data_5WGG # _model_server_result.job_id TVJNpA2PWWetUGVol6coig _model_server_result.datetime_utc '2024-12-26 10:12:50' _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 5wgg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 5WGG # _exptl.entry_id 5WGG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.64 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IRON/SULFUR CLUSTER' _entity.pdbx_number_of_molecules 3 _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 5WGG _cell.length_a 68.917 _cell.length_b 153.766 _cell.length_c 51.822 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WGG _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E 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 metalc ? metalc1 A O SER 11 A SER 8 1_555 H CA CA . A CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc2 A OD1 ASP 31 A ASP 28 1_555 G CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc3 A OD2 ASP 31 A ASP 28 1_555 G CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc4 A O HIS 54 A HIS 51 1_555 G CA CA . A CA 505 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc5 A SG CYS 107 A CYS 104 1_555 D FE2 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc6 A SG CYS 111 A CYS 108 1_555 D FE4 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc7 A SG CYS 114 A CYS 111 1_555 D FE3 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc8 A SG CYS 347 A CYS 344 1_555 C FE4 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc9 A SG CYS 365 A CYS 362 1_555 C FE3 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc10 A SG CYS 403 A CYS 400 1_555 E FE3 SF4 . A SF4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc11 A SG CYS 406 A CYS 403 1_555 E FE1 SF4 . A SF4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc12 A SG CYS 412 A CYS 409 1_555 E FE2 SF4 . A SF4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc13 A SG CYS 416 A CYS 413 1_555 C FE2 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc14 A SG CYS 435 A CYS 432 1_555 E FE4 SF4 . A SF4 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc15 C FE1 SF4 . A SF4 501 1_555 B SG CYS 21 B CYS 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc16 D FE1 SF4 . A SF4 502 1_555 F O SAM . A SAM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc17 D FE1 SF4 . A SF4 502 1_555 F N SAM . A SAM 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc18 E FE4 SF4 . A SF4 503 1_555 I O HOH . A HOH 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc19 G CA CA . A CA 505 1_555 I O HOH . A HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc20 G CA CA . A CA 505 1_555 I O HOH . A HOH 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc21 G CA CA . A CA 505 1_555 I O HOH . A HOH 720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc22 G CA CA . A CA 505 1_555 I O HOH . A HOH 721 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc23 H CA CA . A CA 506 1_555 I O HOH . A HOH 603 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc24 H CA CA . A CA 506 1_555 I O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc25 H CA CA . A CA 506 1_555 I O HOH . A HOH 630 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc26 H CA CA . A CA 506 1_555 I O HOH . A HOH 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc27 H CA CA . A CA 506 1_555 I O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc28 H CA CA . A CA 506 1_555 I O HOH . A HOH 714 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? # _chem_comp.formula 'Fe4 S4' _chem_comp.formula_weight 351.64 _chem_comp.id SF4 _chem_comp.mon_nstd_flag . _chem_comp.name 'IRON/SULFUR CLUSTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 FE1 S2 SF4 sing 341 n n FE1 S3 SF4 sing 342 n n FE1 S4 SF4 sing 343 n n FE2 S1 SF4 sing 344 n n FE2 S3 SF4 sing 345 n n FE2 S4 SF4 sing 346 n n FE3 S1 SF4 sing 347 n n FE3 S2 SF4 sing 348 n n FE3 S4 SF4 sing 349 n n FE4 S1 SF4 sing 350 n n FE4 S2 SF4 sing 351 n n FE4 S3 SF4 sing 352 n n # _atom_sites.entry_id 5WGG _atom_sites.fract_transf_matrix[1][1] 0.01451 _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] 0.006503 _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] 0.019297 _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 C 3 SF4 A 1 501 501 SF4 SF4 . D 3 SF4 A 1 502 502 SF4 SF4 . E 3 SF4 A 1 503 503 SF4 SF4 . F 4 SAM A 1 504 504 SAM SAM . G 5 CA A 1 505 505 CA CA . H 5 CA A 1 506 506 CA CA . I 6 HOH A 1 601 59 HOH HOH . I 6 HOH A 2 602 42 HOH HOH . I 6 HOH A 3 603 17 HOH HOH . I 6 HOH A 4 604 115 HOH HOH . I 6 HOH A 5 605 124 HOH HOH . I 6 HOH A 6 606 128 HOH HOH . I 6 HOH A 7 607 34 HOH HOH . I 6 HOH A 8 608 96 HOH HOH . I 6 HOH A 9 609 89 HOH HOH . I 6 HOH A 10 610 14 HOH HOH . I 6 HOH A 11 611 100 HOH HOH . I 6 HOH A 12 612 93 HOH HOH . I 6 HOH A 13 613 90 HOH HOH . I 6 HOH A 14 614 87 HOH HOH . I 6 HOH A 15 615 69 HOH HOH . I 6 HOH A 16 616 49 HOH HOH . I 6 HOH A 17 617 57 HOH HOH . I 6 HOH A 18 618 53 HOH HOH . I 6 HOH A 19 619 63 HOH HOH . I 6 HOH A 20 620 121 HOH HOH . I 6 HOH A 21 621 43 HOH HOH . I 6 HOH A 22 622 78 HOH HOH . I 6 HOH A 23 623 106 HOH HOH . I 6 HOH A 24 624 80 HOH HOH . I 6 HOH A 25 625 98 HOH HOH . I 6 HOH A 26 626 138 HOH HOH . I 6 HOH A 27 627 50 HOH HOH . I 6 HOH A 28 628 129 HOH HOH . I 6 HOH A 29 629 41 HOH HOH . I 6 HOH A 30 630 2 HOH HOH . I 6 HOH A 31 631 58 HOH HOH . I 6 HOH A 32 632 7 HOH HOH . I 6 HOH A 33 633 15 HOH HOH . I 6 HOH A 34 634 51 HOH HOH . I 6 HOH A 35 635 35 HOH HOH . I 6 HOH A 36 636 83 HOH HOH . I 6 HOH A 37 637 81 HOH HOH . I 6 HOH A 38 638 24 HOH HOH . I 6 HOH A 39 639 66 HOH HOH . I 6 HOH A 40 640 26 HOH HOH . I 6 HOH A 41 641 79 HOH HOH . I 6 HOH A 42 642 3 HOH HOH . I 6 HOH A 43 643 13 HOH HOH . I 6 HOH A 44 644 36 HOH HOH . I 6 HOH A 45 645 94 HOH HOH . I 6 HOH A 46 646 76 HOH HOH . I 6 HOH A 47 647 64 HOH HOH . I 6 HOH A 48 648 19 HOH HOH . I 6 HOH A 49 649 54 HOH HOH . I 6 HOH A 50 650 136 HOH HOH . I 6 HOH A 51 651 60 HOH HOH . I 6 HOH A 52 652 104 HOH HOH . I 6 HOH A 53 653 39 HOH HOH . I 6 HOH A 54 654 91 HOH HOH . I 6 HOH A 55 655 102 HOH HOH . I 6 HOH A 56 656 18 HOH HOH . I 6 HOH A 57 657 8 HOH HOH . I 6 HOH A 58 658 45 HOH HOH . I 6 HOH A 59 659 10 HOH HOH . I 6 HOH A 60 660 30 HOH HOH . I 6 HOH A 61 661 99 HOH HOH . I 6 HOH A 62 662 22 HOH HOH . I 6 HOH A 63 663 120 HOH HOH . I 6 HOH A 64 664 46 HOH HOH . I 6 HOH A 65 665 52 HOH HOH . I 6 HOH A 66 666 110 HOH HOH . I 6 HOH A 67 667 84 HOH HOH . I 6 HOH A 68 668 72 HOH HOH . I 6 HOH A 69 669 33 HOH HOH . I 6 HOH A 70 670 82 HOH HOH . I 6 HOH A 71 671 73 HOH HOH . I 6 HOH A 72 672 5 HOH HOH . I 6 HOH A 73 673 47 HOH HOH . I 6 HOH A 74 674 29 HOH HOH . I 6 HOH A 75 675 21 HOH HOH . I 6 HOH A 76 676 32 HOH HOH . I 6 HOH A 77 677 37 HOH HOH . I 6 HOH A 78 678 23 HOH HOH . I 6 HOH A 79 679 109 HOH HOH . I 6 HOH A 80 680 55 HOH HOH . I 6 HOH A 81 681 142 HOH HOH . I 6 HOH A 82 682 48 HOH HOH . I 6 HOH A 83 683 6 HOH HOH . I 6 HOH A 84 684 139 HOH HOH . I 6 HOH A 85 685 103 HOH HOH . I 6 HOH A 86 686 113 HOH HOH . I 6 HOH A 87 687 11 HOH HOH . I 6 HOH A 88 688 74 HOH HOH . I 6 HOH A 89 689 62 HOH HOH . I 6 HOH A 90 690 4 HOH HOH . I 6 HOH A 91 691 40 HOH HOH . I 6 HOH A 92 692 67 HOH HOH . I 6 HOH A 93 693 68 HOH HOH . I 6 HOH A 94 694 70 HOH HOH . I 6 HOH A 95 695 143 HOH HOH . I 6 HOH A 96 696 119 HOH HOH . I 6 HOH A 97 697 112 HOH HOH . I 6 HOH A 98 698 20 HOH HOH . I 6 HOH A 99 699 88 HOH HOH . I 6 HOH A 100 700 118 HOH HOH . I 6 HOH A 101 701 86 HOH HOH . I 6 HOH A 102 702 1 HOH HOH . I 6 HOH A 103 703 31 HOH HOH . I 6 HOH A 104 704 25 HOH HOH . I 6 HOH A 105 705 105 HOH HOH . I 6 HOH A 106 706 144 HOH HOH . I 6 HOH A 107 707 77 HOH HOH . I 6 HOH A 108 708 137 HOH HOH . I 6 HOH A 109 709 16 HOH HOH . I 6 HOH A 110 710 101 HOH HOH . I 6 HOH A 111 711 85 HOH HOH . I 6 HOH A 112 712 9 HOH HOH . I 6 HOH A 113 713 130 HOH HOH . I 6 HOH A 114 714 12 HOH HOH . I 6 HOH A 115 715 127 HOH HOH . I 6 HOH A 116 716 116 HOH HOH . I 6 HOH A 117 717 131 HOH HOH . I 6 HOH A 118 718 135 HOH HOH . I 6 HOH A 119 719 140 HOH HOH . I 6 HOH A 120 720 27 HOH HOH . I 6 HOH A 121 721 28 HOH HOH . I 6 HOH A 122 722 122 HOH HOH . I 6 HOH A 123 723 141 HOH HOH . I 6 HOH A 124 724 134 HOH HOH . I 6 HOH A 125 725 107 HOH HOH . I 6 HOH A 126 726 117 HOH HOH . I 6 HOH A 127 727 71 HOH HOH . I 6 HOH A 128 728 114 HOH HOH . I 6 HOH A 129 729 123 HOH HOH . I 6 HOH A 130 730 92 HOH HOH . I 6 HOH A 131 731 38 HOH HOH . I 6 HOH A 132 732 65 HOH HOH . I 6 HOH A 133 733 44 HOH HOH . I 6 HOH A 134 734 125 HOH HOH . I 6 HOH A 135 735 132 HOH HOH . J 6 HOH B 1 101 75 HOH HOH . # 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 FE FE1 SF4 . . . E 3 -16.167 11.048 -6.707 1 38.71 ? FE1 SF4 503 A 1 HETATM 2 FE FE2 SF4 . . . E 3 -13.631 12.308 -6.662 1 48.73 ? FE2 SF4 503 A 1 HETATM 3 FE FE3 SF4 . . . E 3 -14.811 11.636 -4.201 1 40.68 ? FE3 SF4 503 A 1 HETATM 4 FE FE4 SF4 . . . E 3 -15.915 13.747 -5.708 1 48.32 ? FE4 SF4 503 A 1 HETATM 5 S S1 SF4 . . . E 3 -13.921 13.5 -4.877 1 52.92 ? S1 SF4 503 A 1 HETATM 6 S S2 SF4 . . . E 3 -16.851 12.009 -4.881 1 43.25 ? S2 SF4 503 A 1 HETATM 7 S S3 SF4 . . . E 3 -15.499 12.892 -7.648 1 51.59 ? S3 SF4 503 A 1 HETATM 8 S S4 SF4 . . . E 3 -14.245 10.396 -5.896 1 49 ? S4 SF4 503 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #