 334 n n 
C21 H212 L3P sing 335 n n 
C21 H211 L3P sing 336 n n 
C22 C23 L3P sing 337 n n 
C22 H222 L3P sing 338 n n 
C22 H221 L3P sing 339 n n 
C23 C24 L3P sing 340 n n 
C23 C25 L3P sing 341 n n 
C23 H23 L3P sing 342 n n 
C24 H243 L3P sing 343 n n 
C24 H242 L3P sing 344 n n 
C24 H241 L3P sing 345 n n 
C25 C26 L3P sing 346 n n 
C25 H252 L3P sing 347 n n 
C25 H251 L3P sing 348 n n 
C26 C27 L3P sing 349 n n 
C26 H262 L3P sing 350 n n 
C26 H261 L3P sing 351 n n 
C27 C28 L3P sing 352 n n 
C27 H272 L3P sing 353 n n 
C27 H271 L3P sing 354 n n 
C28 C29 L3P sing 355 n n 
C28 C30 L3P sing 356 n n 
C28 H28 L3P sing 357 n n 
C29 H293 L3P sing 358 n n 
C29 H292 L3P sing 359 n n 
C29 H291 L3P sing 360 n n 
C30 H303 L3P sing 361 n n 
C30 H302 L3P sing 362 n n 
C30 H301 L3P sing 363 n n 
C41 C42 L3P sing 364 n n 
C41 H412 L3P sing 365 n n 
C41 H411 L3P sing 366 n n 
C42 C43 L3P sing 367 n n 
C42 H422 L3P sing 368 n n 
C42 H421 L3P sing 369 n n 
C43 C44 L3P sing 370 n n 
C43 C45 L3P sing 371 n n 
C43 H43 L3P sing 372 n n 
C44 H443 L3P sing 373 n n 
C44 H442 L3P sing 374 n n 
C44 H441 L3P sing 375 n n 
C45 C46 L3P sing 376 n n 
C45 H452 L3P sing 377 n n 
C45 H451 L3P sing 378 n n 
C46 C47 L3P sing 379 n n 
C46 H462 L3P sing 380 n n 
C46 H461 L3P sing 381 n n 
C47 C48 L3P sing 382 n n 
C47 H472 L3P sing 383 n n 
C47 H471 L3P sing 384 n n 
C48 C49 L3P sing 385 n n 
C48 C50 L3P sing 386 n n 
C48 H48 L3P sing 387 n n 
C49 H493 L3P sing 388 n n 
C49 H492 L3P sing 389 n n 
C49 H491 L3P sing 390 n n 
C50 C51 L3P sing 391 n n 
C50 H502 L3P sing 392 n n 
C50 H501 L3P sing 393 n n 
C51 C52 L3P sing 394 n n 
C51 H512 L3P sing 395 n n 
C51 H511 L3P sing 396 n n 
C52 C53 L3P sing 397 n n 
C52 H522 L3P sing 398 n n 
C52 H521 L3P sing 399 n n 
C53 C54 L3P sing 400 n n 
C53 C55 L3P sing 401 n n 
C53 H53 L3P sing 402 n n 
C54 H543 L3P sing 403 n n 
C54 H542 L3P sing 404 n n 
C54 H541 L3P sing 405 n n 
C55 C56 L3P sing 406 n n 
C55 H552 L3P sing 407 n n 
C55 H551 L3P sing 408 n n 
C56 C57 L3P sing 409 n n 
C56 H562 L3P sing 410 n n 
C56 H561 L3P sing 411 n n 
C57 C58 L3P sing 412 n n 
C57 H572 L3P sing 413 n n 
C57 H571 L3P sing 414 n n 
C58 C59 L3P sing 415 n n 
C58 C60 L3P sing 416 n n 
C58 H58 L3P sing 417 n n 
C59 H593 L3P sing 418 n n 
C59 H592 L3P sing 419 n n 
C59 H591 L3P sing 420 n n 
C60 H603 L3P sing 421 n n 
C60 H602 L3P sing 422 n n 
C60 H601 L3P sing 423 n n 
#
_atom_sites.entry_id                     1X0I 
_atom_sites.fract_transf_matrix[1][1]    0.009743 
_atom_sites.fract_transf_matrix[1][2]    0.005625 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01125 
_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]    0.009171 
_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 SO4 1 1 700 700 SO4 SO4 . 
C 3 RET 1 1 250 250 RET RET . 
D 4 L3P 1 1 260 260 L3P L3P . 
E 5 L2P 1 1 270 270 L2P L2P . 
F 4 L3P 1 1 280 280 L3P L3P . 
G 4 L3P 1 1 290 290 L3P L3P . 
H 6 HOH 1 1 601 601 HOH HOH . 
H 6 HOH 1 2 602 602 HOH HOH . 
H 6 HOH 1 3 603 603 HOH HOH . 
H 6 HOH 1 4 605 605 HOH HOH . 
H 6 HOH 1 5 606 606 HOH HOH . 
H 6 HOH 1 6 607 607 HOH HOH . 
H 6 HOH 1 7 608 608 HOH HOH . 
H 6 HOH 1 8 609 609 HOH HOH . 
H 6 HOH 1 9 610 610 HOH HOH . 
H 6 HOH 1 10 611 611 HOH HOH . 
H 6 HOH 1 11 612 612 HOH HOH . 
H 6 HOH 1 12 613 613 HOH HOH . 
H 6 HOH 1 13 621 621 HOH HOH . 
H 6 HOH 1 14 622 622 HOH HOH . 
H 6 HOH 1 15 623 623 HOH HOH . 
H 6 HOH 1 16 624 624 HOH HOH . 
H 6 HOH 1 17 625 625 HOH HOH . 
H 6 HOH 1 18 626 626 HOH HOH . 
H 6 HOH 1 19 627 627 HOH HOH . 
H 6 HOH 1 20 628 628 HOH HOH . 
H 6 HOH 1 21 631 631 HOH HOH . 
H 6 HOH 1 22 632 632 HOH HOH . 
H 6 HOH 1 23 633 633 HOH HOH . 
H 6 HOH 1 24 634 634 HOH HOH . 
H 6 HOH 1 25 635 635 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 C11 L3P . . . F 4 54.635 4.214 10.847 1 83.35 ? C11 L3P 280 1 1 
HETATM 2 C C12 L3P . . . F 4 53.954 3.488 12.101 1 84.25 ? C12 L3P 280 1 1 
HETATM 3 C C13 L3P . . . F 4 54.818 3.688 13.454 1 85.04 ? C13 L3P 280 1 1 
HETATM 4 C C14 L3P . . . F 4 56.269 3.09 13.278 1 85.17 ? C14 L3P 280 1 1 
HETATM 5 C C15 L3P . . . F 4 54.08 2.954 14.635 1 85.19 ? C15 L3P 280 1 1 
HETATM 6 C C16 L3P . . . F 4 53.62 3.975 15.717 1 84.92 ? C16 L3P 280 1 1 
HETATM 7 C C17 L3P . . . F 4 52.089 3.897 15.883 1 86.85 ? C17 L3P 280 1 1 
HETATM 8 C C18 L3P . . . F 4 51.66 3.044 17.234 1 87.69 ? C18 L3P 280 1 1 
HETATM 9 C C19 L3P . . . F 4 51.281 1.563 16.888 1 88.09 ? C19 L3P 280 1 1 
HETATM 10 C C20 L3P . . . F 4 50.411 3.826 17.929 1 87.91 ? C20 L3P 280 1 1 
HETATM 11 C C21 L3P . . . F 4 50.744 4.402 19.347 1 87.16 ? C21 L3P 280 1 1 
HETATM 12 C C22 L3P . . . F 4 49.445 5.112 19.879 1 87.14 ? C22 L3P 280 1 1 
HETATM 13 C C23 L3P . . . F 4 48.733 4.255 21 1 87.15 ? C23 L3P 280 1 1 
HETATM 14 C C24 L3P . . . F 4 47.46 3.68 20.358 1 88.18 ? C24 L3P 280 1 1 
HETATM 15 C C25 L3P . . . F 4 48.371 5.181 22.278 1 86.28 ? C25 L3P 280 1 1 
HETATM 16 C C26 L3P . . . F 4 47.664 4.352 23.426 1 85.88 ? C26 L3P 280 1 1 
HETATM 17 C C27 L3P . . . F 4 48.755 3.846 24.496 1 86.64 ? C27 L3P 280 1 1 
HETATM 18 C C28 L3P . . . F 4 48.068 2.979 25.657 1 85.75 ? C28 L3P 280 1 1 
HETATM 19 C C29 L3P . . . F 4 48.793 1.705 25.817 1 84.84 ? C29 L3P 280 1 1 
HETATM 20 C C30 L3P . . . F 4 48.097 3.744 26.997 1 85.94 ? C30 L3P 280 1 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           580 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#