data_1QM8 # _model_server_result.job_id CI1JJxgtEL4oyJhkmBLFPw _model_server_result.datetime_utc '2024-11-06 01:53:53' _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 1qm8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":290}' # _entry.id 1QM8 # _exptl.entry_id 1QM8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 807.215 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL _entity.pdbx_number_of_molecules 1 _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 1QM8 _cell.length_a 102.1 _cell.length_b 102.1 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QM8 _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 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 _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 51.05 88.421194 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.1 0 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _chem_comp.formula 'C46 H95 O8 P' _chem_comp.formula_weight 807.215 _chem_comp.id L4P _chem_comp.mon_nstd_flag . _chem_comp.name 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-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 C2 L4P sing 610 n n C1 O1 L4P sing 611 n n C1 H12 L4P sing 612 n n C1 H11 L4P sing 613 n n C2 C3 L4P sing 614 n n C2 O2 L4P sing 615 n n C2 H2 L4P sing 616 n n C3 O3 L4P sing 617 n n C3 H32 L4P sing 618 n n C3 H31 L4P sing 619 n n C4 C5 L4P sing 620 n n C4 O4 L4P sing 621 n n C4 H42 L4P sing 622 n n C4 H41 L4P sing 623 n n C5 C6 L4P sing 624 n n C5 O5 L4P sing 625 n n C5 H5 L4P sing 626 n n C6 O6 L4P sing 627 n n C6 H62 L4P sing 628 n n C6 H61 L4P sing 629 n n O1 C11 L4P sing 630 n n O2 C41 L4P sing 631 n n O3 P1 L4P sing 632 n n O4 P1 L4P sing 633 n n O5 H5O L4P sing 634 n n O6 H6O L4P sing 635 n n O1P P1 L4P doub 636 n n O2P P1 L4P sing 637 n n O2P HOP2 L4P sing 638 n n C11 C12 L4P sing 639 n n C11 H112 L4P sing 640 n n C11 H111 L4P sing 641 n n C12 C13 L4P sing 642 n n C12 H122 L4P sing 643 n n C12 H121 L4P sing 644 n n C13 C14 L4P sing 645 n n C13 C15 L4P sing 646 n n C13 H13 L4P sing 647 n n C14 H143 L4P sing 648 n n C14 H142 L4P sing 649 n n C14 H141 L4P sing 650 n n C15 C16 L4P sing 651 n n C15 H152 L4P sing 652 n n C15 H151 L4P sing 653 n n C16 C17 L4P sing 654 n n C16 H162 L4P sing 655 n n C16 H161 L4P sing 656 n n C17 C18 L4P sing 657 n n C17 H172 L4P sing 658 n n C17 H171 L4P sing 659 n n C18 C19 L4P sing 660 n n C18 C20 L4P sing 661 n n C18 H18 L4P sing 662 n n C19 H193 L4P sing 663 n n C19 H192 L4P sing 664 n n C19 H191 L4P sing 665 n n C20 C21 L4P sing 666 n n C20 H202 L4P sing 667 n n C20 H201 L4P sing 668 n n C21 C22 L4P sing 669 n n C21 H212 L4P sing 670 n n C21 H211 L4P sing 671 n n C22 C23 L4P sing 672 n n C22 H222 L4P sing 673 n n C22 H221 L4P sing 674 n n C23 C24 L4P sing 675 n n C23 C25 L4P sing 676 n n C23 H23 L4P sing 677 n n C24 H243 L4P sing 678 n n C24 H242 L4P sing 679 n n C24 H241 L4P sing 680 n n C25 C26 L4P sing 681 n n C25 H252 L4P sing 682 n n C25 H251 L4P sing 683 n n C26 C27 L4P sing 684 n n C26 H262 L4P sing 685 n n C26 H261 L4P sing 686 n n C27 C28 L4P sing 687 n n C27 H272 L4P sing 688 n n C27 H271 L4P sing 689 n n C28 C29 L4P sing 690 n n C28 C30 L4P sing 691 n n C28 H28 L4P sing 692 n n C29 H293 L4P sing 693 n n C29 H292 L4P sing 694 n n C29 H291 L4P sing 695 n n C30 H303 L4P sing 696 n n C30 H302 L4P sing 697 n n C30 H301 L4P sing 698 n n C41 C42 L4P sing 699 n n C41 H412 L4P sing 700 n n C41 H411 L4P sing 701 n n C42 C43 L4P sing 702 n n C42 H422 L4P sing 703 n n C42 H421 L4P sing 704 n n C43 C44 L4P sing 705 n n C43 C45 L4P sing 706 n n C43 H43 L4P sing 707 n n C44 H443 L4P sing 708 n n C44 H442 L4P sing 709 n n C44 H441 L4P sing 710 n n C45 C46 L4P sing 711 n n C45 H452 L4P sing 712 n n C45 H451 L4P sing 713 n n C46 C47 L4P sing 714 n n C46 H462 L4P sing 715 n n C46 H461 L4P sing 716 n n C47 C48 L4P sing 717 n n C47 H472 L4P sing 718 n n C47 H471 L4P sing 719 n n C48 C49 L4P sing 720 n n C48 C50 L4P sing 721 n n C48 H48 L4P sing 722 n n C49 H493 L4P sing 723 n n C49 H492 L4P sing 724 n n C49 H491 L4P sing 725 n n C50 C51 L4P sing 726 n n C50 H502 L4P sing 727 n n C50 H501 L4P sing 728 n n C51 C52 L4P sing 729 n n C51 H512 L4P sing 730 n n C51 H511 L4P sing 731 n n C52 C53 L4P sing 732 n n C52 H522 L4P sing 733 n n C52 H521 L4P sing 734 n n C53 C54 L4P sing 735 n n C53 C55 L4P sing 736 n n C53 H53 L4P sing 737 n n C54 H543 L4P sing 738 n n C54 H542 L4P sing 739 n n C54 H541 L4P sing 740 n n C55 C56 L4P sing 741 n n C55 H552 L4P sing 742 n n C55 H551 L4P sing 743 n n C56 C57 L4P sing 744 n n C56 H562 L4P sing 745 n n C56 H561 L4P sing 746 n n C57 C58 L4P sing 747 n n C57 H572 L4P sing 748 n n C57 H571 L4P sing 749 n n C58 C59 L4P sing 750 n n C58 C60 L4P sing 751 n n C58 H58 L4P sing 752 n n C59 H593 L4P sing 753 n n C59 H592 L4P sing 754 n n C59 H591 L4P sing 755 n n C60 H603 L4P sing 756 n n C60 H602 L4P sing 757 n n C60 H601 L4P sing 758 n n # _atom_sites.entry_id 1QM8 _atom_sites.fract_transf_matrix[1][1] 0.009794 _atom_sites.fract_transf_matrix[1][2] 0.005655 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011309 _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 . I 8 HOH A 19 2019 2019 HOH HOH . I 8 HOH A 20 2020 2020 HOH HOH . I 8 HOH A 21 2021 2021 HOH HOH . I 8 HOH A 22 2022 2022 HOH HOH . I 8 HOH A 23 2023 2023 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 L4P . . . G 7 37.875 5.249 12.187 1 88.72 ? C1 L4P 290 A 1 HETATM 2 C C2 L4P . . . G 7 37.751 4.697 10.733 1 91.89 ? C2 L4P 290 A 1 HETATM 3 C C3 L4P . . . G 7 37.351 5.841 9.791 1 93.99 ? C3 L4P 290 A 1 HETATM 4 C C4 L4P . . . G 7 34.121 4.966 6.714 1 100 ? C4 L4P 290 A 1 HETATM 5 C C5 L4P . . . G 7 33.306 6.123 6.136 1 100 ? C5 L4P 290 A 1 HETATM 6 C C6 L4P . . . G 7 31.985 5.588 5.582 1 99.83 ? C6 L4P 290 A 1 HETATM 7 O O1 L4P . . . G 7 38.478 4.286 13.077 1 84.75 ? O1 L4P 290 A 1 HETATM 8 O O2 L4P . . . G 7 38.99 4.156 10.236 1 93.58 ? O2 L4P 290 A 1 HETATM 9 O O3 L4P . . . G 7 36.506 5.311 8.751 1 100 ? O3 L4P 290 A 1 HETATM 10 O O4 L4P . . . G 7 35.487 5.085 6.284 1 100 ? O4 L4P 290 A 1 HETATM 11 O O5 L4P . . . G 7 33.036 7.061 7.176 1 100 ? O5 L4P 290 A 1 HETATM 12 O O1P L4P . . . G 7 37.938 5.654 6.649 1 100 ? O1P L4P 290 A 1 HETATM 13 O O2P L4P . . . G 7 36.246 7.319 7.169 1 100 ? O2P L4P 290 A 1 HETATM 14 P P1 L4P . . . G 7 36.572 5.869 7.206 1 100 ? P1 L4P 290 A 1 HETATM 15 C C11 L4P . . . G 7 38.741 4.559 14.454 1 82.04 ? C11 L4P 290 A 1 HETATM 16 C C12 L4P . . . G 7 39.1 3.217 15.125 1 81.11 ? C12 L4P 290 A 1 HETATM 17 C C13 L4P . . . G 7 39.271 3.387 16.656 1 79.6 ? C13 L4P 290 A 1 HETATM 18 C C14 L4P . . . G 7 38.027 4.052 17.283 1 78.74 ? C14 L4P 290 A 1 HETATM 19 C C15 L4P . . . G 7 40.549 4.184 16.984 1 76.23 ? C15 L4P 290 A 1 HETATM 20 C C16 L4P . . . G 7 41.643 3.197 17.423 1 77 ? C16 L4P 290 A 1 HETATM 21 C C17 L4P . . . G 7 42.725 3.954 18.187 1 77.32 ? C17 L4P 290 A 1 HETATM 22 C C18 L4P . . . G 7 43.515 3.007 19.122 1 80.36 ? C18 L4P 290 A 1 HETATM 23 C C19 L4P . . . G 7 44.681 2.356 18.346 1 76.69 ? C19 L4P 290 A 1 HETATM 24 C C20 L4P . . . G 7 42.602 1.931 19.759 1 80.5 ? C20 L4P 290 A 1 HETATM 25 C C21 L4P . . . G 7 43.449 0.785 20.361 1 80.69 ? C21 L4P 290 A 1 HETATM 26 C C22 L4P . . . G 7 44.692 1.348 21.089 1 80.76 ? C22 L4P 290 A 1 HETATM 27 C C23 L4P . . . G 7 45.169 0.339 22.115 1 79.6 ? C23 L4P 290 A 1 HETATM 28 C C24 L4P . . . G 7 44.394 0.517 23.374 1 76.63 ? C24 L4P 290 A 1 HETATM 29 C C25 L4P . . . G 7 46.653 0.508 22.388 1 80.55 ? C25 L4P 290 A 1 HETATM 30 C C26 L4P . . . G 7 46.925 -0.098 23.763 1 85.56 ? C26 L4P 290 A 1 HETATM 31 C C27 L4P . . . G 7 46.508 -1.607 23.764 1 88.17 ? C27 L4P 290 A 1 HETATM 32 C C28 L4P . . . G 7 47.748 -2.418 24.139 1 91.52 ? C28 L4P 290 A 1 HETATM 33 C C29 L4P . . . G 7 47.918 -2.515 25.66 1 89.79 ? C29 L4P 290 A 1 HETATM 34 C C30 L4P . . . G 7 47.817 -3.769 23.451 1 88.26 ? C30 L4P 290 A 1 HETATM 35 C C41 L4P . . . G 7 39.921 3.433 11.065 1 94.43 ? C41 L4P 290 A 1 HETATM 36 C C42 L4P . . . G 7 41.312 3.443 10.383 1 92.53 ? C42 L4P 290 A 1 HETATM 37 C C43 L4P . . . G 7 42.391 2.896 11.351 1 90.47 ? C43 L4P 290 A 1 HETATM 38 C C44 L4P . . . G 7 41.826 1.682 12.14 1 93.53 ? C44 L4P 290 A 1 HETATM 39 C C45 L4P . . . G 7 42.825 4.009 12.326 1 87.52 ? C45 L4P 290 A 1 HETATM 40 C C46 L4P . . . G 7 43.856 3.458 13.316 1 83.33 ? C46 L4P 290 A 1 HETATM 41 C C47 L4P . . . G 7 45.162 4.219 13.144 1 86.61 ? C47 L4P 290 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 41 #