data_8YIN
#
_model_server_result.job_id            hz1zOEjcnOf545J8IM0s0w 
_model_server_result.datetime_utc      '2024-12-26 13:26:59' 
_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          8yin 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":405}' 
#
_entry.id    8YIN 
#
_exptl.entry_id    8YIN 
_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            8YIN 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YIN 
_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 
_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 134 E CYS 164 1_555 E SG CYS 150 E CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
disulf ? disulf2 O SG CYS 134 P CYS 164 1_555 O SG CYS 150 P CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc1 B NE2 HIS 82 C HIS 82 1_555 X FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? 
metalc ? metalc2 B NE2 HIS 96 C HIS 96 1_555 Y FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc3 B NE2 HIS 183 C HIS 183 1_555 X FE HEM . C HEM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? 
metalc ? metalc4 B NE2 HIS 197 C HIS 197 1_555 Y FE HEM . C HEM 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc5 D NE2 HIS 44 D HIS 105 1_555 CA FE HEM . D HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc6 G NE2 HIS 82 N HIS 82 1_555 JA FE HEM . N HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? 
metalc ? metalc7 G NE2 HIS 96 N HIS 96 1_555 GA FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? 
metalc ? metalc8 G NE2 HIS 183 N HIS 183 1_555 JA FE HEM . N HEM 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? 
metalc ? metalc9 G NE2 HIS 197 N HIS 197 1_555 GA FE HEM . N HEM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? 
metalc ? metalc10 M NE2 HIS 44 O HIS 105 1_555 LA FE HEM . O HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
#
_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 560 n n 
O12 P CN5 sing 561 n n 
P O11 CN5 sing 562 n n 
P O13 CN5 sing 563 n n 
O11 C1 CN5 sing 564 n n 
O12 HO12 CN5 sing 565 n n 
O13 CC CN5 sing 566 n n 
C2 C1 CN5 sing 567 n n 
C1 H1 CN5 sing 568 n n 
C1 H1A CN5 sing 569 n n 
C2 C3 CN5 sing 570 n n 
C2 H2 CN5 sing 571 n n 
C2 H2A CN5 sing 572 n n 
O31 C3 CN5 sing 573 n n 
C3 H3 CN5 sing 574 n n 
C3 H3A CN5 sing 575 n n 
O31 C31 CN5 sing 576 n n 
C31 O32 CN5 doub 577 n n 
C32 C31 CN5 sing 578 n n 
C33 C32 CN5 sing 579 n n 
C32 H32 CN5 sing 580 n n 
C32 H32A CN5 sing 581 n n 
C33 C34 CN5 sing 582 n n 
C33 H33 CN5 sing 583 n n 
C33 H33A CN5 sing 584 n n 
C35 C34 CN5 sing 585 n n 
C34 H34 CN5 sing 586 n n 
C34 H34A CN5 sing 587 n n 
C35 C36 CN5 sing 588 n n 
C35 H35 CN5 sing 589 n n 
C35 H35A CN5 sing 590 n n 
C37 C36 CN5 sing 591 n n 
C36 H36 CN5 sing 592 n n 
C36 H36A CN5 sing 593 n n 
C37 C38 CN5 sing 594 n n 
C37 H37 CN5 sing 595 n n 
C37 H37A CN5 sing 596 n n 
C39 C38 CN5 sing 597 n n 
C38 H38 CN5 sing 598 n n 
C38 H38A CN5 sing 599 n n 
C39 C3A CN5 sing 600 n n 
C39 H39 CN5 sing 601 n n 
C39 H39A CN5 sing 602 n n 
C3B C3A CN5 sing 603 n n 
C3A H3AA CN5 sing 604 n n 
C3A H3AB CN5 sing 605 n n 
C3C C3B CN5 sing 606 n n 
C3B H3B CN5 sing 607 n n 
C3B H3BA CN5 sing 608 n n 
C3D C3C CN5 sing 609 n n 
C3C H3C CN5 sing 610 n n 
C3C H3CA CN5 sing 611 n n 
C3E C3D CN5 sing 612 n n 
C3D H3D CN5 sing 613 n n 
C3D H3DA CN5 sing 614 n n 
C3F C3E CN5 sing 615 n n 
C3E H3E CN5 sing 616 n n 
C3E H3EA CN5 sing 617 n n 
C3F H3F CN5 sing 618 n n 
C3F H3FA CN5 sing 619 n n 
C3F H3FB CN5 sing 620 n n 
O3' P' CN5 sing 621 n n 
O1' P' CN5 sing 622 n n 
P' O2' CN5 doub 623 n n 
P' O4' CN5 sing 624 n n 
C1' O1' CN5 sing 625 n n 
CA O3' CN5 sing 626 n n 
O4' HO4' CN5 sing 627 n n 
C2' C1' CN5 sing 628 n n 
C1' H1' CN5 sing 629 n n 
C1' "H1'A" CN5 sing 630 n n 
C2' C3' CN5 sing 631 n n 
C2' H2' CN5 sing 632 n n 
C2' "H2'A" CN5 sing 633 n n 
O41 C3' CN5 sing 634 n n 
C3' H3' CN5 sing 635 n n 
C3' "H3'A" CN5 sing 636 n n 
C41 O41 CN5 sing 637 n n 
O42 C41 CN5 doub 638 n n 
C42 C41 CN5 sing 639 n n 
C42 H42 CN5 sing 640 n n 
C42 H42A CN5 sing 641 n n 
C42 H42B CN5 sing 642 n n 
CB CA CN5 sing 643 n n 
CA HA CN5 sing 644 n n 
CA HAA CN5 sing 645 n n 
OA CB CN5 sing 646 n n 
CC CB CN5 sing 647 n n 
CB HB CN5 sing 648 n n 
OA HOA CN5 sing 649 n n 
CC HC CN5 sing 650 n n 
CC HCA CN5 sing 651 n n 
#
_atom_sites.entry_id                     8YIN 
_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 A 1 501 501 6PH 6PH . 
V 12 CN3 C 1 401 401 CN3 CN3 . 
W 13 9PE C 1 402 402 9PE 9PE . 
X 14 HEM C 1 403 403 HEM HEM . 
Y 14 HEM C 1 404 404 HEM HEM . 
Z 15 CN5 C 1 405 405 CN5 CN5 . 
AA 16 UQ6 C 1 406 406 UQ6 UQ6 . 
BA 17 A1D6O C 1 407 407 A1D6O A1D . 
CA 14 HEM D 1 401 401 HEM HEM . 
DA 11 6PH E 1 301 301 6PH 6PH . 
EA 18 8PE H 1 101 101 8PE 8PE . 
FA 12 CN3 N 1 401 404 CN3 CN3 . 
GA 14 HEM N 1 402 405 HEM HEM . 
HA 16 UQ6 N 1 403 401 UQ6 UQ6 . 
IA 13 9PE N 1 404 402 9PE 9PE . 
JA 14 HEM N 1 405 403 HEM HEM . 
KA 17 A1D6O N 1 406 406 A1D6O A1D . 
LA 14 HEM O 1 401 401 HEM HEM . 
MA 18 8PE S 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 15 150.851 150.642 151.471 1 74.77 ? P CN5 405 C 1 
HETATM 2 O O11 CN5 . . . Z 15 150.572 152.107 152.058 1 74.77 ? O11 CN5 405 C 1 
HETATM 3 O O12 CN5 . . . Z 15 150.886 149.715 152.652 1 74.77 ? O12 CN5 405 C 1 
HETATM 4 O O13 CN5 . . . Z 15 149.537 150.288 150.633 1 74.77 ? O13 CN5 405 C 1 
HETATM 5 O O14 CN5 . . . Z 15 152.019 150.715 150.527 1 74.77 ? O14 CN5 405 C 1 
HETATM 6 C C1 CN5 . . . Z 15 151.649 152.797 152.752 1 74.77 ? C1 CN5 405 C 1 
HETATM 7 C C2 CN5 . . . Z 15 152.368 153.692 151.772 1 74.77 ? C2 CN5 405 C 1 
HETATM 8 C C3 CN5 . . . Z 15 153.759 153.241 151.443 1 74.77 ? C3 CN5 405 C 1 
HETATM 9 O O31 CN5 . . . Z 15 154.682 154.22 151.968 1 74.77 ? O31 CN5 405 C 1 
HETATM 10 O O32 CN5 . . . Z 15 154.209 155.816 150.489 1 74.77 ? O32 CN5 405 C 1 
HETATM 11 C C31 CN5 . . . Z 15 155.006 155.237 151.179 1 74.77 ? C31 CN5 405 C 1 
HETATM 12 C C32 CN5 . . . Z 15 156.473 155.551 151.27 1 74.77 ? C32 CN5 405 C 1 
HETATM 13 C C33 CN5 . . . Z 15 156.757 156.935 151.744 1 74.77 ? C33 CN5 405 C 1 
HETATM 14 C C34 CN5 . . . Z 15 157.45 157.776 150.693 1 74.77 ? C34 CN5 405 C 1 
HETATM 15 C C35 CN5 . . . Z 15 157.085 159.234 150.737 1 74.77 ? C35 CN5 405 C 1 
HETATM 16 C C36 CN5 . . . Z 15 158.11 160.147 150.12 1 74.77 ? C36 CN5 405 C 1 
HETATM 17 C C37 CN5 . . . Z 15 158.175 161.511 150.756 1 74.77 ? C37 CN5 405 C 1 
HETATM 18 C C38 CN5 . . . Z 15 158.486 162.631 149.798 1 74.77 ? C38 CN5 405 C 1 
HETATM 19 C C39 CN5 . . . Z 15 157.506 163.77 149.842 1 74.77 ? C39 CN5 405 C 1 
HETATM 20 C C3A CN5 . . . Z 15 157.293 164.435 148.51 1 74.77 ? C3A CN5 405 C 1 
HETATM 21 C C3B CN5 . . . Z 15 158.536 164.52 147.664 1 74.77 ? C3B CN5 405 C 1 
HETATM 22 C C3C CN5 . . . Z 15 158.912 165.927 147.252 1 74.77 ? C3C CN5 405 C 1 
HETATM 23 C C3D CN5 . . . Z 15 160.332 166.083 146.768 1 74.77 ? C3D CN5 405 C 1 
HETATM 24 C C3E CN5 . . . Z 15 161.287 166.611 147.801 1 74.77 ? C3E CN5 405 C 1 
HETATM 25 C C3F CN5 . . . Z 15 161.163 168.097 148.019 1 74.77 ? C3F CN5 405 C 1 
HETATM 26 P P' CN5 . . . Z 15 149.241 144.111 149.51 1 74.77 ? P' CN5 405 C 1 
HETATM 27 O O1' CN5 . . . Z 15 150.485 143.112 149.341 1 74.77 ? O1' CN5 405 C 1 
HETATM 28 O O2' CN5 . . . Z 15 148.533 144.195 148.188 1 74.77 ? O2' CN5 405 C 1 
HETATM 29 O O3' CN5 . . . Z 15 149.888 145.548 149.825 1 74.77 ? O3' CN5 405 C 1 
HETATM 30 O O4' CN5 . . . Z 15 148.504 143.691 150.748 1 74.77 ? O4' CN5 405 C 1 
HETATM 31 C C1' CN5 . . . Z 15 151.072 142.919 148.023 1 74.77 ? C1' CN5 405 C 1 
HETATM 32 C C2' CN5 . . . Z 15 150.467 141.696 147.379 1 74.77 ? C2' CN5 405 C 1 
HETATM 33 C C3' CN5 . . . Z 15 150.936 140.394 147.961 1 74.77 ? C3' CN5 405 C 1 
HETATM 34 O O41 CN5 . . . Z 15 149.884 139.423 147.762 1 74.77 ? O41 CN5 405 C 1 
HETATM 35 O O42 CN5 . . . Z 15 149.834 137.445 148.761 1 74.77 ? O42 CN5 405 C 1 
HETATM 36 C C41 CN5 . . . Z 15 150.232 138.139 147.872 1 74.77 ? C41 CN5 405 C 1 
HETATM 37 C C42 CN5 . . . Z 15 151.14 137.714 146.775 1 74.77 ? C42 CN5 405 C 1 
HETATM 38 C CA CN5 . . . Z 15 149.015 146.708 149.946 1 74.77 ? CA CN5 405 C 1 
HETATM 39 C CB CN5 . . . Z 15 149.788 147.916 150.416 1 74.77 ? CB CN5 405 C 1 
HETATM 40 O OA CN5 . . . Z 15 150.709 147.537 151.436 1 74.77 ? OA CN5 405 C 1 
HETATM 41 C CC CN5 . . . Z 15 148.887 149.027 150.898 1 74.77 ? CC CN5 405 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    51 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           41 
#