data_8GY3 # _model_server_result.job_id HEdF_IOSu2M4D0HIf9CeKg _model_server_result.datetime_utc '2025-07-05 12:42:31' _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 8gy3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":504}' # _entry.id 8GY3 # _exptl.entry_id 8GY3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 863.343 _entity.id 5 _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 8GY3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GY3 _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_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _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 5 _struct_asym.id G _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 A SG CYS 57 A CYS 57 1_555 D CAB HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? covale ? covale2 A SG CYS 60 A CYS 60 1_555 D CAC HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale3 A SG CYS 207 A CYS 207 1_555 E CAB HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale4 A SG CYS 210 A CYS 210 1_555 E CAC HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale5 A SG CYS 341 A CYS 341 1_555 F CAB HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale6 A SG CYS 344 A CYS 344 1_555 F CAC HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.765 ? metalc ? metalc1 A NE2 HIS 61 A HIS 61 1_555 D FE HEC . A HEC 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc2 A NE2 HIS 211 A HIS 211 1_555 E FE HEC . A HEC 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc3 A NE2 HIS 345 A HIS 345 1_555 F FE HEC . A HEC 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc4 B SG CYS 39 B CYS 39 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 B SG CYS 44 B CYS 44 1_555 H FE1 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc6 B SG CYS 47 B CYS 47 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc7 B SG CYS 59 B CYS 59 1_555 H FE2 FES . B FES 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc8 B SG CYS 97 B CYS 97 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc9 B SG CYS 100 B CYS 100 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc10 B SG CYS 132 B CYS 132 1_555 I FE2 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc11 B SG CYS 134 B CYS 134 1_555 I FE1 FES . B FES 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 523 n n C1 C6 U10 doub 524 n n C1 C1M U10 sing 525 n n C2 C3 U10 sing 526 n n C2 O2 U10 doub 527 n n C3 C4 U10 doub 528 n n C3 O3 U10 sing 529 n n C4 C5 U10 sing 530 n n C4 O4 U10 sing 531 n n C5 C6 U10 sing 532 n n C5 O5 U10 doub 533 n n C6 C7 U10 sing 534 n n C1M H1M1 U10 sing 535 n n C1M H1M2 U10 sing 536 n n C1M H1M3 U10 sing 537 n n C3M O3 U10 sing 538 n n C3M H3M1 U10 sing 539 n n C3M H3M2 U10 sing 540 n n C3M H3M3 U10 sing 541 n n C4M O4 U10 sing 542 n n C4M H4M1 U10 sing 543 n n C4M H4M2 U10 sing 544 n n C4M H4M3 U10 sing 545 n n C7 C8 U10 sing 546 n n C7 H71 U10 sing 547 n n C7 H72 U10 sing 548 n n C8 C9 U10 doub 549 e n C8 H8 U10 sing 550 n n C9 C10 U10 sing 551 n n C9 C11 U10 sing 552 n n C10 H101 U10 sing 553 n n C10 H102 U10 sing 554 n n C10 H103 U10 sing 555 n n C11 C12 U10 sing 556 n n C11 H111 U10 sing 557 n n C11 H112 U10 sing 558 n n C12 C13 U10 sing 559 n n C12 H121 U10 sing 560 n n C12 H122 U10 sing 561 n n C13 C14 U10 doub 562 e n C13 H13 U10 sing 563 n n C14 C15 U10 sing 564 n n C14 C16 U10 sing 565 n n C15 H151 U10 sing 566 n n C15 H152 U10 sing 567 n n C15 H153 U10 sing 568 n n C16 C17 U10 sing 569 n n C16 H161 U10 sing 570 n n C16 H162 U10 sing 571 n n C17 C18 U10 sing 572 n n C17 H171 U10 sing 573 n n C17 H172 U10 sing 574 n n C18 C19 U10 doub 575 e n C18 H18 U10 sing 576 n n C19 C20 U10 sing 577 n n C19 C21 U10 sing 578 n n C20 H201 U10 sing 579 n n C20 H202 U10 sing 580 n n C20 H203 U10 sing 581 n n C21 C22 U10 sing 582 n n C21 H211 U10 sing 583 n n C21 H212 U10 sing 584 n n C22 C23 U10 sing 585 n n C22 H221 U10 sing 586 n n C22 H222 U10 sing 587 n n C23 C24 U10 doub 588 e n C23 H23 U10 sing 589 n n C24 C25 U10 sing 590 n n C24 C26 U10 sing 591 n n C25 H251 U10 sing 592 n n C25 H252 U10 sing 593 n n C25 H253 U10 sing 594 n n C26 C27 U10 sing 595 n n C26 H261 U10 sing 596 n n C26 H262 U10 sing 597 n n C27 C28 U10 sing 598 n n C27 H271 U10 sing 599 n n C27 H272 U10 sing 600 n n C28 C29 U10 doub 601 e n C28 H28 U10 sing 602 n n C29 C30 U10 sing 603 n n C29 C31 U10 sing 604 n n C30 H301 U10 sing 605 n n C30 H302 U10 sing 606 n n C30 H303 U10 sing 607 n n C31 C32 U10 sing 608 n n C31 H311 U10 sing 609 n n C31 H312 U10 sing 610 n n C32 C33 U10 sing 611 n n C32 H321 U10 sing 612 n n C32 H322 U10 sing 613 n n C33 C34 U10 doub 614 e n C33 H33 U10 sing 615 n n C34 C35 U10 sing 616 n n C34 C36 U10 sing 617 n n C35 H351 U10 sing 618 n n C35 H352 U10 sing 619 n n C35 H353 U10 sing 620 n n C36 C37 U10 sing 621 n n C36 H361 U10 sing 622 n n C36 H362 U10 sing 623 n n C37 C38 U10 sing 624 n n C37 H371 U10 sing 625 n n C37 H372 U10 sing 626 n n C38 C39 U10 doub 627 e n C38 H38 U10 sing 628 n n C39 C40 U10 sing 629 n n C39 C41 U10 sing 630 n n C40 H401 U10 sing 631 n n C40 H402 U10 sing 632 n n C40 H403 U10 sing 633 n n C41 C42 U10 sing 634 n n C41 H411 U10 sing 635 n n C41 H412 U10 sing 636 n n C42 C43 U10 sing 637 n n C42 H421 U10 sing 638 n n C42 H422 U10 sing 639 n n C43 C44 U10 doub 640 e n C43 H43 U10 sing 641 n n C44 C45 U10 sing 642 n n C44 C46 U10 sing 643 n n C45 H451 U10 sing 644 n n C45 H452 U10 sing 645 n n C45 H453 U10 sing 646 n n C46 C47 U10 sing 647 n n C46 H461 U10 sing 648 n n C46 H462 U10 sing 649 n n C47 C48 U10 sing 650 n n C47 H471 U10 sing 651 n n C47 H472 U10 sing 652 n n C48 C49 U10 doub 653 e n C48 H48 U10 sing 654 n n C49 C50 U10 sing 655 n n C49 C51 U10 sing 656 n n C50 H501 U10 sing 657 n n C50 H502 U10 sing 658 n n C50 H503 U10 sing 659 n n C51 C52 U10 sing 660 n n C51 H511 U10 sing 661 n n C51 H512 U10 sing 662 n n C52 C53 U10 sing 663 n n C52 H521 U10 sing 664 n n C52 H522 U10 sing 665 n n C53 C54 U10 doub 666 n n C53 H53 U10 sing 667 n n C54 C55 U10 sing 668 n n C54 C56 U10 sing 669 n n C55 H551 U10 sing 670 n n C55 H552 U10 sing 671 n n C55 H553 U10 sing 672 n n C56 H561 U10 sing 673 n n C56 H562 U10 sing 674 n n C56 H563 U10 sing 675 n n # _atom_sites.entry_id 8GY3 _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 HEC A 1 501 501 HEC HEC . E 4 HEC A 1 502 502 HEC HEC . F 4 HEC A 1 503 503 HEC HEC . G 5 U10 A 1 504 504 U10 U10 . H 6 FES B 1 201 201 FES FES . I 6 FES B 1 202 202 FES FES . J 7 PCD C 1 801 801 PCD PCD . # 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 . . . G 5 107.746 152.025 94.375 1 133.61 ? C1 U10 504 A 1 HETATM 2 C C2 U10 . . . G 5 106.651 152.678 93.829 1 134.45 ? C2 U10 504 A 1 HETATM 3 C C3 U10 . . . G 5 106.348 152.515 92.481 1 135.2 ? C3 U10 504 A 1 HETATM 4 C C4 U10 . . . G 5 107.149 151.7 91.678 1 135.39 ? C4 U10 504 A 1 HETATM 5 C C5 U10 . . . G 5 108.248 151.059 92.239 1 131.22 ? C5 U10 504 A 1 HETATM 6 C C6 U10 . . . G 5 108.55 151.217 93.586 1 129.69 ? C6 U10 504 A 1 HETATM 7 C C1M U10 . . . G 5 108.065 152.206 95.829 1 131.7 ? C1M U10 504 A 1 HETATM 8 C C3M U10 . . . G 5 104.166 153.116 92.089 1 129.73 ? C3M U10 504 A 1 HETATM 9 C C4M U10 . . . G 5 106.113 151.361 89.643 1 131.51 ? C4M U10 504 A 1 HETATM 10 C C7 U10 . . . G 5 109.927 150.873 94.097 1 126.91 ? C7 U10 504 A 1 HETATM 11 C C8 U10 . . . G 5 110.055 149.377 94.234 1 127.12 ? C8 U10 504 A 1 HETATM 12 C C9 U10 . . . G 5 111.383 148.763 94.14 1 130.6 ? C9 U10 504 A 1 HETATM 13 C C10 U10 . . . G 5 112.483 149.262 95.025 1 130.2 ? C10 U10 504 A 1 HETATM 14 C C11 U10 . . . G 5 111.63 147.637 93.167 1 131.65 ? C11 U10 504 A 1 HETATM 15 C C12 U10 . . . G 5 111.594 146.302 93.895 1 129.39 ? C12 U10 504 A 1 HETATM 16 C C13 U10 . . . G 5 112.962 145.953 94.42 1 130.44 ? C13 U10 504 A 1 HETATM 17 C C14 U10 . . . G 5 113.129 145.248 95.695 1 131.45 ? C14 U10 504 A 1 HETATM 18 C C15 U10 . . . G 5 111.935 144.922 96.537 1 131.51 ? C15 U10 504 A 1 HETATM 19 C C16 U10 . . . G 5 114.51 144.84 96.141 1 130.06 ? C16 U10 504 A 1 HETATM 20 C C17 U10 . . . G 5 115.235 146.034 96.745 1 128.53 ? C17 U10 504 A 1 HETATM 21 C C18 U10 . . . G 5 116.701 145.898 96.424 1 127.39 ? C18 U10 504 A 1 HETATM 22 C C19 U10 . . . G 5 117.721 146.129 97.453 1 129.41 ? C19 U10 504 A 1 HETATM 23 C C20 U10 . . . G 5 117.359 146.788 98.75 1 130.59 ? C20 U10 504 A 1 HETATM 24 C C21 U10 . . . G 5 119.138 145.693 97.19 1 129.5 ? C21 U10 504 A 1 HETATM 25 C C22 U10 . . . G 5 119.692 144.943 98.393 1 126.2 ? C22 U10 504 A 1 HETATM 26 C C23 U10 . . . G 5 120.773 144.018 97.892 1 129.94 ? C23 U10 504 A 1 HETATM 27 C C24 U10 . . . G 5 122.121 144.022 98.474 1 134.86 ? C24 U10 504 A 1 HETATM 28 C C25 U10 . . . G 5 122.351 144.546 99.861 1 129.49 ? C25 U10 504 A 1 HETATM 29 C C26 U10 . . . G 5 123.265 143.491 97.646 1 131.53 ? C26 U10 504 A 1 HETATM 30 C C27 U10 . . . G 5 124.48 143.194 98.513 1 131.51 ? C27 U10 504 A 1 HETATM 31 C C28 U10 . . . G 5 124.486 141.728 98.866 1 131.64 ? C28 U10 504 A 1 HETATM 32 C C29 U10 . . . G 5 125.693 140.922 98.643 1 135.52 ? C29 U10 504 A 1 HETATM 33 C C30 U10 . . . G 5 126.768 141.425 97.727 1 130.65 ? C30 U10 504 A 1 HETATM 34 C C31 U10 . . . G 5 125.851 139.586 99.328 1 133.99 ? C31 U10 504 A 1 HETATM 35 C C32 U10 . . . G 5 124.477 139.005 99.638 1 133.29 ? C32 U10 504 A 1 HETATM 36 C C33 U10 . . . G 5 124.594 138.073 100.818 1 131.83 ? C33 U10 504 A 1 HETATM 37 C C34 U10 . . . G 5 124.533 138.595 102.19 1 132.59 ? C34 U10 504 A 1 HETATM 38 C C35 U10 . . . G 5 124.032 139.985 102.447 1 129.23 ? C35 U10 504 A 1 HETATM 39 C C36 U10 . . . G 5 124.975 137.723 103.339 1 132.76 ? C36 U10 504 A 1 HETATM 40 C C37 U10 . . . G 5 126.472 137.897 103.56 1 131.71 ? C37 U10 504 A 1 HETATM 41 C C38 U10 . . . G 5 126.938 136.931 104.622 1 129.53 ? C38 U10 504 A 1 HETATM 42 C C39 U10 . . . G 5 126.617 137.163 106.038 1 129.67 ? C39 U10 504 A 1 HETATM 43 O O2 U10 . . . G 5 106.212 153.661 94.423 1 134.91 ? O2 U10 504 A 1 HETATM 44 O O3 U10 . . . G 5 105.56 153.307 91.963 1 136.69 ? O3 U10 504 A 1 HETATM 45 O O4 U10 . . . G 5 107.154 151.86 90.456 1 138.29 ? O4 U10 504 A 1 HETATM 46 O O5 U10 . . . G 5 108.885 150.255 91.561 1 128.97 ? O5 U10 504 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 46 #