data_8XCM # _model_server_result.job_id GC7oWx7mW6qIbFanV3VurQ _model_server_result.datetime_utc '2025-07-31 00:04:13' _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 8xcm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":504}' # _entry.id 8XCM # _exptl.entry_id 8XCM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 863.343 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UBIQUINONE-10 _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 8XCM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XCM _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 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 # _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 x,y,z _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 7 _struct_asym.id I _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 covale ? covale1 C CB CYS 52 C CYS 52 1_555 H CBB HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? covale ? covale2 C SG CYS 55 C CYS 55 1_555 H CBC HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.767 ? covale ? covale3 C N TYR 115 C TYR 115 1_555 H O2D HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale4 C SG CYS 201 C CYS 201 1_555 G CAB HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale5 C SG CYS 204 C CYS 204 1_555 G CBC HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? covale ? covale6 C CB CYS 343 C CYS 343 1_555 F CAB HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale7 C SG CYS 343 C CYS 343 1_555 F CAB HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? covale ? covale8 C SG CYS 346 C CYS 346 1_555 F CBC HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale9 C CG ASP 375 C ASP 375 1_555 G O1D HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale10 C CG1 ILE 393 C ILE 393 1_555 F O2D HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.377 ? metalc ? metalc1 A SG CYS 216 A CYS 216 1_555 E FE4 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc2 A SG CYS 222 A CYS 222 1_555 E FE3 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc3 A SG CYS 226 A CYS 226 1_555 E FE1 F3S . A F3S 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc4 C NE2 HIS 56 C HIS 56 1_555 H FE HEC . C HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc5 C NE2 HIS 205 C HIS 205 1_555 G FE HEC . C HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 C NE2 HIS 347 C HIS 347 1_555 F FE HEC . C HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _chem_comp.formula 'C59 H90 O4' _chem_comp.formula_weight 863.343 _chem_comp.id U10 _chem_comp.mon_nstd_flag . _chem_comp.name UBIQUINONE-10 _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Coenzyme Q10' # 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 U10 sing 540 n n C1 C6 U10 doub 541 n n C1 C1M U10 sing 542 n n C2 C3 U10 sing 543 n n C2 O2 U10 doub 544 n n C3 C4 U10 doub 545 n n C3 O3 U10 sing 546 n n C4 C5 U10 sing 547 n n C4 O4 U10 sing 548 n n C5 C6 U10 sing 549 n n C5 O5 U10 doub 550 n n C6 C7 U10 sing 551 n n C1M H1M1 U10 sing 552 n n C1M H1M2 U10 sing 553 n n C1M H1M3 U10 sing 554 n n C3M O3 U10 sing 555 n n C3M H3M1 U10 sing 556 n n C3M H3M2 U10 sing 557 n n C3M H3M3 U10 sing 558 n n C4M O4 U10 sing 559 n n C4M H4M1 U10 sing 560 n n C4M H4M2 U10 sing 561 n n C4M H4M3 U10 sing 562 n n C7 C8 U10 sing 563 n n C7 H71 U10 sing 564 n n C7 H72 U10 sing 565 n n C8 C9 U10 doub 566 e n C8 H8 U10 sing 567 n n C9 C10 U10 sing 568 n n C9 C11 U10 sing 569 n n C10 H101 U10 sing 570 n n C10 H102 U10 sing 571 n n C10 H103 U10 sing 572 n n C11 C12 U10 sing 573 n n C11 H111 U10 sing 574 n n C11 H112 U10 sing 575 n n C12 C13 U10 sing 576 n n C12 H121 U10 sing 577 n n C12 H122 U10 sing 578 n n C13 C14 U10 doub 579 e n C13 H13 U10 sing 580 n n C14 C15 U10 sing 581 n n C14 C16 U10 sing 582 n n C15 H151 U10 sing 583 n n C15 H152 U10 sing 584 n n C15 H153 U10 sing 585 n n C16 C17 U10 sing 586 n n C16 H161 U10 sing 587 n n C16 H162 U10 sing 588 n n C17 C18 U10 sing 589 n n C17 H171 U10 sing 590 n n C17 H172 U10 sing 591 n n C18 C19 U10 doub 592 e n C18 H18 U10 sing 593 n n C19 C20 U10 sing 594 n n C19 C21 U10 sing 595 n n C20 H201 U10 sing 596 n n C20 H202 U10 sing 597 n n C20 H203 U10 sing 598 n n C21 C22 U10 sing 599 n n C21 H211 U10 sing 600 n n C21 H212 U10 sing 601 n n C22 C23 U10 sing 602 n n C22 H221 U10 sing 603 n n C22 H222 U10 sing 604 n n C23 C24 U10 doub 605 e n C23 H23 U10 sing 606 n n C24 C25 U10 sing 607 n n C24 C26 U10 sing 608 n n C25 H251 U10 sing 609 n n C25 H252 U10 sing 610 n n C25 H253 U10 sing 611 n n C26 C27 U10 sing 612 n n C26 H261 U10 sing 613 n n C26 H262 U10 sing 614 n n C27 C28 U10 sing 615 n n C27 H271 U10 sing 616 n n C27 H272 U10 sing 617 n n C28 C29 U10 doub 618 e n C28 H28 U10 sing 619 n n C29 C30 U10 sing 620 n n C29 C31 U10 sing 621 n n C30 H301 U10 sing 622 n n C30 H302 U10 sing 623 n n C30 H303 U10 sing 624 n n C31 C32 U10 sing 625 n n C31 H311 U10 sing 626 n n C31 H312 U10 sing 627 n n C32 C33 U10 sing 628 n n C32 H321 U10 sing 629 n n C32 H322 U10 sing 630 n n C33 C34 U10 doub 631 e n C33 H33 U10 sing 632 n n C34 C35 U10 sing 633 n n C34 C36 U10 sing 634 n n C35 H351 U10 sing 635 n n C35 H352 U10 sing 636 n n C35 H353 U10 sing 637 n n C36 C37 U10 sing 638 n n C36 H361 U10 sing 639 n n C36 H362 U10 sing 640 n n C37 C38 U10 sing 641 n n C37 H371 U10 sing 642 n n C37 H372 U10 sing 643 n n C38 C39 U10 doub 644 e n C38 H38 U10 sing 645 n n C39 C40 U10 sing 646 n n C39 C41 U10 sing 647 n n C40 H401 U10 sing 648 n n C40 H402 U10 sing 649 n n C40 H403 U10 sing 650 n n C41 C42 U10 sing 651 n n C41 H411 U10 sing 652 n n C41 H412 U10 sing 653 n n C42 C43 U10 sing 654 n n C42 H421 U10 sing 655 n n C42 H422 U10 sing 656 n n C43 C44 U10 doub 657 e n C43 H43 U10 sing 658 n n C44 C45 U10 sing 659 n n C44 C46 U10 sing 660 n n C45 H451 U10 sing 661 n n C45 H452 U10 sing 662 n n C45 H453 U10 sing 663 n n C46 C47 U10 sing 664 n n C46 H461 U10 sing 665 n n C46 H462 U10 sing 666 n n C47 C48 U10 sing 667 n n C47 H471 U10 sing 668 n n C47 H472 U10 sing 669 n n C48 C49 U10 doub 670 e n C48 H48 U10 sing 671 n n C49 C50 U10 sing 672 n n C49 C51 U10 sing 673 n n C50 H501 U10 sing 674 n n C50 H502 U10 sing 675 n n C50 H503 U10 sing 676 n n C51 C52 U10 sing 677 n n C51 H511 U10 sing 678 n n C51 H512 U10 sing 679 n n C52 C53 U10 sing 680 n n C52 H521 U10 sing 681 n n C52 H522 U10 sing 682 n n C53 C54 U10 doub 683 n n C53 H53 U10 sing 684 n n C54 C55 U10 sing 685 n n C54 C56 U10 sing 686 n n C55 H551 U10 sing 687 n n C55 H552 U10 sing 688 n n C55 H553 U10 sing 689 n n C56 H561 U10 sing 690 n n C56 H562 U10 sing 691 n n C56 H563 U10 sing 692 n n # _atom_sites.entry_id 8XCM _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 D 4 FAD A 1 601 601 FAD FAD . E 5 F3S A 1 602 602 F3S F3S . F 6 HEC C 1 501 501 HEC HEC . G 6 HEC C 1 502 502 HEC HEC . H 6 HEC C 1 503 503 HEC HEC . I 7 U10 C 1 504 504 U10 U10 . # 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 U10 . . . I 7 123.505 79.895 117.339 1 177.39 ? C1 U10 504 C 1 HETATM 2 C C2 U10 . . . I 7 124.2 78.968 118.106 1 180.37 ? C2 U10 504 C 1 HETATM 3 C C3 U10 . . . I 7 124.578 77.746 117.56 1 183.57 ? C3 U10 504 C 1 HETATM 4 C C4 U10 . . . I 7 124.221 77.453 116.245 1 181.6 ? C4 U10 504 C 1 HETATM 5 C C5 U10 . . . I 7 123.532 78.385 115.478 1 174.75 ? C5 U10 504 C 1 HETATM 6 C C6 U10 . . . I 7 123.16 79.609 116.019 1 172.77 ? C6 U10 504 C 1 HETATM 7 C C1M U10 . . . I 7 123.128 81.204 117.968 1 179.35 ? C1M U10 504 C 1 HETATM 8 C C3M U10 . . . I 7 126.817 77.787 118.073 1 176.54 ? C3M U10 504 C 1 HETATM 9 C C4M U10 . . . I 7 123.953 75.164 116.396 1 178.72 ? C4M U10 504 C 1 HETATM 10 C C7 U10 . . . I 7 122.003 80.335 115.369 1 173.97 ? C7 U10 504 C 1 HETATM 11 C C8 U10 . . . I 7 122.45 81.606 114.679 1 173.73 ? C8 U10 504 C 1 HETATM 12 C C9 U10 . . . I 7 122.726 81.661 113.237 1 174.17 ? C9 U10 504 C 1 HETATM 13 C C10 U10 . . . I 7 123.504 80.565 112.574 1 175.4 ? C10 U10 504 C 1 HETATM 14 C C11 U10 . . . I 7 122.236 82.842 112.431 1 175.47 ? C11 U10 504 C 1 HETATM 15 C C12 U10 . . . I 7 123.265 83.233 111.376 1 173.96 ? C12 U10 504 C 1 HETATM 16 C C13 U10 . . . I 7 122.803 84.475 110.648 1 173.55 ? C13 U10 504 C 1 HETATM 17 C C14 U10 . . . I 7 123.76 85.552 110.353 1 173.79 ? C14 U10 504 C 1 HETATM 18 C C15 U10 . . . I 7 125.148 85.471 110.913 1 177.32 ? C15 U10 504 C 1 HETATM 19 C C16 U10 . . . I 7 123.374 86.739 109.498 1 173.63 ? C16 U10 504 C 1 HETATM 20 C C17 U10 . . . I 7 121.884 86.738 109.174 1 174.9 ? C17 U10 504 C 1 HETATM 21 C C18 U10 . . . I 7 121.69 87.279 107.776 1 173.18 ? C18 U10 504 C 1 HETATM 22 C C19 U10 . . . I 7 120.356 87.344 107.16 1 172.29 ? C19 U10 504 C 1 HETATM 23 C C20 U10 . . . I 7 119.132 87.078 107.982 1 172.66 ? C20 U10 504 C 1 HETATM 24 C C21 U10 . . . I 7 120.212 87.674 105.693 1 175.79 ? C21 U10 504 C 1 HETATM 25 C C22 U10 . . . I 7 118.925 88.452 105.445 1 174.41 ? C22 U10 504 C 1 HETATM 26 C C23 U10 . . . I 7 119.125 89.897 105.832 1 173.81 ? C23 U10 504 C 1 HETATM 27 C C24 U10 . . . I 7 118.683 90.973 104.935 1 173.37 ? C24 U10 504 C 1 HETATM 28 C C25 U10 . . . I 7 117.846 90.646 103.734 1 174.17 ? C25 U10 504 C 1 HETATM 29 C C26 U10 . . . I 7 119.077 92.4 105.235 1 174.52 ? C26 U10 504 C 1 HETATM 30 C C27 U10 . . . I 7 118.75 93.307 104.054 1 174.94 ? C27 U10 504 C 1 HETATM 31 C C28 U10 . . . I 7 120.003 93.51 103.236 1 177.03 ? C28 U10 504 C 1 HETATM 32 C C29 U10 . . . I 7 120.074 94.559 102.209 1 174.82 ? C29 U10 504 C 1 HETATM 33 C C30 U10 . . . I 7 119.096 95.695 102.227 1 174.61 ? C30 U10 504 C 1 HETATM 34 C C31 U10 . . . I 7 121.141 94.5 101.142 1 172.63 ? C31 U10 504 C 1 HETATM 35 O O2 U10 . . . I 7 124.196 79.097 119.33 1 180.49 ? O2 U10 504 C 1 HETATM 36 O O3 U10 . . . I 7 125.549 77.17 118.055 1 184.96 ? O3 U10 504 C 1 HETATM 37 O O4 U10 . . . I 7 124.424 76.336 115.764 1 183.88 ? O4 U10 504 C 1 HETATM 38 O O5 U10 . . . I 7 122.974 78.001 114.452 1 175.14 ? O5 U10 504 C 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 38 #