data_8YHQ
#
_model_server_result.job_id            lG182r_VGE7b9ceNzOlQPQ 
_model_server_result.datetime_utc      '2024-12-26 12:49:40' 
_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":"Z","auth_seq_id":406}' 
#
_entry.id    8YHQ 
#
_exptl.entry_id    8YHQ 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              634.631 
_entity.id                          15 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate' 
_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                      15 
_struct_asym.id                             Z 
_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           'C26 H52 O13 P2' 
_chem_comp.formula_weight    634.631 
_chem_comp.id                CN5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate' 
_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
O14 P CN5 doub 652 n n 
O12 P CN5 sing 653 n n 
P O11 CN5 sing 654 n n 
P O13 CN5 sing 655 n n 
O11 C1 CN5 sing 656 n n 
O12 HO12 CN5 sing 657 n n 
O13 CC CN5 sing 658 n n 
C2 C1 CN5 sing 659 n n 
C1 H1 CN5 sing 660 n n 
C1 H1A CN5 sing 661 n n 
C2 C3 CN5 sing 662 n n 
C2 H2 CN5 sing 663 n n 
C2 H2A CN5 sing 664 n n 
O31 C3 CN5 sing 665 n n 
C3 H3 CN5 sing 666 n n 
C3 H3A CN5 sing 667 n n 
O31 C31 CN5 sing 668 n n 
C31 O32 CN5 doub 669 n n 
C32 C31 CN5 sing 670 n n 
C33 C32 CN5 sing 671 n n 
C32 H32 CN5 sing 672 n n 
C32 H32A CN5 sing 673 n n 
C33 C34 CN5 sing 674 n n 
C33 H33 CN5 sing 675 n n 
C33 H33A CN5 sing 676 n n 
C35 C34 CN5 sing 677 n n 
C34 H34 CN5 sing 678 n n 
C34 H34A CN5 sing 679 n n 
C35 C36 CN5 sing 680 n n 
C35 H35 CN5 sing 681 n n 
C35 H35A CN5 sing 682 n n 
C37 C36 CN5 sing 683 n n 
C36 H36 CN5 sing 684 n n 
C36 H36A CN5 sing 685 n n 
C37 C38 CN5 sing 686 n n 
C37 H37 CN5 sing 687 n n 
C37 H37A CN5 sing 688 n n 
C39 C38 CN5 sing 689 n n 
C38 H38 CN5 sing 690 n n 
C38 H38A CN5 sing 691 n n 
C39 C3A CN5 sing 692 n n 
C39 H39 CN5 sing 693 n n 
C39 H39A CN5 sing 694 n n 
C3B C3A CN5 sing 695 n n 
C3A H3AA CN5 sing 696 n n 
C3A H3AB CN5 sing 697 n n 
C3C C3B CN5 sing 698 n n 
C3B H3B CN5 sing 699 n n 
C3B H3BA CN5 sing 700 n n 
C3D C3C CN5 sing 701 n n 
C3C H3C CN5 sing 702 n n 
C3C H3CA CN5 sing 703 n n 
C3E C3D CN5 sing 704 n n 
C3D H3D CN5 sing 705 n n 
C3D H3DA CN5 sing 706 n n 
C3F C3E CN5 sing 707 n n 
C3E H3E CN5 sing 708 n n 
C3E H3EA CN5 sing 709 n n 
C3F H3F CN5 sing 710 n n 
C3F H3FA CN5 sing 711 n n 
C3F H3FB CN5 sing 712 n n 
O3' P' CN5 sing 713 n n 
O1' P' CN5 sing 714 n n 
P' O2' CN5 doub 715 n n 
P' O4' CN5 sing 716 n n 
C1' O1' CN5 sing 717 n n 
CA O3' CN5 sing 718 n n 
O4' HO4' CN5 sing 719 n n 
C2' C1' CN5 sing 720 n n 
C1' H1' CN5 sing 721 n n 
C1' "H1'A" CN5 sing 722 n n 
C2' C3' CN5 sing 723 n n 
C2' H2' CN5 sing 724 n n 
C2' "H2'A" CN5 sing 725 n n 
O41 C3' CN5 sing 726 n n 
C3' H3' CN5 sing 727 n n 
C3' "H3'A" CN5 sing 728 n n 
C41 O41 CN5 sing 729 n n 
O42 C41 CN5 doub 730 n n 
C42 C41 CN5 sing 731 n n 
C42 H42 CN5 sing 732 n n 
C42 H42A CN5 sing 733 n n 
C42 H42B CN5 sing 734 n n 
CB CA CN5 sing 735 n n 
CA HA CN5 sing 736 n n 
CA HAA CN5 sing 737 n n 
OA CB CN5 sing 738 n n 
CC CB CN5 sing 739 n n 
CB HB CN5 sing 740 n n 
OA HOA CN5 sing 741 n n 
CC HC CN5 sing 742 n n 
CC HCA CN5 sing 743 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 CN5 . . . Z 15 136.015 136.534 131.312 1 41.29 ? P CN5 406 C 1 
HETATM 2 O O11 CN5 . . . Z 15 136.99 137.263 130.265 1 41.29 ? O11 CN5 406 C 1 
HETATM 3 O O12 CN5 . . . Z 15 136.677 136.259 132.627 1 41.29 ? O12 CN5 406 C 1 
HETATM 4 O O13 CN5 . . . Z 15 135.634 135.137 130.618 1 41.29 ? O13 CN5 406 C 1 
HETATM 5 O O14 CN5 . . . Z 15 134.73 137.31 131.271 1 41.29 ? O14 CN5 406 C 1 
HETATM 6 C C1 CN5 . . . Z 15 138.365 137.547 130.623 1 41.29 ? C1 CN5 406 C 1 
HETATM 7 C C2 CN5 . . . Z 15 138.504 139.031 130.833 1 41.29 ? C2 CN5 406 C 1 
HETATM 8 C C3 CN5 . . . Z 15 138.329 139.885 129.638 1 41.29 ? C3 CN5 406 C 1 
HETATM 9 O O31 CN5 . . . Z 15 136.913 140.115 129.558 1 41.29 ? O31 CN5 406 C 1 
HETATM 10 O O32 CN5 . . . Z 15 135.406 141.445 130.497 1 41.29 ? O32 CN5 406 C 1 
HETATM 11 C C31 CN5 . . . Z 15 136.465 141.293 129.956 1 41.29 ? C31 CN5 406 C 1 
HETATM 12 C C32 CN5 . . . Z 15 137.416 142.377 129.617 1 41.29 ? C32 CN5 406 C 1 
HETATM 13 C C33 CN5 . . . Z 15 136.761 143.697 129.615 1 41.29 ? C33 CN5 406 C 1 
HETATM 14 C C34 CN5 . . . Z 15 136.389 144.131 128.222 1 41.29 ? C34 CN5 406 C 1 
HETATM 15 C C35 CN5 . . . Z 15 137.381 145.069 127.602 1 41.29 ? C35 CN5 406 C 1 
HETATM 16 C C36 CN5 . . . Z 15 137.106 146.513 127.888 1 41.29 ? C36 CN5 406 C 1 
HETATM 17 C C37 CN5 . . . Z 15 136.265 147.208 126.838 1 41.29 ? C37 CN5 406 C 1 
HETATM 18 C C38 CN5 . . . Z 15 136.296 148.716 126.903 1 41.29 ? C38 CN5 406 C 1 
HETATM 19 C C39 CN5 . . . Z 15 137.666 149.323 126.734 1 41.29 ? C39 CN5 406 C 1 
HETATM 20 C C3A CN5 . . . Z 15 137.682 150.837 126.739 1 41.29 ? C3A CN5 406 C 1 
HETATM 21 C C3B CN5 . . . Z 15 138.639 151.456 127.739 1 41.29 ? C3B CN5 406 C 1 
HETATM 22 C C3C CN5 . . . Z 15 138.142 152.73 128.381 1 41.29 ? C3C CN5 406 C 1 
HETATM 23 C C3D CN5 . . . Z 15 137.237 152.545 129.582 1 41.29 ? C3D CN5 406 C 1 
HETATM 24 C C3E CN5 . . . Z 15 137.394 153.599 130.645 1 41.29 ? C3E CN5 406 C 1 
HETATM 25 C C3F CN5 . . . Z 15 136.28 153.765 131.649 1 41.29 ? C3F CN5 406 C 1 
HETATM 26 P P' CN5 . . . Z 15 131.355 131.135 130.531 1 41.29 ? P' CN5 406 C 1 
HETATM 27 O O1' CN5 . . . Z 15 131.374 129.549 130.753 1 41.29 ? O1' CN5 406 C 1 
HETATM 28 O O2' CN5 . . . Z 15 131.646 131.395 129.091 1 41.29 ? O2' CN5 406 C 1 
HETATM 29 O O3' CN5 . . . Z 15 132.628 131.703 131.33 1 41.29 ? O3' CN5 406 C 1 
HETATM 30 O O4' CN5 . . . Z 15 130.07 131.608 131.132 1 41.29 ? O4' CN5 406 C 1 
HETATM 31 C C1' CN5 . . . Z 15 130.791 128.646 129.778 1 41.29 ? C1' CN5 406 C 1 
HETATM 32 C C2' CN5 . . . Z 15 131.794 127.546 129.543 1 41.29 ? C2' CN5 406 C 1 
HETATM 33 C C3' CN5 . . . Z 15 131.244 126.173 129.699 1 41.29 ? C3' CN5 406 C 1 
HETATM 34 O O41 CN5 . . . Z 15 132.166 125.235 129.107 1 41.29 ? O41 CN5 406 C 1 
HETATM 35 O O42 CN5 . . . Z 15 131.54 123.375 128.03 1 41.29 ? O42 CN5 406 C 1 
HETATM 36 C C41 CN5 . . . Z 15 131.706 124.561 128.048 1 41.29 ? C41 CN5 406 C 1 
HETATM 37 C C42 CN5 . . . Z 15 131.422 125.483 126.917 1 41.29 ? C42 CN5 406 C 1 
HETATM 38 C CA CN5 . . . Z 15 132.662 133.108 131.692 1 41.29 ? CA CN5 406 C 1 
HETATM 39 C CB CN5 . . . Z 15 134.002 133.831 131.719 1 41.29 ? CB CN5 406 C 1 
HETATM 40 O OA CN5 . . . Z 15 134.178 134.53 132.952 1 41.29 ? OA CN5 406 C 1 
HETATM 41 C CC CN5 . . . Z 15 134.241 134.747 130.544 1 41.29 ? CC CN5 406 C 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           41 
#