data_8YSK # _model_server_result.job_id S4rL9ZZGLnQXgPesWlsT3A _model_server_result.datetime_utc '2025-02-12 03:57:04' _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 8ysk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 8YSK # _exptl.entry_id 8YSK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 101.137 _cell.angle_beta 106.903 _cell.angle_gamma 95.429 _cell.entry_id 8YSK _cell.length_a 35.274 _cell.length_b 46.091 _cell.length_c 59.889 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSK _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # 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 OD1 ASP 78 A ASP 78 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc3 A OD2 ASP 78 A ASP 78 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc4 A OD2 ASP 80 A ASP 80 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc5 A OD1 ASP 80 A ASP 80 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc6 A OD2 ASP 129 A ASP 129 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc7 B O2A UTP . A UTP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc8 B O2B UTP . A UTP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc9 B O1G UTP . A UTP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc10 C MN MN . A MN 402 1_555 E O HOH . A HOH 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc11 C MN MN . A MN 402 1_555 E O HOH . A HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc12 D MN MN . A MN 403 1_555 E O HOH . A HOH 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 8YSK _atom_sites.fract_transf_matrix[1][1] 0.028349 _atom_sites.fract_transf_matrix[1][2] 0.002694 _atom_sites.fract_transf_matrix[1][3] 0.009497 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021794 _atom_sites.fract_transf_matrix[2][3] 0.00519 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01794 _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 B 2 UTP A 1 401 401 UTP UTP . C 3 MN A 1 402 403 MN MN . D 3 MN A 1 403 404 MN MN . E 4 HOH A 1 501 550 HOH HOH . E 4 HOH A 2 502 645 HOH HOH . E 4 HOH A 3 503 686 HOH HOH . E 4 HOH A 4 504 643 HOH HOH . E 4 HOH A 5 505 519 HOH HOH . E 4 HOH A 6 506 570 HOH HOH . E 4 HOH A 7 507 625 HOH HOH . E 4 HOH A 8 508 538 HOH HOH . E 4 HOH A 9 509 555 HOH HOH . E 4 HOH A 10 510 640 HOH HOH . E 4 HOH A 11 511 591 HOH HOH . E 4 HOH A 12 512 693 HOH HOH . E 4 HOH A 13 513 527 HOH HOH . E 4 HOH A 14 514 509 HOH HOH . E 4 HOH A 15 515 537 HOH HOH . E 4 HOH A 16 516 664 HOH HOH . E 4 HOH A 17 517 642 HOH HOH . E 4 HOH A 18 518 586 HOH HOH . E 4 HOH A 19 519 505 HOH HOH . E 4 HOH A 20 520 584 HOH HOH . E 4 HOH A 21 521 546 HOH HOH . E 4 HOH A 22 522 518 HOH HOH . E 4 HOH A 23 523 542 HOH HOH . E 4 HOH A 24 524 644 HOH HOH . E 4 HOH A 25 525 532 HOH HOH . E 4 HOH A 26 526 638 HOH HOH . E 4 HOH A 27 527 590 HOH HOH . E 4 HOH A 28 528 582 HOH HOH . E 4 HOH A 29 529 662 HOH HOH . E 4 HOH A 30 530 611 HOH HOH . E 4 HOH A 31 531 517 HOH HOH . E 4 HOH A 32 532 605 HOH HOH . E 4 HOH A 33 533 673 HOH HOH . E 4 HOH A 34 534 579 HOH HOH . E 4 HOH A 35 535 513 HOH HOH . E 4 HOH A 36 536 539 HOH HOH . E 4 HOH A 37 537 674 HOH HOH . E 4 HOH A 38 538 655 HOH HOH . E 4 HOH A 39 539 567 HOH HOH . E 4 HOH A 40 540 565 HOH HOH . E 4 HOH A 41 541 504 HOH HOH . E 4 HOH A 42 542 688 HOH HOH . E 4 HOH A 43 543 502 HOH HOH . E 4 HOH A 44 544 627 HOH HOH . E 4 HOH A 45 545 683 HOH HOH . E 4 HOH A 46 546 575 HOH HOH . E 4 HOH A 47 547 547 HOH HOH . E 4 HOH A 48 548 657 HOH HOH . E 4 HOH A 49 549 618 HOH HOH . E 4 HOH A 50 550 501 HOH HOH . E 4 HOH A 51 551 522 HOH HOH . E 4 HOH A 52 552 616 HOH HOH . E 4 HOH A 53 553 556 HOH HOH . E 4 HOH A 54 554 553 HOH HOH . E 4 HOH A 55 555 503 HOH HOH . E 4 HOH A 56 556 506 HOH HOH . E 4 HOH A 57 557 630 HOH HOH . E 4 HOH A 58 558 511 HOH HOH . E 4 HOH A 59 559 600 HOH HOH . E 4 HOH A 60 560 620 HOH HOH . E 4 HOH A 61 561 576 HOH HOH . E 4 HOH A 62 562 615 HOH HOH . E 4 HOH A 63 563 602 HOH HOH . E 4 HOH A 64 564 578 HOH HOH . E 4 HOH A 65 565 500 HOH HOH . E 4 HOH A 66 566 561 HOH HOH . E 4 HOH A 67 567 667 HOH HOH . E 4 HOH A 68 568 563 HOH HOH . E 4 HOH A 69 569 557 HOH HOH . E 4 HOH A 70 570 636 HOH HOH . E 4 HOH A 71 571 603 HOH HOH . E 4 HOH A 72 572 684 HOH HOH . E 4 HOH A 73 573 541 HOH HOH . E 4 HOH A 74 574 595 HOH HOH . E 4 HOH A 75 575 599 HOH HOH . E 4 HOH A 76 576 631 HOH HOH . E 4 HOH A 77 577 589 HOH HOH . E 4 HOH A 78 578 652 HOH HOH . E 4 HOH A 79 579 641 HOH HOH . E 4 HOH A 80 580 648 HOH HOH . E 4 HOH A 81 581 594 HOH HOH . E 4 HOH A 82 582 551 HOH HOH . E 4 HOH A 83 583 520 HOH HOH . E 4 HOH A 84 584 650 HOH HOH . E 4 HOH A 85 585 577 HOH HOH . E 4 HOH A 86 586 508 HOH HOH . E 4 HOH A 87 587 609 HOH HOH . E 4 HOH A 88 588 526 HOH HOH . E 4 HOH A 89 589 639 HOH HOH . E 4 HOH A 90 590 610 HOH HOH . E 4 HOH A 91 591 621 HOH HOH . E 4 HOH A 92 592 510 HOH HOH . E 4 HOH A 93 593 512 HOH HOH . E 4 HOH A 94 594 628 HOH HOH . E 4 HOH A 95 595 507 HOH HOH . E 4 HOH A 96 596 571 HOH HOH . E 4 HOH A 97 597 666 HOH HOH . E 4 HOH A 98 598 624 HOH HOH . E 4 HOH A 99 599 523 HOH HOH . E 4 HOH A 100 600 549 HOH HOH . E 4 HOH A 101 601 679 HOH HOH . E 4 HOH A 102 602 535 HOH HOH . E 4 HOH A 103 603 564 HOH HOH . E 4 HOH A 104 604 623 HOH HOH . E 4 HOH A 105 605 516 HOH HOH . E 4 HOH A 106 606 680 HOH HOH . E 4 HOH A 107 607 515 HOH HOH . E 4 HOH A 108 608 566 HOH HOH . E 4 HOH A 109 609 651 HOH HOH . E 4 HOH A 110 610 676 HOH HOH . E 4 HOH A 111 611 529 HOH HOH . E 4 HOH A 112 612 572 HOH HOH . E 4 HOH A 113 613 629 HOH HOH . E 4 HOH A 114 614 665 HOH HOH . E 4 HOH A 115 615 622 HOH HOH . E 4 HOH A 116 616 634 HOH HOH . E 4 HOH A 117 617 525 HOH HOH . E 4 HOH A 118 618 552 HOH HOH . E 4 HOH A 119 619 521 HOH HOH . E 4 HOH A 120 620 574 HOH HOH . E 4 HOH A 121 621 573 HOH HOH . E 4 HOH A 122 622 540 HOH HOH . E 4 HOH A 123 623 583 HOH HOH . E 4 HOH A 124 624 659 HOH HOH . E 4 HOH A 125 625 661 HOH HOH . E 4 HOH A 126 626 604 HOH HOH . E 4 HOH A 127 627 588 HOH HOH . E 4 HOH A 128 628 587 HOH HOH . E 4 HOH A 129 629 524 HOH HOH . E 4 HOH A 130 630 682 HOH HOH . E 4 HOH A 131 631 593 HOH HOH . E 4 HOH A 132 632 617 HOH HOH . E 4 HOH A 133 633 672 HOH HOH . E 4 HOH A 134 634 585 HOH HOH . E 4 HOH A 135 635 592 HOH HOH . E 4 HOH A 136 636 530 HOH HOH . E 4 HOH A 137 637 568 HOH HOH . E 4 HOH A 138 638 613 HOH HOH . E 4 HOH A 139 639 681 HOH HOH . E 4 HOH A 140 640 528 HOH HOH . E 4 HOH A 141 641 608 HOH HOH . E 4 HOH A 142 642 671 HOH HOH . E 4 HOH A 143 643 597 HOH HOH . E 4 HOH A 144 644 637 HOH HOH . E 4 HOH A 145 645 663 HOH HOH . E 4 HOH A 146 646 619 HOH HOH . E 4 HOH A 147 647 656 HOH HOH . E 4 HOH A 148 648 534 HOH HOH . E 4 HOH A 149 649 558 HOH HOH . E 4 HOH A 150 650 536 HOH HOH . E 4 HOH A 151 651 531 HOH HOH . E 4 HOH A 152 652 545 HOH HOH . E 4 HOH A 153 653 548 HOH HOH . E 4 HOH A 154 654 543 HOH HOH . E 4 HOH A 155 655 596 HOH HOH . E 4 HOH A 156 656 692 HOH HOH . E 4 HOH A 157 657 544 HOH HOH . E 4 HOH A 158 658 614 HOH HOH . E 4 HOH A 159 659 514 HOH HOH . E 4 HOH A 160 660 654 HOH HOH . E 4 HOH A 161 661 653 HOH HOH . E 4 HOH A 162 662 632 HOH HOH . E 4 HOH A 163 663 685 HOH HOH . E 4 HOH A 164 664 559 HOH HOH . E 4 HOH A 165 665 691 HOH HOH . E 4 HOH A 166 666 646 HOH HOH . E 4 HOH A 167 667 580 HOH HOH . E 4 HOH A 168 668 690 HOH HOH . E 4 HOH A 169 669 554 HOH HOH . E 4 HOH A 170 670 581 HOH HOH . E 4 HOH A 171 671 560 HOH HOH . E 4 HOH A 172 672 670 HOH HOH . E 4 HOH A 173 673 687 HOH HOH . E 4 HOH A 174 674 533 HOH HOH . E 4 HOH A 175 675 612 HOH HOH . E 4 HOH A 176 676 668 HOH HOH . E 4 HOH A 177 677 606 HOH HOH . E 4 HOH A 178 678 689 HOH HOH . E 4 HOH A 179 679 678 HOH HOH . E 4 HOH A 180 680 598 HOH HOH . E 4 HOH A 181 681 562 HOH HOH . E 4 HOH A 182 682 669 HOH HOH . E 4 HOH A 183 683 607 HOH HOH . E 4 HOH A 184 684 677 HOH HOH . E 4 HOH A 185 685 626 HOH HOH . E 4 HOH A 186 686 649 HOH HOH . E 4 HOH A 187 687 647 HOH HOH . E 4 HOH A 188 688 658 HOH HOH . E 4 HOH A 189 689 660 HOH HOH . E 4 HOH A 190 690 569 HOH HOH . E 4 HOH A 191 691 601 HOH HOH . E 4 HOH A 192 692 675 HOH HOH . E 4 HOH A 193 693 635 HOH HOH . E 4 HOH A 194 694 633 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x -0.352 _atom_site.Cartn_y 1.948 _atom_site.Cartn_z -4.319 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 24.81 _atom_site.pdbx_formal_charge 0 _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 403 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #