data_5B6X # _model_server_result.job_id qBFxEWYo95h57PMv6QwQ3g _model_server_result.datetime_utc '2024-11-23 00:44:31' _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 5b6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":608}' # _entry.id 5B6X # _exptl.entry_id 5B6X _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 5B6X _cell.length_a 62.5 _cell.length_b 62.5 _cell.length_c 112 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B6X _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,R _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 -62.5 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 -31.25 -54.126588 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 300 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.311 ? covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 300 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.31 ? # _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 5B6X _atom_sites.fract_transf_matrix[1][1] 0.016 _atom_sites.fract_transf_matrix[1][2] 0.009238 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018475 _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] 0.008929 _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 1 300 300 RET RET . C 3 L2P A 1 600 600 L2P L2P . D 4 TRD A 1 601 601 TRD TRD . E 5 D10 A 1 602 602 D10 D10 . F 6 HP6 A 1 603 603 HP6 HP6 . G 7 OCT A 1 604 604 OCT OCT . H 7 OCT A 1 605 605 OCT OCT . I 8 MYS A 1 606 606 MYS MYS . J 9 UND A 1 607 607 UND UND . K 3 L2P A 1 608 608 L2P L2P . L 3 L2P A 1 609 609 L2P L2P . M 8 MYS A 1 610 610 MYS MYS . N 10 DD9 A 1 611 611 DD9 DD9 . O 11 C14 A 1 612 612 C14 C14 . P 7 OCT A 1 613 613 OCT OCT . Q 9 UND A 1 614 614 UND UND . R 12 HOH A 1 400 400 HOH HOH . R 12 HOH A 2 401 401 HOH HOH . R 12 HOH A 3 402 402 HOH HOH . R 12 HOH A 4 403 403 HOH HOH . R 12 HOH A 5 404 404 HOH HOH . R 12 HOH A 6 405 405 HOH HOH . R 12 HOH A 7 406 406 HOH HOH . R 12 HOH A 8 407 407 HOH HOH . R 12 HOH A 9 408 408 HOH HOH . R 12 HOH A 10 414 414 HOH HOH . R 12 HOH A 11 425 425 HOH HOH . R 12 HOH A 12 424 424 HOH HOH . R 12 HOH A 13 433 433 HOH HOH . R 12 HOH A 14 438 438 HOH HOH . R 12 HOH A 15 441 441 HOH HOH . R 12 HOH A 16 442 442 HOH HOH . R 12 HOH A 17 443 443 HOH HOH . R 12 HOH A 18 452 452 HOH HOH . R 12 HOH A 19 453 453 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 . . . K 3 -11.229 1.497 -18.323 1 77.15 ? C1 L2P 608 A 1 HETATM 2 O O1 L2P . . . K 3 -10.915 2.216 -17.136 1 94.48 ? O1 L2P 608 A 1 HETATM 3 C C11 L2P . . . K 3 -12.052 2.573 -16.356 1 86.51 ? C11 L2P 608 A 1 HETATM 4 C C12 L2P . . . K 3 -11.587 2.786 -14.885 1 86.66 ? C12 L2P 608 A 1 HETATM 5 C C13 L2P . . . K 3 -12.776 3.058 -13.945 1 85.06 ? C13 L2P 608 A 1 HETATM 6 C C14 L2P . . . K 3 -13.709 4.071 -14.601 1 88.09 ? C14 L2P 608 A 1 HETATM 7 C C15 L2P . . . K 3 -12.234 3.587 -12.606 1 73.91 ? C15 L2P 608 A 1 HETATM 8 C C16 L2P . . . K 3 -13.407 3.957 -11.643 1 73.25 ? C16 L2P 608 A 1 HETATM 9 C C17 L2P . . . K 3 -13.081 3.539 -10.18 1 79.89 ? C17 L2P 608 A 1 HETATM 10 C C18 L2P . . . K 3 -12.381 4.677 -9.422 1 79.18 ? C18 L2P 608 A 1 HETATM 11 C C19 L2P . . . K 3 -10.879 4.41 -9.384 1 104.05 ? C19 L2P 608 A 1 HETATM 12 C C20 L2P . . . K 3 -12.943 4.725 -7.993 1 90.77 ? C20 L2P 608 A 1 HETATM 13 C C21 L2P . . . K 3 -12.478 6.013 -7.249 1 81.94 ? C21 L2P 608 A 1 HETATM 14 C C22 L2P . . . K 3 -12.791 5.887 -5.725 1 77.45 ? C22 L2P 608 A 1 HETATM 15 C C23 L2P . . . K 3 -14.266 5.526 -5.479 1 82.98 ? C23 L2P 608 A 1 HETATM 16 C C24 L2P . . . K 3 -15.17 6.624 -6.037 1 89.84 ? C24 L2P 608 A 1 HETATM 17 C C25 L2P . . . K 3 -14.5 5.374 -3.968 1 96.34 ? C25 L2P 608 A 1 HETATM 18 C C26 L2P . . . K 3 -15.587 4.292 -3.698 1 92.29 ? C26 L2P 608 A 1 HETATM 19 C C27 L2P . . . K 3 -17.001 4.938 -3.746 1 88.82 ? C27 L2P 608 A 1 HETATM 20 C C28 L2P . . . K 3 -17.79 4.693 -2.431 1 78.71 ? C28 L2P 608 A 1 HETATM 21 C C29 L2P . . . K 3 -17.066 5.339 -1.223 1 87.7 ? C29 L2P 608 A 1 HETATM 22 C C30 L2P . . . K 3 -19.186 5.348 -2.574 1 76.74 ? C30 L2P 608 A 1 HETATM 23 H H12 L2P . . . K 3 -12.123 1.732 -18.616 1 92.59 ? H12 L2P 608 A 1 HETATM 24 H H11 L2P . . . K 3 -11.187 0.544 -18.145 1 92.59 ? H11 L2P 608 A 1 HETATM 25 H H112 L2P . . . K 3 -12.71 1.861 -16.391 1 103.81 ? H112 L2P 608 A 1 HETATM 26 H H111 L2P . . . K 3 -12.439 3.394 -16.699 1 103.81 ? H111 L2P 608 A 1 HETATM 27 H H122 L2P . . . K 3 -10.979 3.541 -14.852 1 103.99 ? H122 L2P 608 A 1 HETATM 28 H H121 L2P . . . K 3 -11.121 1.991 -14.583 1 103.99 ? H121 L2P 608 A 1 HETATM 29 H H13 L2P . . . K 3 -13.259 2.231 -13.791 1 102.08 ? H13 L2P 608 A 1 HETATM 30 H H143 L2P . . . K 3 -13.185 4.724 -15.091 1 105.7 ? H143 L2P 608 A 1 HETATM 31 H H142 L2P . . . K 3 -14.307 3.612 -15.212 1 105.7 ? H142 L2P 608 A 1 HETATM 32 H H141 L2P . . . K 3 -14.229 4.522 -13.917 1 105.7 ? H141 L2P 608 A 1 HETATM 33 H H152 L2P . . . K 3 -11.694 4.376 -12.769 1 88.7 ? H152 L2P 608 A 1 HETATM 34 H H151 L2P . . . K 3 -11.684 2.904 -12.192 1 88.7 ? H151 L2P 608 A 1 HETATM 35 H H162 L2P . . . K 3 -14.213 3.501 -11.932 1 87.9 ? H162 L2P 608 A 1 HETATM 36 H H161 L2P . . . K 3 -13.555 4.915 -11.675 1 87.9 ? H161 L2P 608 A 1 HETATM 37 H H172 L2P . . . K 3 -12.501 2.762 -10.193 1 95.87 ? H172 L2P 608 A 1 HETATM 38 H H171 L2P . . . K 3 -13.906 3.313 -9.723 1 95.87 ? H171 L2P 608 A 1 HETATM 39 H H18 L2P . . . K 3 -12.552 5.521 -9.869 1 95.02 ? H18 L2P 608 A 1 HETATM 40 H H193 L2P . . . K 3 -10.411 5.227 -9.153 1 124.86 ? H193 L2P 608 A 1 HETATM 41 H H192 L2P . . . K 3 -10.688 3.729 -8.72 1 124.86 ? H192 L2P 608 A 1 HETATM 42 H H191 L2P . . . K 3 -10.583 4.103 -10.255 1 124.86 ? H191 L2P 608 A 1 HETATM 43 H H202 L2P . . . K 3 -12.634 3.946 -7.504 1 108.92 ? H202 L2P 608 A 1 HETATM 44 H H201 L2P . . . K 3 -13.912 4.713 -8.032 1 108.92 ? H201 L2P 608 A 1 HETATM 45 H H212 L2P . . . K 3 -11.523 6.13 -7.373 1 98.32 ? H212 L2P 608 A 1 HETATM 46 H H211 L2P . . . K 3 -12.946 6.781 -7.612 1 98.32 ? H211 L2P 608 A 1 HETATM 47 H H222 L2P . . . K 3 -12.595 6.732 -5.291 1 92.94 ? H222 L2P 608 A 1 HETATM 48 H H221 L2P . . . K 3 -12.228 5.196 -5.342 1 92.94 ? H221 L2P 608 A 1 HETATM 49 H H23 L2P . . . K 3 -14.469 4.687 -5.921 1 99.57 ? H23 L2P 608 A 1 HETATM 50 H H243 L2P . . . K 3 -16.093 6.428 -5.813 1 107.81 ? H243 L2P 608 A 1 HETATM 51 H H242 L2P . . . K 3 -14.918 7.478 -5.651 1 107.81 ? H242 L2P 608 A 1 HETATM 52 H H241 L2P . . . K 3 -15.073 6.664 -7.001 1 107.81 ? H241 L2P 608 A 1 HETATM 53 H H252 L2P . . . K 3 -13.671 5.11 -3.54 1 115.61 ? H252 L2P 608 A 1 HETATM 54 H H251 L2P . . . K 3 -14.794 6.223 -3.602 1 115.61 ? H251 L2P 608 A 1 HETATM 55 H H262 L2P . . . K 3 -15.526 3.599 -4.374 1 110.75 ? H262 L2P 608 A 1 HETATM 56 H H261 L2P . . . K 3 -15.441 3.901 -2.822 1 110.75 ? H261 L2P 608 A 1 HETATM 57 H H272 L2P . . . K 3 -16.907 5.893 -3.885 1 106.58 ? H272 L2P 608 A 1 HETATM 58 H H271 L2P . . . K 3 -17.497 4.558 -4.488 1 106.58 ? H271 L2P 608 A 1 HETATM 59 H H28 L2P . . . K 3 -17.889 3.74 -2.282 1 94.46 ? H28 L2P 608 A 1 HETATM 60 H H293 L2P . . . K 3 -17.54 5.118 -0.406 1 105.24 ? H293 L2P 608 A 1 HETATM 61 H H292 L2P . . . K 3 -17.047 6.302 -1.335 1 105.24 ? H292 L2P 608 A 1 HETATM 62 H H291 L2P . . . K 3 -16.158 5.001 -1.172 1 105.24 ? H291 L2P 608 A 1 HETATM 63 H H303 L2P . . . K 3 -19.082 6.293 -2.766 1 92.09 ? H303 L2P 608 A 1 HETATM 64 H H302 L2P . . . K 3 -19.681 5.238 -1.747 1 92.09 ? H302 L2P 608 A 1 HETATM 65 H H301 L2P . . . K 3 -19.67 4.923 -3.299 1 92.09 ? H301 L2P 608 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 65 #