data_1DZE # _model_server_result.job_id cRREMSiv7G141NEiq0jM8A _model_server_result.datetime_utc '2024-11-18 00:45:28' _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 1dze # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":300}' # _entry.id 1DZE # _exptl.entry_id 1DZE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DI-PHYTANYL-GLYCEROL _entity.pdbx_number_of_molecules 2 _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 1DZE _cell.length_a 102.4 _cell.length_b 102.4 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DZE _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 PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.2 88.681001 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.4 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 GAL MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC A 400 GLC 2 n B MAN 2 B 2 MAN A 410 MAN 2 n B GAL 3 B 3 GAL A 420 GAL # 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 C C15 RET . A RET 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 325 n n C1 C2 L2P sing 326 n n C1 H12 L2P sing 327 n n C1 H11 L2P sing 328 n n O1 C11 L2P sing 329 n n C2 O2 L2P sing 330 n n C2 C3 L2P sing 331 n n C2 H2 L2P sing 332 n n O2 C41 L2P sing 333 n n C3 O3 L2P sing 334 n n C3 H32 L2P sing 335 n n C3 H31 L2P sing 336 n n O3 H3O L2P sing 337 n n C11 C12 L2P sing 338 n n C11 H112 L2P sing 339 n n C11 H111 L2P sing 340 n n C12 C13 L2P sing 341 n n C12 H122 L2P sing 342 n n C12 H121 L2P sing 343 n n C13 C14 L2P sing 344 n n C13 C15 L2P sing 345 n n C13 H13 L2P sing 346 n n C14 H143 L2P sing 347 n n C14 H142 L2P sing 348 n n C14 H141 L2P sing 349 n n C15 C16 L2P sing 350 n n C15 H152 L2P sing 351 n n C15 H151 L2P sing 352 n n C16 C17 L2P sing 353 n n C16 H162 L2P sing 354 n n C16 H161 L2P sing 355 n n C17 C18 L2P sing 356 n n C17 H172 L2P sing 357 n n C17 H171 L2P sing 358 n n C18 C19 L2P sing 359 n n C18 C20 L2P sing 360 n n C18 H18 L2P sing 361 n n C19 H193 L2P sing 362 n n C19 H192 L2P sing 363 n n C19 H191 L2P sing 364 n n C20 C21 L2P sing 365 n n C20 H202 L2P sing 366 n n C20 H201 L2P sing 367 n n C21 C22 L2P sing 368 n n C21 H212 L2P sing 369 n n C21 H211 L2P sing 370 n n C22 C23 L2P sing 371 n n C22 H222 L2P sing 372 n n C22 H221 L2P sing 373 n n C23 C24 L2P sing 374 n n C23 C25 L2P sing 375 n n C23 H23 L2P sing 376 n n C24 H243 L2P sing 377 n n C24 H242 L2P sing 378 n n C24 H241 L2P sing 379 n n C25 C26 L2P sing 380 n n C25 H252 L2P sing 381 n n C25 H251 L2P sing 382 n n C26 C27 L2P sing 383 n n C26 H262 L2P sing 384 n n C26 H261 L2P sing 385 n n C27 C28 L2P sing 386 n n C27 H272 L2P sing 387 n n C27 H271 L2P sing 388 n n C28 C29 L2P sing 389 n n C28 C30 L2P sing 390 n n C28 H28 L2P sing 391 n n C29 H293 L2P sing 392 n n C29 H292 L2P sing 393 n n C29 H291 L2P sing 394 n n C30 H303 L2P sing 395 n n C30 H302 L2P sing 396 n n C30 H301 L2P sing 397 n n C41 C42 L2P sing 398 n n C41 H412 L2P sing 399 n n C41 H411 L2P sing 400 n n C42 C43 L2P sing 401 n n C42 H422 L2P sing 402 n n C42 H421 L2P sing 403 n n C43 C44 L2P sing 404 n n C43 C45 L2P sing 405 n n C43 H43 L2P sing 406 n n C44 H443 L2P sing 407 n n C44 H442 L2P sing 408 n n C44 H441 L2P sing 409 n n C45 C46 L2P sing 410 n n C45 H452 L2P sing 411 n n C45 H451 L2P sing 412 n n C46 C47 L2P sing 413 n n C46 H462 L2P sing 414 n n C46 H461 L2P sing 415 n n C47 C48 L2P sing 416 n n C47 H472 L2P sing 417 n n C47 H471 L2P sing 418 n n C48 C49 L2P sing 419 n n C48 C50 L2P sing 420 n n C48 H48 L2P sing 421 n n C49 H493 L2P sing 422 n n C49 H492 L2P sing 423 n n C49 H491 L2P sing 424 n n C50 C51 L2P sing 425 n n C50 H502 L2P sing 426 n n C50 H501 L2P sing 427 n n C51 C52 L2P sing 428 n n C51 H512 L2P sing 429 n n C51 H511 L2P sing 430 n n C52 C53 L2P sing 431 n n C52 H522 L2P sing 432 n n C52 H521 L2P sing 433 n n C53 C54 L2P sing 434 n n C53 C55 L2P sing 435 n n C53 H53 L2P sing 436 n n C54 H543 L2P sing 437 n n C54 H542 L2P sing 438 n n C54 H541 L2P sing 439 n n C55 C56 L2P sing 440 n n C55 H552 L2P sing 441 n n C55 H551 L2P sing 442 n n C56 C57 L2P sing 443 n n C56 H562 L2P sing 444 n n C56 H561 L2P sing 445 n n C57 C58 L2P sing 446 n n C57 H572 L2P sing 447 n n C57 H571 L2P sing 448 n n C58 C59 L2P sing 449 n n C58 C60 L2P sing 450 n n C58 H58 L2P sing 451 n n C59 H593 L2P sing 452 n n C59 H592 L2P sing 453 n n C59 H591 L2P sing 454 n n C60 H603 L2P sing 455 n n C60 H602 L2P sing 456 n n C60 H601 L2P sing 457 n n # _atom_sites.entry_id 1DZE _atom_sites.fract_transf_matrix[1][1] 0.009766 _atom_sites.fract_transf_matrix[1][2] 0.005638 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011276 _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] 0.008905 _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 C 3 RET A 1 250 250 RET RET . D 4 L1P A 1 260 260 L1P L1P . E 5 L2P A 1 270 270 L2P L2P . F 6 L3P A 1 280 280 L3P L3P . G 7 L4P A 1 290 290 L4P L4P . H 5 L2P A 1 300 300 L2P L2P . I 8 HOH A 1 2001 2001 HOH HOH . I 8 HOH A 2 2002 2002 HOH HOH . I 8 HOH A 3 2003 2003 HOH HOH . I 8 HOH A 4 2004 2004 HOH HOH . I 8 HOH A 5 2005 2005 HOH HOH . I 8 HOH A 6 2006 2006 HOH HOH . I 8 HOH A 7 2007 2007 HOH HOH . I 8 HOH A 8 2008 2008 HOH HOH . I 8 HOH A 9 2009 2009 HOH HOH . I 8 HOH A 10 2010 2010 HOH HOH . I 8 HOH A 11 2011 2011 HOH HOH . I 8 HOH A 12 2012 2012 HOH HOH . I 8 HOH A 13 2013 2013 HOH HOH . I 8 HOH A 14 2014 2014 HOH HOH . I 8 HOH A 15 2015 2015 HOH HOH . I 8 HOH A 16 2016 2016 HOH HOH . I 8 HOH A 17 2017 2017 HOH HOH . I 8 HOH A 18 2018 2018 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 . . . H 5 20.817 39.037 40.244 1 61.83 ? C1 L2P 300 A 1 HETATM 2 O O1 L2P . . . H 5 21.203 39.894 39.184 1 61.15 ? O1 L2P 300 A 1 HETATM 3 C C2 L2P . . . H 5 22.063 38.3 40.719 1 59.35 ? C2 L2P 300 A 1 HETATM 4 O O2 L2P . . . H 5 21.892 36.87 40.634 1 66.43 ? O2 L2P 300 A 1 HETATM 5 C C3 L2P . . . H 5 22.359 38.709 42.161 1 63.19 ? C3 L2P 300 A 1 HETATM 6 O O3 L2P . . . H 5 22.335 40.139 42.259 1 75.81 ? O3 L2P 300 A 1 HETATM 7 C C11 L2P . . . H 5 21.457 39.337 37.904 1 57.96 ? C11 L2P 300 A 1 HETATM 8 C C12 L2P . . . H 5 20.374 39.828 36.954 1 60.04 ? C12 L2P 300 A 1 HETATM 9 C C13 L2P . . . H 5 20.475 39.079 35.632 1 58.16 ? C13 L2P 300 A 1 HETATM 10 C C14 L2P . . . H 5 20.451 37.571 35.897 1 58.79 ? C14 L2P 300 A 1 HETATM 11 C C15 L2P . . . H 5 21.778 39.466 34.928 1 54.71 ? C15 L2P 300 A 1 HETATM 12 C C16 L2P . . . H 5 21.556 39.434 33.415 1 55.74 ? C16 L2P 300 A 1 HETATM 13 C C17 L2P . . . H 5 22.348 40.565 32.756 1 60.75 ? C17 L2P 300 A 1 HETATM 14 C C41 L2P . . . H 5 20.818 36.264 39.892 1 64.1 ? C41 L2P 300 A 1 HETATM 15 C C42 L2P . . . H 5 20.448 34.932 40.561 1 50.16 ? C42 L2P 300 A 1 HETATM 16 C C43 L2P . . . H 5 18.974 34.615 40.314 1 37.19 ? C43 L2P 300 A 1 HETATM 17 C C44 L2P . . . H 5 18.342 34.045 41.584 1 40.09 ? C44 L2P 300 A 1 HETATM 18 C C45 L2P . . . H 5 18.88 33.581 39.206 1 35.18 ? C45 L2P 300 A 1 HETATM 19 C C46 L2P . . . H 5 18.489 34.308 37.932 1 46.17 ? C46 L2P 300 A 1 HETATM 20 C C47 L2P . . . H 5 18.914 33.486 36.725 1 50.81 ? C47 L2P 300 A 1 HETATM 21 C C48 L2P . . . H 5 18.015 33.868 35.555 1 61.38 ? C48 L2P 300 A 1 HETATM 22 C C49 L2P . . . H 5 17.013 32.739 35.295 1 62.2 ? C49 L2P 300 A 1 HETATM 23 C C50 L2P . . . H 5 18.863 34.155 34.298 1 74.09 ? C50 L2P 300 A 1 HETATM 24 C C51 L2P . . . H 5 19.562 32.875 33.807 1 77.12 ? C51 L2P 300 A 1 HETATM 25 C C52 L2P . . . H 5 20.448 33.188 32.586 1 71.97 ? C52 L2P 300 A 1 HETATM 26 C C53 L2P . . . H 5 21.105 31.89 32.085 1 69.85 ? C53 L2P 300 A 1 HETATM 27 C C54 L2P . . . H 5 22.023 31.34 33.17 1 75.73 ? C54 L2P 300 A 1 HETATM 28 C C55 L2P . . . H 5 21.939 32.171 30.832 1 66.41 ? C55 L2P 300 A 1 HETATM 29 C C56 L2P . . . H 5 21.392 31.342 29.666 1 60.22 ? C56 L2P 300 A 1 HETATM 30 C C57 L2P . . . H 5 22.416 30.276 29.273 1 57.11 ? C57 L2P 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #