data_8YHQ # _model_server_result.job_id 0fL4pONnU7HPmQXyCrzfcw _model_server_result.datetime_utc '2024-12-26 13:06:30' _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 8yhq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HA","auth_seq_id":404}' # _entry.id 8YHQ # _exptl.entry_id 8YHQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 834.862 _entity.id 19 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate' _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 90 _cell.entry_id 8YHQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YHQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 19 _struct_asym.id HA _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 E SG CYS 129 E CYS 159 1_555 E SG CYS 134 E CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? disulf ? disulf2 E SG CYS 148 E CYS 178 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? disulf ? disulf3 F SG CYS 29 F CYS 101 1_555 F SG CYS 51 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? disulf ? disulf4 N SG CYS 134 N CYS 164 1_555 N SG CYS 150 N CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? disulf ? disulf5 P SG CYS 29 O CYS 101 1_555 P SG CYS 51 O CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 W FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 X FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 G NE2 HIS 82 L HIS 82 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc7 G NE2 HIS 96 L HIS 96 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc8 G NE2 HIS 183 L HIS 183 1_555 GA FE HEM . L HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc9 G NE2 HIS 197 L HIS 197 1_555 IA FE HEM . L HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc10 M NE2 HIS 44 M HIS 105 1_555 KA FE HEM . M HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _chem_comp.formula 'C36 H68 O17 P2' _chem_comp.formula_weight 834.862 _chem_comp.id CN3 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CARDIOLIPIN # 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 P O11 CN3 sing 530 n n P O13 CN3 sing 531 n n O11 C1 CN3 sing 532 n n O12 P CN3 sing 533 n n O12 HO12 CN3 sing 534 n n O13 CC CN3 sing 535 n n O14 P CN3 doub 536 n n C1 C2 CN3 sing 537 n n C1 H1 CN3 sing 538 n n C1 H1A CN3 sing 539 n n C2 H2 CN3 sing 540 n n C3 C2 CN3 sing 541 n n C3 O31 CN3 sing 542 n n C3 H3 CN3 sing 543 n n C3 H3A CN3 sing 544 n n O32 C31 CN3 doub 545 n n C31 O31 CN3 sing 546 n n C31 C32 CN3 sing 547 n n C32 C33 CN3 sing 548 n n C32 H32 CN3 sing 549 n n C33 H33 CN3 sing 550 n n C33 H33A CN3 sing 551 n n O21 C2 CN3 sing 552 n n O21 C21 CN3 sing 553 n n C21 O22 CN3 doub 554 n n C21 C22 CN3 sing 555 n n C22 C23 CN3 sing 556 n n C22 H22 CN3 sing 557 n n C22 H22A CN3 sing 558 n n C23 H23 CN3 sing 559 n n C23 H23A CN3 sing 560 n n C24 C23 CN3 sing 561 n n C24 H24 CN3 sing 562 n n C24 H24A CN3 sing 563 n n C24 H24B CN3 sing 564 n n P' O3' CN3 sing 565 n n P' O1' CN3 sing 566 n n P' O4' CN3 sing 567 n n O1' C1' CN3 sing 568 n n O2' P' CN3 doub 569 n n O3' CA CN3 sing 570 n n O4' HO4' CN3 sing 571 n n C1' C2' CN3 sing 572 n n C1' H1' CN3 sing 573 n n C1' "H1'A" CN3 sing 574 n n C2' O51 CN3 sing 575 n n C2' H2' CN3 sing 576 n n C3' C2' CN3 sing 577 n n C3' O41 CN3 sing 578 n n C3' H3' CN3 sing 579 n n C3' "H3'A" CN3 sing 580 n n O42 C41 CN3 doub 581 n n C41 O41 CN3 sing 582 n n C41 C42 CN3 sing 583 n n C42 H42 CN3 sing 584 n n C42 H42A CN3 sing 585 n n C43 C42 CN3 sing 586 n n C43 H43 CN3 sing 587 n n C43 H43A CN3 sing 588 n n C44 C43 CN3 sing 589 n n C44 H44 CN3 sing 590 n n C44 H44A CN3 sing 591 n n C45 C44 CN3 sing 592 n n C45 C46 CN3 sing 593 n n C45 H45 CN3 sing 594 n n C45 H45A CN3 sing 595 n n C46 H46 CN3 sing 596 n n C46 H46A CN3 sing 597 n n C47 C46 CN3 sing 598 n n C47 C48 CN3 sing 599 n n C47 H47 CN3 sing 600 n n C47 H47A CN3 sing 601 n n C48 C49 CN3 sing 602 n n C48 H48 CN3 sing 603 n n C48 H48A CN3 sing 604 n n C49 H49 CN3 sing 605 n n C49 H49A CN3 sing 606 n n C4A C49 CN3 sing 607 n n C4A C4B CN3 sing 608 n n C4A H4A CN3 sing 609 n n C4A H4AA CN3 sing 610 n n C4B H4B CN3 sing 611 n n C4B H4BA CN3 sing 612 n n C4B H4BB CN3 sing 613 n n O51 C51 CN3 sing 614 n n C51 O52 CN3 doub 615 n n C51 C52 CN3 sing 616 n n C52 C53 CN3 sing 617 n n C52 H52 CN3 sing 618 n n C52 H52A CN3 sing 619 n n C53 C54 CN3 sing 620 n n C53 H53 CN3 sing 621 n n C53 H53A CN3 sing 622 n n C54 H54 CN3 sing 623 n n C54 H54A CN3 sing 624 n n C55 C54 CN3 sing 625 n n C55 H55 CN3 sing 626 n n C55 H55A CN3 sing 627 n n C56 C55 CN3 sing 628 n n C56 C57 CN3 sing 629 n n C56 H56 CN3 sing 630 n n C56 H56A CN3 sing 631 n n C57 H57 CN3 sing 632 n n C57 H57A CN3 sing 633 n n C58 C57 CN3 sing 634 n n C58 C59 CN3 sing 635 n n C58 H58 CN3 sing 636 n n C58 H58A CN3 sing 637 n n C59 H59 CN3 sing 638 n n C59 H59A CN3 sing 639 n n C59 H59B CN3 sing 640 n n CA HA CN3 sing 641 n n CA HAA CN3 sing 642 n n CB CA CN3 sing 643 n n CB OA CN3 sing 644 n n CB HB CN3 sing 645 n n OA HOA CN3 sing 646 n n CC CB CN3 sing 647 n n CC HC CN3 sing 648 n n CC HCA CN3 sing 649 n n C32 H67 CN3 sing 650 n n C33 H68 CN3 sing 651 n n # _atom_sites.entry_id 8YHQ _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 U 11 6PH C 1 401 402 6PH 6PH . V 12 9PE C 1 402 403 9PE 9PE . W 13 HEM C 1 403 404 HEM HEM . X 13 HEM C 1 404 405 HEM HEM . Y 14 8PE C 1 405 406 8PE 8PE . Z 15 CN5 C 1 406 407 CN5 CN5 . AA 16 UQ6 C 1 407 408 UQ6 UQ6 . BA 17 A1D6K C 1 408 401 A1D6K A1D . CA 13 HEM D 1 401 402 HEM HEM . DA 18 7PH D 1 402 401 7PH 7PH . EA 16 UQ6 L 1 401 402 UQ6 UQ6 . FA 12 9PE L 1 402 403 9PE 9PE . GA 13 HEM L 1 403 404 HEM HEM . HA 19 CN3 L 1 404 405 CN3 CN3 . IA 13 HEM L 1 405 406 HEM HEM . JA 17 A1D6K L 1 406 401 A1D6K A1D . KA 13 HEM M 1 401 401 HEM HEM . LA 11 6PH N 1 401 401 6PH 6PH . MA 18 7PH N 1 402 402 7PH 7PH . NA 14 8PE Q 1 101 101 8PE 8PE . # 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 P P CN3 . . . HA 19 156.501 161.335 130.516 1 22.06 ? P CN3 404 L 1 HETATM 2 O O11 CN3 . . . HA 19 156.101 162.221 129.195 1 22.06 ? O11 CN3 404 L 1 HETATM 3 O O12 CN3 . . . HA 19 155.322 160.492 130.922 1 22.06 ? O12 CN3 404 L 1 HETATM 4 O O13 CN3 . . . HA 19 157.776 160.372 130.132 1 22.06 ? O13 CN3 404 L 1 HETATM 5 O O14 CN3 . . . HA 19 156.886 162.245 131.652 1 22.06 ? O14 CN3 404 L 1 HETATM 6 C C1 CN3 . . . HA 19 155.591 161.516 128.106 1 22.06 ? C1 CN3 404 L 1 HETATM 7 C C2 CN3 . . . HA 19 156.583 161.544 126.958 1 22.06 ? C2 CN3 404 L 1 HETATM 8 C C3 CN3 . . . HA 19 156.044 160.621 125.877 1 22.06 ? C3 CN3 404 L 1 HETATM 9 O O31 CN3 . . . HA 19 156.851 159.491 125.783 1 22.06 ? O31 CN3 404 L 1 HETATM 10 O O32 CN3 . . . HA 19 155.257 158.442 124.586 1 22.06 ? O32 CN3 404 L 1 HETATM 11 C C31 CN3 . . . HA 19 156.223 158.359 125.262 1 22.06 ? C31 CN3 404 L 1 HETATM 12 C C32 CN3 . . . HA 19 156.804 156.997 125.6 1 22.06 ? C32 CN3 404 L 1 HETATM 13 C C33 CN3 . . . HA 19 156.704 156.05 124.416 1 22.06 ? C33 CN3 404 L 1 HETATM 14 O O21 CN3 . . . HA 19 156.68 162.861 126.495 1 22.06 ? O21 CN3 404 L 1 HETATM 15 O O22 CN3 . . . HA 19 158.561 162.345 125.378 1 22.06 ? O22 CN3 404 L 1 HETATM 16 C C21 CN3 . . . HA 19 157.784 163.183 125.696 1 22.06 ? C21 CN3 404 L 1 HETATM 17 C C22 CN3 . . . HA 19 157.954 164.639 125.251 1 22.06 ? C22 CN3 404 L 1 HETATM 18 C C23 CN3 . . . HA 19 158.591 164.766 123.861 1 22.06 ? C23 CN3 404 L 1 HETATM 19 C C24 CN3 . . . HA 19 157.533 165.072 122.803 1 22.06 ? C24 CN3 404 L 1 HETATM 20 P P' CN3 . . . HA 19 160.027 155.088 130.606 1 22.06 ? P' CN3 404 L 1 HETATM 21 O O1' CN3 . . . HA 19 159.912 154.633 129.038 1 22.06 ? O1' CN3 404 L 1 HETATM 22 O O2' CN3 . . . HA 19 158.734 154.786 131.31 1 22.06 ? O2' CN3 404 L 1 HETATM 23 O O3' CN3 . . . HA 19 160.339 156.701 130.654 1 22.06 ? O3' CN3 404 L 1 HETATM 24 O O4' CN3 . . . HA 19 161.156 154.332 131.25 1 22.06 ? O4' CN3 404 L 1 HETATM 25 C C1' CN3 . . . HA 19 160.918 155.095 128.191 1 22.06 ? C1' CN3 404 L 1 HETATM 26 C C2' CN3 . . . HA 19 161.354 153.975 127.26 1 22.06 ? C2' CN3 404 L 1 HETATM 27 C C3' CN3 . . . HA 19 160.288 153.719 126.208 1 22.06 ? C3' CN3 404 L 1 HETATM 28 O O41 CN3 . . . HA 19 159.84 152.405 126.351 1 22.06 ? O41 CN3 404 L 1 HETATM 29 O O42 CN3 . . . HA 19 157.851 151.821 125.502 1 22.06 ? O42 CN3 404 L 1 HETATM 30 C C41 CN3 . . . HA 19 159.008 151.973 125.32 1 22.06 ? C41 CN3 404 L 1 HETATM 31 C C42 CN3 . . . HA 19 159.609 151.721 123.946 1 22.06 ? C42 CN3 404 L 1 HETATM 32 C C43 CN3 . . . HA 19 158.942 152.666 122.956 1 22.06 ? C43 CN3 404 L 1 HETATM 33 C C44 CN3 . . . HA 19 157.698 151.984 122.402 1 22.06 ? C44 CN3 404 L 1 HETATM 34 C C45 CN3 . . . HA 19 156.612 153.005 122.063 1 22.06 ? C45 CN3 404 L 1 HETATM 35 C C46 CN3 . . . HA 19 155.971 152.612 120.743 1 22.06 ? C46 CN3 404 L 1 HETATM 36 C C47 CN3 . . . HA 19 154.578 153.213 120.636 1 22.06 ? C47 CN3 404 L 1 HETATM 37 C C48 CN3 . . . HA 19 153.921 153.106 119.254 1 22.06 ? C48 CN3 404 L 1 HETATM 38 C C49 CN3 . . . HA 19 154.332 151.968 118.304 1 22.06 ? C49 CN3 404 L 1 HETATM 39 C C4A CN3 . . . HA 19 154.973 152.562 117.052 1 22.06 ? C4A CN3 404 L 1 HETATM 40 C C4B CN3 . . . HA 19 155.677 151.479 116.234 1 22.06 ? C4B CN3 404 L 1 HETATM 41 O O51 CN3 . . . HA 19 162.542 154.377 126.645 1 22.06 ? O51 CN3 404 L 1 HETATM 42 O O52 CN3 . . . HA 19 163.889 152.961 127.81 1 22.06 ? O52 CN3 404 L 1 HETATM 43 C C51 CN3 . . . HA 19 163.675 153.569 126.813 1 22.06 ? C51 CN3 404 L 1 HETATM 44 C C52 CN3 . . . HA 19 164.665 153.497 125.663 1 22.06 ? C52 CN3 404 L 1 HETATM 45 C C53 CN3 . . . HA 19 163.988 154.067 124.421 1 22.06 ? C53 CN3 404 L 1 HETATM 46 C C54 CN3 . . . HA 19 164.864 153.841 123.193 1 22.06 ? C54 CN3 404 L 1 HETATM 47 C C55 CN3 . . . HA 19 164.631 152.435 122.64 1 22.06 ? C55 CN3 404 L 1 HETATM 48 C C56 CN3 . . . HA 19 163.371 152.344 121.776 1 22.06 ? C56 CN3 404 L 1 HETATM 49 C C57 CN3 . . . HA 19 163.573 151.327 120.652 1 22.06 ? C57 CN3 404 L 1 HETATM 50 C C58 CN3 . . . HA 19 162.273 150.587 120.364 1 22.06 ? C58 CN3 404 L 1 HETATM 51 C C59 CN3 . . . HA 19 162.402 149.854 119.03 1 22.06 ? C59 CN3 404 L 1 HETATM 52 C CA CN3 . . . HA 19 159.291 157.573 130.955 1 22.06 ? CA CN3 404 L 1 HETATM 53 C CB CN3 . . . HA 19 159.675 159.012 130.626 1 22.06 ? CB CN3 404 L 1 HETATM 54 O OA CN3 . . . HA 19 160.91 159.31 131.207 1 22.06 ? OA CN3 404 L 1 HETATM 55 C CC CN3 . . . HA 19 158.615 159.965 131.166 1 22.06 ? CC CN3 404 L 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 55 #