data_4DQW # _model_server_result.job_id j33rd2ld1WiBE_clygofjA _model_server_result.datetime_utc '2024-11-24 14:09:05' _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 4dqw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":504}' # _entry.id 4DQW # _exptl.entry_id 4DQW _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 4 _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 4DQW _cell.length_a 108.96 _cell.length_b 108.96 _cell.length_c 194.39 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DQW _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_445 -x-1,-y-1,z -1 0 0 0 -1 0 0 0 1 -108.96 -108.96 0 3 'crystal symmetry operation' 3_455 -y-1,x,z 0 -1 0 1 0 0 0 0 1 -108.96 0 0 4 'crystal symmetry operation' 4_545 y,-x-1,z 0 1 0 -1 0 0 0 0 1 0 -108.96 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N ? 3 J N N ? 3 L 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 OE2 GLU 200 A GLU 180 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc2 A OE1 GLU 200 A GLU 180 1_555 F MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 C O1B ATP . A ATP 501 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 C O1G ATP . A ATP 501 1_555 D MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc5 C O1G ATP . A ATP 501 1_555 F MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc6 C O3G ATP . A ATP 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc7 D MN MN . A MN 502 1_555 E O2B ATP . A ATP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc8 D MN MN . A MN 502 1_555 E O1G ATP . A ATP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc9 E O1G ATP . A ATP 503 1_555 F MN MN . A MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc10 F MN MN . A MN 504 1_555 I O1G ATP . B ATP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc11 F MN MN . A MN 504 1_555 N O HOH . B HOH 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc12 B OE2 GLU 200 B GLU 180 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc13 B OE1 GLU 200 B GLU 180 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc14 I O3G ATP . B ATP 501 1_555 J MN MN . B MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc15 I O3B ATP . B ATP 501 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc16 I O1B ATP . B ATP 501 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc17 I O3G ATP . B ATP 501 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc18 J MN MN . B MN 502 1_555 K O1G ATP . B ATP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc19 J MN MN . B MN 502 1_555 N O HOH . B HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc20 K O1G ATP . B ATP 503 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.762 ? metalc ? metalc21 K O2B ATP . B ATP 503 1_555 L MN MN . B MN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? # _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 4DQW _atom_sites.fract_transf_matrix[1][1] 0.009178 _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] 0.009178 _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] 0.005144 _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 2 ATP A 1 501 1 ATP ATP . D 3 MN A 1 502 2 MN MN . E 2 ATP A 1 503 3 ATP ATP . F 3 MN A 1 504 4 MN MN . G 4 PO4 A 1 505 1 PO4 PO4 . H 5 GOL A 1 506 1 GOL GOL . I 2 ATP B 1 501 5 ATP ATP . J 3 MN B 1 502 6 MN MN . K 2 ATP B 1 503 7 ATP ATP . L 3 MN B 1 504 8 MN MN . M 6 HOH A 1 601 1 HOH HOH . M 6 HOH A 2 602 332 HOH HOH . M 6 HOH A 3 603 352 HOH HOH . M 6 HOH A 4 604 672 HOH HOH . M 6 HOH A 5 605 334 HOH HOH . M 6 HOH A 6 606 5 HOH HOH . M 6 HOH A 7 607 335 HOH HOH . M 6 HOH A 8 608 7 HOH HOH . M 6 HOH A 9 609 10 HOH HOH . M 6 HOH A 10 610 346 HOH HOH . M 6 HOH A 11 611 311 HOH HOH . M 6 HOH A 12 612 323 HOH HOH . M 6 HOH A 13 613 413 HOH HOH . M 6 HOH A 14 614 15 HOH HOH . M 6 HOH A 15 615 16 HOH HOH . M 6 HOH A 16 616 318 HOH HOH . M 6 HOH A 17 617 22 HOH HOH . M 6 HOH A 18 618 24 HOH HOH . M 6 HOH A 19 619 26 HOH HOH . M 6 HOH A 20 620 29 HOH HOH . M 6 HOH A 21 621 30 HOH HOH . M 6 HOH A 22 622 31 HOH HOH . M 6 HOH A 23 623 39 HOH HOH . M 6 HOH A 24 624 340 HOH HOH . M 6 HOH A 25 625 42 HOH HOH . M 6 HOH A 26 626 343 HOH HOH . M 6 HOH A 27 627 47 HOH HOH . M 6 HOH A 28 628 48 HOH HOH . M 6 HOH A 29 629 49 HOH HOH . M 6 HOH A 30 630 52 HOH HOH . M 6 HOH A 31 631 54 HOH HOH . M 6 HOH A 32 632 58 HOH HOH . M 6 HOH A 33 633 60 HOH HOH . M 6 HOH A 34 634 560 HOH HOH . M 6 HOH A 35 635 63 HOH HOH . M 6 HOH A 36 636 66 HOH HOH . M 6 HOH A 37 637 67 HOH HOH . M 6 HOH A 38 638 570 HOH HOH . M 6 HOH A 39 639 71 HOH HOH . M 6 HOH A 40 640 72 HOH HOH . M 6 HOH A 41 641 572 HOH HOH . M 6 HOH A 42 642 74 HOH HOH . M 6 HOH A 43 643 77 HOH HOH . M 6 HOH A 44 644 79 HOH HOH . M 6 HOH A 45 645 579 HOH HOH . M 6 HOH A 46 646 84 HOH HOH . M 6 HOH A 47 647 85 HOH HOH . M 6 HOH A 48 648 88 HOH HOH . M 6 HOH A 49 649 89 HOH HOH . M 6 HOH A 50 650 93 HOH HOH . M 6 HOH A 51 651 94 HOH HOH . M 6 HOH A 52 652 95 HOH HOH . M 6 HOH A 53 653 96 HOH HOH . M 6 HOH A 54 654 97 HOH HOH . M 6 HOH A 55 655 98 HOH HOH . M 6 HOH A 56 656 99 HOH HOH . M 6 HOH A 57 657 100 HOH HOH . M 6 HOH A 58 658 102 HOH HOH . M 6 HOH A 59 659 103 HOH HOH . M 6 HOH A 60 660 104 HOH HOH . M 6 HOH A 61 661 110 HOH HOH . M 6 HOH A 62 662 111 HOH HOH . M 6 HOH A 63 663 115 HOH HOH . M 6 HOH A 64 664 116 HOH HOH . M 6 HOH A 65 665 117 HOH HOH . M 6 HOH A 66 666 118 HOH HOH . M 6 HOH A 67 667 119 HOH HOH . M 6 HOH A 68 668 121 HOH HOH . M 6 HOH A 69 669 123 HOH HOH . M 6 HOH A 70 670 128 HOH HOH . M 6 HOH A 71 671 129 HOH HOH . M 6 HOH A 72 672 130 HOH HOH . M 6 HOH A 73 673 131 HOH HOH . M 6 HOH A 74 674 132 HOH HOH . M 6 HOH A 75 675 138 HOH HOH . M 6 HOH A 76 676 140 HOH HOH . M 6 HOH A 77 677 141 HOH HOH . M 6 HOH A 78 678 142 HOH HOH . M 6 HOH A 79 679 148 HOH HOH . M 6 HOH A 80 680 149 HOH HOH . M 6 HOH A 81 681 150 HOH HOH . M 6 HOH A 82 682 151 HOH HOH . M 6 HOH A 83 683 152 HOH HOH . M 6 HOH A 84 684 153 HOH HOH . M 6 HOH A 85 685 154 HOH HOH . M 6 HOH A 86 686 158 HOH HOH . M 6 HOH A 87 687 159 HOH HOH . M 6 HOH A 88 688 990 HOH HOH . M 6 HOH A 89 689 925 HOH HOH . M 6 HOH A 90 690 932 HOH HOH . M 6 HOH A 91 691 933 HOH HOH . M 6 HOH A 92 692 938 HOH HOH . M 6 HOH A 93 693 946 HOH HOH . M 6 HOH A 94 694 964 HOH HOH . M 6 HOH A 95 695 965 HOH HOH . M 6 HOH A 96 696 968 HOH HOH . M 6 HOH A 97 697 995 HOH HOH . M 6 HOH A 98 698 996 HOH HOH . M 6 HOH A 99 699 997 HOH HOH . M 6 HOH A 100 700 999 HOH HOH . N 6 HOH B 1 601 139 HOH HOH . N 6 HOH B 2 602 2 HOH HOH . N 6 HOH B 3 603 331 HOH HOH . N 6 HOH B 4 604 362 HOH HOH . N 6 HOH B 5 605 3 HOH HOH . N 6 HOH B 6 606 4 HOH HOH . N 6 HOH B 7 607 354 HOH HOH . N 6 HOH B 8 608 6 HOH HOH . N 6 HOH B 9 609 337 HOH HOH . N 6 HOH B 10 610 8 HOH HOH . N 6 HOH B 11 611 338 HOH HOH . N 6 HOH B 12 612 9 HOH HOH . N 6 HOH B 13 613 339 HOH HOH . N 6 HOH B 14 614 11 HOH HOH . N 6 HOH B 15 615 319 HOH HOH . N 6 HOH B 16 616 12 HOH HOH . N 6 HOH B 17 617 313 HOH HOH . N 6 HOH B 18 618 513 HOH HOH . N 6 HOH B 19 619 14 HOH HOH . N 6 HOH B 20 620 17 HOH HOH . N 6 HOH B 21 621 18 HOH HOH . N 6 HOH B 22 622 19 HOH HOH . N 6 HOH B 23 623 20 HOH HOH . N 6 HOH B 24 624 21 HOH HOH . N 6 HOH B 25 625 23 HOH HOH . N 6 HOH B 26 626 27 HOH HOH . N 6 HOH B 27 627 34 HOH HOH . N 6 HOH B 28 628 35 HOH HOH . N 6 HOH B 29 629 36 HOH HOH . N 6 HOH B 30 630 440 HOH HOH . N 6 HOH B 31 631 41 HOH HOH . N 6 HOH B 32 632 342 HOH HOH . N 6 HOH B 33 633 43 HOH HOH . N 6 HOH B 34 634 44 HOH HOH . N 6 HOH B 35 635 46 HOH HOH . N 6 HOH B 36 636 446 HOH HOH . N 6 HOH B 37 637 50 HOH HOH . N 6 HOH B 38 638 51 HOH HOH . N 6 HOH B 39 639 53 HOH HOH . N 6 HOH B 40 640 55 HOH HOH . N 6 HOH B 41 641 56 HOH HOH . N 6 HOH B 42 642 57 HOH HOH . N 6 HOH B 43 643 59 HOH HOH . N 6 HOH B 44 644 460 HOH HOH . N 6 HOH B 45 645 515 HOH HOH . N 6 HOH B 46 646 61 HOH HOH . N 6 HOH B 47 647 62 HOH HOH . N 6 HOH B 48 648 65 HOH HOH . N 6 HOH B 49 649 64 HOH HOH . N 6 HOH B 50 650 69 HOH HOH . N 6 HOH B 51 651 73 HOH HOH . N 6 HOH B 52 652 573 HOH HOH . N 6 HOH B 53 653 75 HOH HOH . N 6 HOH B 54 654 76 HOH HOH . N 6 HOH B 55 655 78 HOH HOH . N 6 HOH B 56 656 80 HOH HOH . N 6 HOH B 57 657 81 HOH HOH . N 6 HOH B 58 658 82 HOH HOH . N 6 HOH B 59 659 83 HOH HOH . N 6 HOH B 60 660 86 HOH HOH . N 6 HOH B 61 661 87 HOH HOH . N 6 HOH B 62 662 90 HOH HOH . N 6 HOH B 63 663 91 HOH HOH . N 6 HOH B 64 664 92 HOH HOH . N 6 HOH B 65 665 101 HOH HOH . N 6 HOH B 66 666 105 HOH HOH . N 6 HOH B 67 667 107 HOH HOH . N 6 HOH B 68 668 108 HOH HOH . N 6 HOH B 69 669 109 HOH HOH . N 6 HOH B 70 670 112 HOH HOH . N 6 HOH B 71 671 113 HOH HOH . N 6 HOH B 72 672 114 HOH HOH . N 6 HOH B 73 673 120 HOH HOH . N 6 HOH B 74 674 122 HOH HOH . N 6 HOH B 75 675 124 HOH HOH . N 6 HOH B 76 676 126 HOH HOH . N 6 HOH B 77 677 127 HOH HOH . N 6 HOH B 78 678 133 HOH HOH . N 6 HOH B 79 679 134 HOH HOH . N 6 HOH B 80 680 135 HOH HOH . N 6 HOH B 81 681 137 HOH HOH . N 6 HOH B 82 682 144 HOH HOH . N 6 HOH B 83 683 145 HOH HOH . N 6 HOH B 84 684 147 HOH HOH . N 6 HOH B 85 685 155 HOH HOH . N 6 HOH B 86 686 156 HOH HOH . N 6 HOH B 87 687 157 HOH HOH . N 6 HOH B 88 688 160 HOH HOH . N 6 HOH B 89 689 161 HOH HOH . N 6 HOH B 90 690 162 HOH HOH . N 6 HOH B 91 691 163 HOH HOH . N 6 HOH B 92 692 928 HOH HOH . N 6 HOH B 93 693 930 HOH HOH . N 6 HOH B 94 694 936 HOH HOH . N 6 HOH B 95 695 937 HOH HOH . N 6 HOH B 96 696 951 HOH HOH . N 6 HOH B 97 697 953 HOH HOH . N 6 HOH B 98 698 955 HOH HOH . N 6 HOH B 99 699 970 HOH HOH . N 6 HOH B 100 700 971 HOH HOH . N 6 HOH B 101 701 991 HOH HOH . N 6 HOH B 102 702 992 HOH HOH . N 6 HOH B 103 703 993 HOH HOH . N 6 HOH B 104 704 994 HOH HOH . N 6 HOH B 105 705 998 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 L _atom_site.label_entity_id 3 _atom_site.Cartn_x -7.309 _atom_site.Cartn_y -34.657 _atom_site.Cartn_z 37.665 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 53.99 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 504 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #