data_8YIN # _model_server_result.job_id k7j0yYaGTtHwRFAdyz_ELw _model_server_result.datetime_utc '2024-12-26 12:44:54' _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":"FA","auth_seq_id":401}' # _entry.id 8YIN # _exptl.entry_id 8YIN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 834.862 _entity.id 12 _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 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 12 V N N ? 12 FA 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 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 '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 438 n n P O13 CN3 sing 439 n n O11 C1 CN3 sing 440 n n O12 P CN3 sing 441 n n O12 HO12 CN3 sing 442 n n O13 CC CN3 sing 443 n n O14 P CN3 doub 444 n n C1 C2 CN3 sing 445 n n C1 H1 CN3 sing 446 n n C1 H1A CN3 sing 447 n n C2 H2 CN3 sing 448 n n C3 C2 CN3 sing 449 n n C3 O31 CN3 sing 450 n n C3 H3 CN3 sing 451 n n C3 H3A CN3 sing 452 n n O32 C31 CN3 doub 453 n n C31 O31 CN3 sing 454 n n C31 C32 CN3 sing 455 n n C32 C33 CN3 sing 456 n n C32 H32 CN3 sing 457 n n C33 H33 CN3 sing 458 n n C33 H33A CN3 sing 459 n n O21 C2 CN3 sing 460 n n O21 C21 CN3 sing 461 n n C21 O22 CN3 doub 462 n n C21 C22 CN3 sing 463 n n C22 C23 CN3 sing 464 n n C22 H22 CN3 sing 465 n n C22 H22A CN3 sing 466 n n C23 H23 CN3 sing 467 n n C23 H23A CN3 sing 468 n n C24 C23 CN3 sing 469 n n C24 H24 CN3 sing 470 n n C24 H24A CN3 sing 471 n n C24 H24B CN3 sing 472 n n P' O3' CN3 sing 473 n n P' O1' CN3 sing 474 n n P' O4' CN3 sing 475 n n O1' C1' CN3 sing 476 n n O2' P' CN3 doub 477 n n O3' CA CN3 sing 478 n n O4' HO4' CN3 sing 479 n n C1' C2' CN3 sing 480 n n C1' H1' CN3 sing 481 n n C1' "H1'A" CN3 sing 482 n n C2' O51 CN3 sing 483 n n C2' H2' CN3 sing 484 n n C3' C2' CN3 sing 485 n n C3' O41 CN3 sing 486 n n C3' H3' CN3 sing 487 n n C3' "H3'A" CN3 sing 488 n n O42 C41 CN3 doub 489 n n C41 O41 CN3 sing 490 n n C41 C42 CN3 sing 491 n n C42 H42 CN3 sing 492 n n C42 H42A CN3 sing 493 n n C43 C42 CN3 sing 494 n n C43 H43 CN3 sing 495 n n C43 H43A CN3 sing 496 n n C44 C43 CN3 sing 497 n n C44 H44 CN3 sing 498 n n C44 H44A CN3 sing 499 n n C45 C44 CN3 sing 500 n n C45 C46 CN3 sing 501 n n C45 H45 CN3 sing 502 n n C45 H45A CN3 sing 503 n n C46 H46 CN3 sing 504 n n C46 H46A CN3 sing 505 n n C47 C46 CN3 sing 506 n n C47 C48 CN3 sing 507 n n C47 H47 CN3 sing 508 n n C47 H47A CN3 sing 509 n n C48 C49 CN3 sing 510 n n C48 H48 CN3 sing 511 n n C48 H48A CN3 sing 512 n n C49 H49 CN3 sing 513 n n C49 H49A CN3 sing 514 n n C4A C49 CN3 sing 515 n n C4A C4B CN3 sing 516 n n C4A H4A CN3 sing 517 n n C4A H4AA CN3 sing 518 n n C4B H4B CN3 sing 519 n n C4B H4BA CN3 sing 520 n n C4B H4BB CN3 sing 521 n n O51 C51 CN3 sing 522 n n C51 O52 CN3 doub 523 n n C51 C52 CN3 sing 524 n n C52 C53 CN3 sing 525 n n C52 H52 CN3 sing 526 n n C52 H52A CN3 sing 527 n n C53 C54 CN3 sing 528 n n C53 H53 CN3 sing 529 n n C53 H53A CN3 sing 530 n n C54 H54 CN3 sing 531 n n C54 H54A CN3 sing 532 n n C55 C54 CN3 sing 533 n n C55 H55 CN3 sing 534 n n C55 H55A CN3 sing 535 n n C56 C55 CN3 sing 536 n n C56 C57 CN3 sing 537 n n C56 H56 CN3 sing 538 n n C56 H56A CN3 sing 539 n n C57 H57 CN3 sing 540 n n C57 H57A CN3 sing 541 n n C58 C57 CN3 sing 542 n n C58 C59 CN3 sing 543 n n C58 H58 CN3 sing 544 n n C58 H58A CN3 sing 545 n n C59 H59 CN3 sing 546 n n C59 H59A CN3 sing 547 n n C59 H59B CN3 sing 548 n n CA HA CN3 sing 549 n n CA HAA CN3 sing 550 n n CB CA CN3 sing 551 n n CB OA CN3 sing 552 n n CB HB CN3 sing 553 n n OA HOA CN3 sing 554 n n CC CB CN3 sing 555 n n CC HC CN3 sing 556 n n CC HCA CN3 sing 557 n n C32 H67 CN3 sing 558 n n C33 H68 CN3 sing 559 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 CN3 . . . FA 12 179.461 176.805 150.735 1 58.07 ? P CN3 401 N 1 HETATM 2 O O11 CN3 . . . FA 12 179.532 177.621 149.304 1 58.07 ? O11 CN3 401 N 1 HETATM 3 O O12 CN3 . . . FA 12 178.031 176.416 151.03 1 58.07 ? O12 CN3 401 N 1 HETATM 4 O O13 CN3 . . . FA 12 180.399 175.457 150.655 1 58.07 ? O13 CN3 401 N 1 HETATM 5 O O14 CN3 . . . FA 12 179.99 177.685 151.839 1 58.07 ? O14 CN3 401 N 1 HETATM 6 C C1 CN3 . . . FA 12 178.85 177.127 148.188 1 58.07 ? C1 CN3 401 N 1 HETATM 7 C C2 CN3 . . . FA 12 179.76 176.164 147.431 1 58.07 ? C2 CN3 401 N 1 HETATM 8 C C3 CN3 . . . FA 12 179.096 175.724 146.131 1 58.07 ? C3 CN3 401 N 1 HETATM 9 O O31 CN3 . . . FA 12 178.099 174.795 146.426 1 58.07 ? O31 CN3 401 N 1 HETATM 10 O O32 CN3 . . . FA 12 177.235 173.025 145.387 1 58.07 ? O32 CN3 401 N 1 HETATM 11 C C31 CN3 . . . FA 12 178.21 173.557 145.789 1 58.07 ? C31 CN3 401 N 1 HETATM 12 C C32 CN3 . . . FA 12 179.564 172.875 145.62 1 58.07 ? C32 CN3 401 N 1 HETATM 13 C C33 CN3 . . . FA 12 179.367 171.513 144.96 1 58.07 ? C33 CN3 401 N 1 HETATM 14 O O21 CN3 . . . FA 12 180.976 176.791 147.145 1 58.07 ? O21 CN3 401 N 1 HETATM 15 O O22 CN3 . . . FA 12 182.277 174.998 147.508 1 58.07 ? O22 CN3 401 N 1 HETATM 16 C C21 CN3 . . . FA 12 182 175.903 146.792 1 58.07 ? C21 CN3 401 N 1 HETATM 17 C C22 CN3 . . . FA 12 182.767 176.103 145.486 1 58.07 ? C22 CN3 401 N 1 HETATM 18 C C23 CN3 . . . FA 12 182.588 174.88 144.589 1 58.07 ? C23 CN3 401 N 1 HETATM 19 C C24 CN3 . . . FA 12 182.072 175.319 143.221 1 58.07 ? C24 CN3 401 N 1 HETATM 20 P P' CN3 . . . FA 12 182.456 170.111 151.24 1 58.07 ? P' CN3 401 N 1 HETATM 21 O O1' CN3 . . . FA 12 183.062 169.702 149.767 1 58.07 ? O1' CN3 401 N 1 HETATM 22 O O2' CN3 . . . FA 12 180.974 169.832 151.277 1 58.07 ? O2' CN3 401 N 1 HETATM 23 O O3' CN3 . . . FA 12 182.726 171.712 151.512 1 58.07 ? O3' CN3 401 N 1 HETATM 24 O O4' CN3 . . . FA 12 183.15 169.285 152.29 1 58.07 ? O4' CN3 401 N 1 HETATM 25 C C1' CN3 . . . FA 12 182.322 170.046 148.634 1 58.07 ? C1' CN3 401 N 1 HETATM 26 C C2' CN3 . . . FA 12 182.521 168.994 147.548 1 58.07 ? C2' CN3 401 N 1 HETATM 27 C C3' CN3 . . . FA 12 181.158 168.537 147.041 1 58.07 ? C3' CN3 401 N 1 HETATM 28 O O41 CN3 . . . FA 12 181.296 167.448 146.182 1 58.07 ? O41 CN3 401 N 1 HETATM 29 O O42 CN3 . . . FA 12 179.132 167.131 145.709 1 58.07 ? O42 CN3 401 N 1 HETATM 30 C C41 CN3 . . . FA 12 180.224 167.323 145.295 1 58.07 ? C41 CN3 401 N 1 HETATM 31 C C42 CN3 . . . FA 12 180.464 167.441 143.792 1 58.07 ? C42 CN3 401 N 1 HETATM 32 C C43 CN3 . . . FA 12 179.204 167.039 143.028 1 58.07 ? C43 CN3 401 N 1 HETATM 33 C C44 CN3 . . . FA 12 178.541 168.285 142.445 1 58.07 ? C44 CN3 401 N 1 HETATM 34 C C45 CN3 . . . FA 12 177.662 167.89 141.261 1 58.07 ? C45 CN3 401 N 1 HETATM 35 C C46 CN3 . . . FA 12 177.406 169.108 140.376 1 58.07 ? C46 CN3 401 N 1 HETATM 36 C C47 CN3 . . . FA 12 176.004 169.048 139.771 1 58.07 ? C47 CN3 401 N 1 HETATM 37 C C48 CN3 . . . FA 12 175.86 167.794 138.915 1 58.07 ? C48 CN3 401 N 1 HETATM 38 C C49 CN3 . . . FA 12 176.717 167.931 137.659 1 58.07 ? C49 CN3 401 N 1 HETATM 39 C C4A CN3 . . . FA 12 177.141 166.542 137.19 1 58.07 ? C4A CN3 401 N 1 HETATM 40 C C4B CN3 . . . FA 12 177.403 166.567 135.687 1 58.07 ? C4B CN3 401 N 1 HETATM 41 O O51 CN3 . . . FA 12 183.249 169.568 146.504 1 58.07 ? O51 CN3 401 N 1 HETATM 42 O O52 CN3 . . . FA 12 185.144 168.717 147.36 1 58.07 ? O52 CN3 401 N 1 HETATM 43 C C51 CN3 . . . FA 12 184.568 169.114 146.402 1 58.07 ? C51 CN3 401 N 1 HETATM 44 C C52 CN3 . . . FA 12 185.27 169.138 145.047 1 58.07 ? C52 CN3 401 N 1 HETATM 45 C C53 CN3 . . . FA 12 185.562 167.709 144.604 1 58.07 ? C53 CN3 401 N 1 HETATM 46 C C54 CN3 . . . FA 12 185.598 167.651 143.081 1 58.07 ? C54 CN3 401 N 1 HETATM 47 C C55 CN3 . . . FA 12 184.332 166.974 142.564 1 58.07 ? C55 CN3 401 N 1 HETATM 48 C C56 CN3 . . . FA 12 184.722 165.995 141.462 1 58.07 ? C56 CN3 401 N 1 HETATM 49 C C57 CN3 . . . FA 12 183.477 165.442 140.776 1 58.07 ? C57 CN3 401 N 1 HETATM 50 C C58 CN3 . . . FA 12 183.921 164.508 139.654 1 58.07 ? C58 CN3 401 N 1 HETATM 51 C C59 CN3 . . . FA 12 182.786 164.326 138.65 1 58.07 ? C59 CN3 401 N 1 HETATM 52 C CA CN3 . . . FA 12 181.637 172.59 151.48 1 58.07 ? CA CN3 401 N 1 HETATM 53 C CB CN3 . . . FA 12 182.131 174.034 151.44 1 58.07 ? CB CN3 401 N 1 HETATM 54 O OA CN3 . . . FA 12 183.189 174.197 152.34 1 58.07 ? OA CN3 401 N 1 HETATM 55 C CC CN3 . . . FA 12 180.997 174.98 151.823 1 58.07 ? CC CN3 401 N 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 55 #