data_1X0I # _model_server_result.job_id rYMjGlXN3A_zY4w2tLc42g _model_server_result.datetime_utc '2024-11-23 23:57:18' _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":"D","auth_seq_id":260}' # _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 C1 L3P . . . D 4 36.933 38.816 38.145 1 72.55 ? C1 L3P 260 1 1 HETATM 2 C C2 L3P . . . D 4 36.751 40.049 39.061 1 79.81 ? C2 L3P 260 1 1 HETATM 3 C C3 L3P . . . D 4 38.028 40.243 39.92 1 81.51 ? C3 L3P 260 1 1 HETATM 4 O O1 L3P . . . D 4 35.774 38.567 37.273 1 66.01 ? O1 L3P 260 1 1 HETATM 5 O O2 L3P . . . D 4 36.487 41.275 38.213 1 84.35 ? O2 L3P 260 1 1 HETATM 6 O O3 L3P . . . D 4 37.578 40.882 41.213 1 85.66 ? O3 L3P 260 1 1 HETATM 7 O O4 L3P . . . D 4 38.394 43.403 41.334 0.5 85.94 ? O4 L3P 260 1 1 HETATM 8 O O1P L3P . . . D 4 39.644 41.722 42.505 0.5 86.26 ? O1P L3P 260 1 1 HETATM 9 O O2P L3P . . . D 4 37.418 42.508 43.514 0.5 85.7 ? O2P L3P 260 1 1 HETATM 10 P P1 L3P . . . D 4 38.299 42.135 42.136 0.5 86.16 ? P1 L3P 260 1 1 HETATM 11 C C11 L3P . . . D 4 35.917 37.88 35.988 1 60.68 ? C11 L3P 260 1 1 HETATM 12 C C12 L3P . . . D 4 36.069 38.94 34.89 1 62.73 ? C12 L3P 260 1 1 HETATM 13 C C13 L3P . . . D 4 36.288 38.427 33.478 1 64.27 ? C13 L3P 260 1 1 HETATM 14 C C14 L3P . . . D 4 37.571 37.612 33.401 1 65.7 ? C14 L3P 260 1 1 HETATM 15 C C15 L3P . . . D 4 36.351 39.65 32.56 1 67.29 ? C15 L3P 260 1 1 HETATM 16 C C16 L3P . . . D 4 36.571 39.343 31.109 1 68.39 ? C16 L3P 260 1 1 HETATM 17 C C17 L3P . . . D 4 36.544 40.654 30.348 1 71.23 ? C17 L3P 260 1 1 HETATM 18 C C18 L3P . . . D 4 36.352 40.548 28.801 1 72.82 ? C18 L3P 260 1 1 HETATM 19 C C19 L3P . . . D 4 37.525 39.839 28.122 1 73 ? C19 L3P 260 1 1 HETATM 20 C C20 L3P . . . D 4 36.274 41.932 28.16 1 75.32 ? C20 L3P 260 1 1 HETATM 21 C C21 L3P . . . D 4 34.826 42.294 27.821 1 77.88 ? C21 L3P 260 1 1 HETATM 22 C C22 L3P . . . D 4 34.545 42.155 26.3 1 78.33 ? C22 L3P 260 1 1 HETATM 23 C C23 L3P . . . D 4 33.634 40.921 25.998 1 78.9 ? C23 L3P 260 1 1 HETATM 24 C C24 L3P . . . D 4 34.411 39.828 25.267 1 77.82 ? C24 L3P 260 1 1 HETATM 25 C C25 L3P . . . D 4 32.448 41.312 25.116 1 78.26 ? C25 L3P 260 1 1 HETATM 26 C C26 L3P . . . D 4 31.19 40.651 25.699 1 76.47 ? C26 L3P 260 1 1 HETATM 27 C C27 L3P . . . D 4 30.402 39.902 24.596 1 74.82 ? C27 L3P 260 1 1 HETATM 28 C C28 L3P . . . D 4 29.133 40.695 24.202 1 74.02 ? C28 L3P 260 1 1 HETATM 29 C C29 L3P . . . D 4 29.336 41.324 22.835 1 74.69 ? C29 L3P 260 1 1 HETATM 30 C C30 L3P . . . D 4 27.908 39.769 24.126 1 73.81 ? C30 L3P 260 1 1 HETATM 31 C C41 L3P . . . D 4 36.254 42.698 38.7 1 86.67 ? C41 L3P 260 1 1 HETATM 32 C C42 L3P . . . D 4 34.816 42.99 39.327 1 87.44 ? C42 L3P 260 1 1 HETATM 33 C C43 L3P . . . D 4 34.522 44.534 39.31 1 88.43 ? C43 L3P 260 1 1 HETATM 34 C C44 L3P . . . D 4 34.38 45.085 40.732 1 88.01 ? C44 L3P 260 1 1 HETATM 35 C C45 L3P . . . D 4 33.226 44.806 38.553 1 89.07 ? C45 L3P 260 1 1 HETATM 36 C C46 L3P . . . D 4 33.593 45.02 37.094 1 88.89 ? C46 L3P 260 1 1 HETATM 37 C C47 L3P . . . D 4 32.384 45.287 36.264 1 88.9 ? C47 L3P 260 1 1 HETATM 38 C C48 L3P . . . D 4 32.769 45.49 34.807 1 89.29 ? C48 L3P 260 1 1 HETATM 39 C C49 L3P . . . D 4 33.755 46.643 34.515 1 88.91 ? C49 L3P 260 1 1 HETATM 40 C C50 L3P . . . D 4 31.525 45.729 34.05 1 90.08 ? C50 L3P 260 1 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 576 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #