data_3EDL
#
_model_server_result.job_id            R_nyvTMzUBcjkokHxFsGzQ 
_model_server_result.datetime_utc      '2025-07-12 21:18:25' 
_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          3edl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":501}' 
#
_entry.id    3EDL 
#
_exptl.entry_id    3EDL 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              24.305 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MAGNESIUM ION' 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 165-meric 165 'representative helical assembly' 1 
? pentameric 5 'helical asymmetric unit' 2 
? pentameric 5 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 1 (1-33) 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 3 H 
#
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]
H 'transform to helical frame' ? ? 1 0 0 0 1 0 0 0 1 -300 -300 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? 0.693402 -0.720551 0 0.720551 0.693402 0 0 0 1 308.14478 -124.18588 -104.614 
3 'helical symmetry operation' ? ? 0.925134 -0.379641 0 0.379641 0.925134 0 0 0 1 136.35217 -91.43249 -93.60078 
4 'helical symmetry operation' ? ? 0.999668 0.025777 0 -0.025777 0.999668 0 0 0 1 -7.63349 7.83287 -82.58757 
5 'helical symmetry operation' ? ? 0.904339 0.426816 0 -0.426816 0.904339 0 0 0 1 -99.34628 156.74307 -71.57435 
6 'helical symmetry operation' ? ? 0.655345 0.75533 0 -0.75533 0.655345 0 0 0 1 -123.20241 329.99539 -60.56113 
7 'helical symmetry operation' ? ? 0.294996 0.955499 0 -0.955499 0.294996 0 0 0 1 -75.14825 498.15094 -49.54792 
8 'helical symmetry operation' ? ? -0.115479 0.99331 0 -0.99331 -0.115479 0 0 0 1 36.65085 632.63678 -38.5347 
9 'helical symmetry operation' ? ? -0.506332 0.862339 0 -0.862339 -0.506332 0 0 0 1 193.19807 710.6012 -27.52149 
10 'helical symmetry operation' ? ? -0.811149 0.584839 0 -0.584839 -0.811149 0 0 0 1 367.89301 718.79651 -16.50827 
11 'helical symmetry operation' ? ? -0.978136 0.207964 0 -0.207964 -0.978136 0 0 0 1 531.05164 655.83026 -5.49506 
12 'helical symmetry operation' ? ? -0.978919 -0.204248 0 0.204248 -0.978919 0 0 0 1 654.95007 532.40149 5.51816 
13 'helical symmetry operation' ? ? -0.813365 -0.581754 0 0.581754 -0.813365 0 0 0 1 718.53564 369.48322 16.53138 
14 'helical symmetry operation' ? ? -0.509604 -0.860409 0 0.860409 -0.509604 0 0 0 1 711.00391 194.75842 27.54459 
15 'helical symmetry operation' ? ? -0.119251 -0.992864 0 0.992864 -0.119251 0 0 0 1 633.63464 37.9162 38.55781 
16 'helical symmetry operation' ? ? 0.291364 -0.956612 0 0.956612 0.291364 0 0 0 1 499.5744 -74.39291 49.57103 
17 'helical symmetry operation' ? ? 0.652471 -0.757813 0 0.757813 0.652471 0 0 0 1 331.60263 -123.08542 60.58424 
18 'helical symmetry operation' ? ? 0.674302 -0.738455 0 0.738455 0.674302 0 0 0 1 319.24588 -123.82732 -22.024 
19 'helical symmetry operation' ? ? 0.914879 -0.403728 0 0.403728 0.914879 0 0 0 1 146.65477 -95.58215 -11.01078 
20 'helical symmetry operation' ? ? 1 -0.0004 0 0.0004 1 0 0 0 1 0.11997 -0.11992 0.00243 
21 'helical symmetry operation' ? ? 0.915202 0.402996 0 -0.402996 0.915202 0 0 0 1 -95.4594 146.33849 11.01565 
22 'helical symmetry operation' ? ? 0.674893 0.737916 0 -0.737916 0.674893 0 0 0 1 -123.84258 318.90698 22.02886 
23 'helical symmetry operation' ? ? 0.319906 0.947449 0 -0.947449 0.319906 0 0 0 1 -80.20668 488.26279 33.04208 
24 'helical symmetry operation' ? ? -0.089438 0.995992 0 -0.995992 -0.089438 0 0 0 1 28.03368 625.62909 44.0553 
25 'helical symmetry operation' ? ? -0.483585 0.875297 0 -0.875297 -0.483585 0 0 0 1 182.48639 707.66473 55.06851 
26 'helical symmetry operation' ? ? -0.795562 0.605872 0 -0.605872 -0.795562 0 0 0 1 356.90692 720.43024 66.08173 
27 'helical symmetry operation' ? ? -0.972357 0.233498 0 -0.233498 -0.972357 0 0 0 1 521.6579 661.75653 77.09494 
28 'helical symmetry operation' ? ? -0.98393 -0.178553 0 0.178553 -0.98393 0 0 0 1 648.74487 541.61334 88.10816 
29 'helical symmetry operation' ? ? -0.828315 -0.560263 0 0.560263 -0.828315 0 0 0 1 716.57336 380.41541 99.12138 
30 'helical symmetry operation' ? ? -0.531952 -0.846774 0 0.846774 -0.531952 0 0 0 1 713.61798 205.55331 110.13459 
31 'helical symmetry operation' ? ? -0.145201 -0.989402 0 0.989402 -0.145201 0 0 0 1 640.38086 46.73955 121.1478 
32 'helical symmetry operation' ? ? 0.266223 -0.963911 0 0.963911 0.266223 0 0 0 1 509.30649 -69.04037 132.16103 
33 'helical symmetry operation' ? ? 0.632411 -0.774633 0 0.774633 0.632411 0 0 0 1 342.66687 -122.11318 143.17424 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 G N N 
? 6 K N N 
? 6 M 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 G MG MG . A MG 501 1_555 H O1G GTP . B GTP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc2 C OG1 THR 97 D THR 169 1_555 K MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc3 L O2G ANP . D ANP 500 1_555 K MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc4 L O1B ANP . D ANP 500 1_555 K MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc5 K MG MG . D MG 501 1_555 Q O HOH . D HOH 667 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc6 K MG MG . D MG 501 1_555 Q O HOH . D HOH 668 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc7 K MG MG . D MG 501 1_555 Q O HOH . D HOH 673 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc8 M MG MG . F MG 503 1_555 N O2B GTP . F GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc9 M MG MG . F MG 503 1_555 N O3G GTP . F GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? 
#
_chem_comp.formula           'Mg 2' 
_chem_comp.formula_weight    24.305 
_chem_comp.id                MG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MAGNESIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     3EDL 
_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
F 5 ZN A 1 900 900 ZN ZN . 
G 6 MG A 1 501 501 MG MG . 
H 7 GTP B 1 500 500 GTP GTP . 
I 8 GDP B 1 600 600 GDP GDP . 
J 9 TA1 B 1 601 601 TA1 TA1 . 
K 6 MG D 1 501 501 MG MG . 
L 10 ANP D 1 500 500 ANP ANP . 
M 6 MG F 1 503 503 MG MG . 
N 7 GTP F 1 601 601 GTP GTP . 
O 8 GDP F 1 603 603 GDP GDP . 
P 11 CN2 G 1 701 701 CN2 CN2 . 
Q 12 HOH D 1 600 600 HOH HOH . 
Q 12 HOH D 2 601 601 HOH HOH . 
Q 12 HOH D 3 602 602 HOH HOH . 
Q 12 HOH D 4 603 603 HOH HOH . 
Q 12 HOH D 5 604 604 HOH HOH . 
Q 12 HOH D 6 605 605 HOH HOH . 
Q 12 HOH D 7 607 607 HOH HOH . 
Q 12 HOH D 8 608 608 HOH HOH . 
Q 12 HOH D 9 609 609 HOH HOH . 
Q 12 HOH D 10 610 610 HOH HOH . 
Q 12 HOH D 11 611 611 HOH HOH . 
Q 12 HOH D 12 612 612 HOH HOH . 
Q 12 HOH D 13 613 613 HOH HOH . 
Q 12 HOH D 14 614 614 HOH HOH . 
Q 12 HOH D 15 615 615 HOH HOH . 
Q 12 HOH D 16 617 617 HOH HOH . 
Q 12 HOH D 17 618 618 HOH HOH . 
Q 12 HOH D 18 619 619 HOH HOH . 
Q 12 HOH D 19 620 620 HOH HOH . 
Q 12 HOH D 20 621 621 HOH HOH . 
Q 12 HOH D 21 622 622 HOH HOH . 
Q 12 HOH D 22 623 623 HOH HOH . 
Q 12 HOH D 23 624 624 HOH HOH . 
Q 12 HOH D 24 625 625 HOH HOH . 
Q 12 HOH D 25 626 626 HOH HOH . 
Q 12 HOH D 26 627 627 HOH HOH . 
Q 12 HOH D 27 628 628 HOH HOH . 
Q 12 HOH D 28 629 629 HOH HOH . 
Q 12 HOH D 29 630 630 HOH HOH . 
Q 12 HOH D 30 631 631 HOH HOH . 
Q 12 HOH D 31 632 632 HOH HOH . 
Q 12 HOH D 32 633 633 HOH HOH . 
Q 12 HOH D 33 634 634 HOH HOH . 
Q 12 HOH D 34 635 635 HOH HOH . 
Q 12 HOH D 35 636 636 HOH HOH . 
Q 12 HOH D 36 637 637 HOH HOH . 
Q 12 HOH D 37 638 638 HOH HOH . 
Q 12 HOH D 38 639 639 HOH HOH . 
Q 12 HOH D 39 640 640 HOH HOH . 
Q 12 HOH D 40 641 641 HOH HOH . 
Q 12 HOH D 41 642 642 HOH HOH . 
Q 12 HOH D 42 643 643 HOH HOH . 
Q 12 HOH D 43 644 644 HOH HOH . 
Q 12 HOH D 44 645 645 HOH HOH . 
Q 12 HOH D 45 646 646 HOH HOH . 
Q 12 HOH D 46 647 647 HOH HOH . 
Q 12 HOH D 47 648 648 HOH HOH . 
Q 12 HOH D 48 650 650 HOH HOH . 
Q 12 HOH D 49 651 651 HOH HOH . 
Q 12 HOH D 50 652 652 HOH HOH . 
Q 12 HOH D 51 653 653 HOH HOH . 
Q 12 HOH D 52 654 654 HOH HOH . 
Q 12 HOH D 53 655 655 HOH HOH . 
Q 12 HOH D 54 656 656 HOH HOH . 
Q 12 HOH D 55 657 657 HOH HOH . 
Q 12 HOH D 56 658 658 HOH HOH . 
Q 12 HOH D 57 659 659 HOH HOH . 
Q 12 HOH D 58 660 660 HOH HOH . 
Q 12 HOH D 59 661 661 HOH HOH . 
Q 12 HOH D 60 662 662 HOH HOH . 
Q 12 HOH D 61 665 665 HOH HOH . 
Q 12 HOH D 62 666 666 HOH HOH . 
Q 12 HOH D 63 667 667 HOH HOH . 
Q 12 HOH D 64 668 668 HOH HOH . 
Q 12 HOH D 65 669 669 HOH HOH . 
Q 12 HOH D 66 670 670 HOH HOH . 
Q 12 HOH D 67 671 671 HOH HOH . 
Q 12 HOH D 68 673 673 HOH HOH . 
Q 12 HOH D 69 678 678 HOH HOH . 
Q 12 HOH D 70 679 679 HOH HOH . 
Q 12 HOH D 71 680 680 HOH HOH . 
Q 12 HOH D 72 681 681 HOH HOH . 
Q 12 HOH D 73 682 682 HOH HOH . 
Q 12 HOH D 74 683 683 HOH HOH . 
Q 12 HOH D 75 684 684 HOH HOH . 
Q 12 HOH D 76 685 685 HOH HOH . 
Q 12 HOH D 77 686 686 HOH HOH . 
Q 12 HOH D 78 687 687 HOH HOH . 
Q 12 HOH D 79 688 688 HOH HOH . 
Q 12 HOH D 80 689 689 HOH HOH . 
Q 12 HOH D 81 690 690 HOH HOH . 
Q 12 HOH D 82 691 691 HOH HOH . 
Q 12 HOH D 83 692 692 HOH HOH . 
Q 12 HOH D 84 693 693 HOH HOH . 
Q 12 HOH D 85 695 695 HOH HOH . 
Q 12 HOH D 86 696 696 HOH HOH . 
Q 12 HOH D 87 697 697 HOH HOH . 
Q 12 HOH D 88 699 699 HOH HOH . 
Q 12 HOH D 89 700 700 HOH HOH . 
Q 12 HOH D 90 701 701 HOH HOH . 
Q 12 HOH D 91 702 702 HOH HOH . 
Q 12 HOH D 92 703 703 HOH HOH . 
Q 12 HOH D 93 704 704 HOH HOH . 
Q 12 HOH D 94 705 705 HOH HOH . 
Q 12 HOH D 95 707 707 HOH HOH . 
Q 12 HOH D 96 708 708 HOH HOH . 
Q 12 HOH D 97 709 709 HOH HOH . 
Q 12 HOH D 98 710 710 HOH HOH . 
R 12 HOH F 1 606 606 HOH HOH . 
R 12 HOH F 2 616 616 HOH HOH . 
R 12 HOH F 3 649 649 HOH HOH . 
R 12 HOH F 4 663 663 HOH HOH . 
R 12 HOH F 5 664 664 HOH HOH . 
R 12 HOH F 6 672 672 HOH HOH . 
R 12 HOH F 7 694 694 HOH HOH . 
R 12 HOH F 8 698 698 HOH HOH . 
R 12 HOH F 9 706 706 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           MG 
_atom_site.label_atom_id         MG 
_atom_site.label_comp_id         MG 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         G 
_atom_site.label_entity_id       6 
_atom_site.Cartn_x               205.895 
_atom_site.Cartn_y               379.973 
_atom_site.Cartn_z               79.14 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        18.63 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          MG 
_atom_site.auth_comp_id          MG 
_atom_site.auth_seq_id           501 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#