data_6GAD # _model_server_result.job_id L5-Z5Y9o25juXxnJ6NiooQ _model_server_result.datetime_utc '2024-11-16 23:36:51' _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 6gad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":311}' # _entry.id 6GAD # _exptl.entry_id 6GAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.157 _entity.id 3 _entity.src_method nat _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 6GAD _cell.length_a 62.1 _cell.length_b 62.1 _cell.length_c 110.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GAD _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 -62.1 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 -31.05 -53.780178 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 301 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.343 ? covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.309 ? # _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 # _atom_sites.entry_id 6GAD _atom_sites.fract_transf_matrix[1][1] 0.016103 _atom_sites.fract_transf_matrix[1][2] 0.009297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018594 _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] 0.00905 _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 1 401 636 HOH HOH . Q 12 HOH A 2 402 611 HOH HOH . Q 12 HOH A 3 403 627 HOH HOH . Q 12 HOH A 4 404 618 HOH HOH . Q 12 HOH A 5 405 613 HOH HOH . Q 12 HOH A 6 406 616 HOH HOH . Q 12 HOH A 7 407 610 HOH HOH . Q 12 HOH A 8 408 402 HOH HOH . Q 12 HOH A 9 409 631 HOH HOH . Q 12 HOH A 10 410 617 HOH HOH . Q 12 HOH A 11 411 406 HOH HOH . Q 12 HOH A 12 412 403 HOH HOH . Q 12 HOH A 13 413 401 HOH HOH . Q 12 HOH A 14 414 620 HOH HOH . Q 12 HOH A 15 415 630 HOH HOH . Q 12 HOH A 16 416 633 HOH HOH . Q 12 HOH A 17 417 614 HOH HOH . Q 12 HOH A 18 418 609 HOH HOH . Q 12 HOH A 19 419 606 HOH HOH . Q 12 HOH A 20 420 635 HOH HOH . Q 12 HOH A 21 421 407 HOH HOH . Q 12 HOH A 22 422 612 HOH HOH . Q 12 HOH A 23 423 626 HOH HOH . Q 12 HOH A 24 424 404 HOH HOH . Q 12 HOH A 25 425 501 HOH HOH . Q 12 HOH A 26 426 619 HOH HOH . Q 12 HOH A 27 427 622 HOH HOH . Q 12 HOH A 28 428 615 HOH HOH . Q 12 HOH A 29 429 628 HOH HOH . Q 12 HOH A 30 430 624 HOH HOH . Q 12 HOH A 31 431 621 HOH HOH . Q 12 HOH A 32 432 629 HOH HOH . Q 12 HOH A 33 433 623 HOH HOH . Q 12 HOH A 34 434 634 HOH HOH . Q 12 HOH A 35 435 638 HOH HOH . Q 12 HOH A 36 436 637 HOH HOH . Q 12 HOH A 37 437 632 HOH HOH . Q 12 HOH A 38 438 625 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 -26.438 -22.124 -13.63 1 50.49 ? C1 L2P 311 A 1 HETATM 2 O O1 L2P . . . L 3 -27.313 -21.201 -12.948 1 53.97 ? O1 L2P 311 A 1 HETATM 3 C C2 L2P . . . L 3 -26.217 -21.681 -15.077 1 47.46 ? C2 L2P 311 A 1 HETATM 4 O O2 L2P . . . L 3 -26.559 -20.294 -15.201 1 55.94 ? O2 L2P 311 A 1 HETATM 5 C C3 L2P . . . L 3 -27.081 -22.506 -15.971 1 53.5 ? C3 L2P 311 A 1 HETATM 6 O O3 L2P . . . L 3 -26.87 -23.878 -15.716 1 52.29 ? O3 L2P 311 A 1 HETATM 7 C C11 L2P . . . L 3 -28.386 -21.829 -12.208 1 51.34 ? C11 L2P 311 A 1 HETATM 8 C C12 L2P . . . L 3 -28.219 -21.565 -10.714 1 53.27 ? C12 L2P 311 A 1 HETATM 9 C C13 L2P . . . L 3 -27.043 -22.356 -10.183 1 54.36 ? C13 L2P 311 A 1 HETATM 10 C C14 L2P . . . L 3 -27.184 -23.805 -10.581 1 48.47 ? C14 L2P 311 A 1 HETATM 11 C C15 L2P . . . L 3 -27.006 -22.266 -8.665 1 48.94 ? C15 L2P 311 A 1 HETATM 12 C C16 L2P . . . L 3 -25.651 -22.789 -8.169 1 52.38 ? C16 L2P 311 A 1 HETATM 13 C C17 L2P . . . L 3 -25.69 -22.931 -6.627 1 53.85 ? C17 L2P 311 A 1 HETATM 14 C C18 L2P . . . L 3 -24.422 -23.573 -6.136 1 47.17 ? C18 L2P 311 A 1 HETATM 15 C C19 L2P . . . L 3 -24.124 -24.754 -6.994 1 51.5 ? C19 L2P 311 A 1 HETATM 16 C C20 L2P . . . L 3 -24.597 -24.077 -4.681 1 49.06 ? C20 L2P 311 A 1 HETATM 17 C C21 L2P . . . L 3 -23.448 -25.043 -4.337 1 43.81 ? C21 L2P 311 A 1 HETATM 18 C C22 L2P . . . L 3 -23.556 -25.556 -2.89 1 40.61 ? C22 L2P 311 A 1 HETATM 19 C C23 L2P . . . L 3 -23.7 -24.383 -1.953 1 41.66 ? C23 L2P 311 A 1 HETATM 20 C C24 L2P . . . L 3 -22.471 -23.533 -2.047 1 43.31 ? C24 L2P 311 A 1 HETATM 21 C C25 L2P . . . L 3 -23.86 -24.868 -0.5 1 37.47 ? C25 L2P 311 A 1 HETATM 22 C C26 L2P . . . L 3 -24.624 -23.791 0.313 1 38.82 ? C26 L2P 311 A 1 HETATM 23 C C27 L2P . . . L 3 -24.07 -23.721 1.752 1 37.93 ? C27 L2P 311 A 1 HETATM 24 C C28 L2P . . . L 3 -25.223 -23.572 2.783 1 38.77 ? C28 L2P 311 A 1 HETATM 25 C C29 L2P . . . L 3 -24.733 -22.777 3.984 1 44.1 ? C29 L2P 311 A 1 HETATM 26 C C30 L2P . . . L 3 -26.383 -22.817 2.155 1 51.33 ? C30 L2P 311 A 1 HETATM 27 C C41 L2P . . . L 3 -26.059 -19.663 -16.408 1 51.43 ? C41 L2P 311 A 1 HETATM 28 C C42 L2P . . . L 3 -25.076 -18.531 -16.033 1 44.64 ? C42 L2P 311 A 1 HETATM 29 C C43 L2P . . . L 3 -25.819 -17.419 -15.281 1 47.37 ? C43 L2P 311 A 1 HETATM 30 C C44 L2P . . . L 3 -25.298 -16.085 -15.74 1 47.04 ? C44 L2P 311 A 1 HETATM 31 C C45 L2P . . . L 3 -25.609 -17.617 -13.788 1 46.92 ? C45 L2P 311 A 1 HETATM 32 C C46 L2P . . . L 3 -25.412 -16.29 -13.017 1 44.63 ? C46 L2P 311 A 1 HETATM 33 C C47 L2P . . . L 3 -26.304 -16.263 -11.748 1 46.49 ? C47 L2P 311 A 1 HETATM 34 C C48 L2P . . . L 3 -25.702 -17.118 -10.62 1 43.54 ? C48 L2P 311 A 1 HETATM 35 C C49 L2P . . . L 3 -26.539 -18.331 -10.44 1 50.43 ? C49 L2P 311 A 1 HETATM 36 C C50 L2P . . . L 3 -25.704 -16.323 -9.317 1 46.07 ? C50 L2P 311 A 1 HETATM 37 C C51 L2P . . . L 3 -25.343 -17.251 -8.133 1 46.41 ? C51 L2P 311 A 1 HETATM 38 C C52 L2P . . . L 3 -26.334 -17.025 -6.964 1 51.86 ? C52 L2P 311 A 1 HETATM 39 C C53 L2P . . . L 3 -26.265 -18.151 -5.924 1 50.39 ? C53 L2P 311 A 1 HETATM 40 C C54 L2P . . . L 3 -25.743 -19.403 -6.563 1 49.22 ? C54 L2P 311 A 1 HETATM 41 C C55 L2P . . . L 3 -27.649 -18.424 -5.358 1 52.3 ? C55 L2P 311 A 1 HETATM 42 C C56 L2P . . . L 3 -27.724 -19.858 -4.753 1 53.28 ? C56 L2P 311 A 1 HETATM 43 C C57 L2P . . . L 3 -28.906 -20.63 -5.37 1 51.53 ? C57 L2P 311 A 1 HETATM 44 C C58 L2P . . . L 3 -29.136 -21.986 -4.677 1 51.26 ? C58 L2P 311 A 1 HETATM 45 C C59 L2P . . . L 3 -29.347 -23.061 -5.718 1 50.4 ? C59 L2P 311 A 1 HETATM 46 C C60 L2P . . . L 3 -27.939 -22.388 -3.776 1 48.73 ? C60 L2P 311 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 46 #