data_2ZDY # _model_server_result.job_id EI54-8TEu5P6pZtZkSfvrQ _model_server_result.datetime_utc '2024-11-14 17:38:39' _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 2zdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2ZDY # _exptl.entry_id 2ZDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 99.66 _cell.angle_gamma 90 _cell.entry_id 2ZDY _cell.length_a 70.713 _cell.length_b 69.09 _cell.length_c 81.492 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 D N N ? 3 G 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 ASN 241 A ASN 258 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc2 C MG MG . A MG 500 1_555 D O2B ADP . A ADP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc3 C MG MG . A MG 500 1_555 D O1A ADP . A ADP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc4 C MG MG . A MG 500 1_555 H O HOH . A HOH 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc5 B OD1 ASN 241 B ASN 258 1_555 F MG MG . B MG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc6 F MG MG . B MG 1500 1_555 G O3B ADP . B ADP 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc7 F MG MG . B MG 1500 1_555 G O1A ADP . B ADP 1501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 2ZDY _atom_sites.fract_transf_matrix[1][1] 0.014142 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002408 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014474 _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] 0.012448 _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 MG A 1 500 500 MG MG . D 3 ADP A 1 501 501 ADP ADP . E 4 EPE A 1 600 600 EPE EPE . F 2 MG B 1 1500 1500 MG MG . G 3 ADP B 1 1501 1501 ADP ADP . H 5 HOH A 1 601 2 HOH HOH . H 5 HOH A 2 602 4 HOH HOH . H 5 HOH A 3 603 6 HOH HOH . H 5 HOH A 4 604 7 HOH HOH . H 5 HOH A 5 605 8 HOH HOH . H 5 HOH A 6 606 11 HOH HOH . H 5 HOH A 7 607 12 HOH HOH . H 5 HOH A 8 608 14 HOH HOH . H 5 HOH A 9 609 15 HOH HOH . H 5 HOH A 10 610 17 HOH HOH . H 5 HOH A 11 611 19 HOH HOH . H 5 HOH A 12 612 21 HOH HOH . H 5 HOH A 13 613 24 HOH HOH . H 5 HOH A 14 614 25 HOH HOH . H 5 HOH A 15 615 27 HOH HOH . H 5 HOH A 16 616 28 HOH HOH . H 5 HOH A 17 617 31 HOH HOH . H 5 HOH A 18 618 34 HOH HOH . H 5 HOH A 19 619 35 HOH HOH . H 5 HOH A 20 620 36 HOH HOH . H 5 HOH A 21 621 37 HOH HOH . H 5 HOH A 22 622 39 HOH HOH . H 5 HOH A 23 623 42 HOH HOH . H 5 HOH A 24 624 43 HOH HOH . H 5 HOH A 25 625 46 HOH HOH . H 5 HOH A 26 626 47 HOH HOH . H 5 HOH A 27 627 48 HOH HOH . H 5 HOH A 28 628 51 HOH HOH . H 5 HOH A 29 629 54 HOH HOH . H 5 HOH A 30 630 55 HOH HOH . H 5 HOH A 31 631 56 HOH HOH . H 5 HOH A 32 632 59 HOH HOH . H 5 HOH A 33 633 60 HOH HOH . H 5 HOH A 34 634 61 HOH HOH . H 5 HOH A 35 635 62 HOH HOH . H 5 HOH A 36 636 65 HOH HOH . H 5 HOH A 37 637 66 HOH HOH . H 5 HOH A 38 638 69 HOH HOH . H 5 HOH A 39 639 70 HOH HOH . H 5 HOH A 40 640 71 HOH HOH . H 5 HOH A 41 641 72 HOH HOH . H 5 HOH A 42 642 73 HOH HOH . H 5 HOH A 43 643 78 HOH HOH . H 5 HOH A 44 644 80 HOH HOH . H 5 HOH A 45 645 81 HOH HOH . H 5 HOH A 46 646 82 HOH HOH . H 5 HOH A 47 647 84 HOH HOH . H 5 HOH A 48 648 85 HOH HOH . H 5 HOH A 49 649 86 HOH HOH . H 5 HOH A 50 650 87 HOH HOH . H 5 HOH A 51 651 89 HOH HOH . H 5 HOH A 52 652 90 HOH HOH . H 5 HOH A 53 653 91 HOH HOH . H 5 HOH A 54 654 93 HOH HOH . H 5 HOH A 55 655 94 HOH HOH . H 5 HOH A 56 656 97 HOH HOH . H 5 HOH A 57 657 99 HOH HOH . H 5 HOH A 58 658 101 HOH HOH . H 5 HOH A 59 659 102 HOH HOH . H 5 HOH A 60 660 103 HOH HOH . H 5 HOH A 61 661 104 HOH HOH . H 5 HOH A 62 662 105 HOH HOH . H 5 HOH A 63 663 106 HOH HOH . H 5 HOH A 64 664 107 HOH HOH . H 5 HOH A 65 665 108 HOH HOH . H 5 HOH A 66 666 109 HOH HOH . H 5 HOH A 67 667 110 HOH HOH . H 5 HOH A 68 668 111 HOH HOH . H 5 HOH A 69 669 112 HOH HOH . H 5 HOH A 70 670 115 HOH HOH . H 5 HOH A 71 671 117 HOH HOH . H 5 HOH A 72 672 118 HOH HOH . H 5 HOH A 73 673 119 HOH HOH . H 5 HOH A 74 674 123 HOH HOH . H 5 HOH A 75 675 124 HOH HOH . H 5 HOH A 76 676 125 HOH HOH . H 5 HOH A 77 677 126 HOH HOH . H 5 HOH A 78 678 128 HOH HOH . H 5 HOH A 79 679 129 HOH HOH . H 5 HOH A 80 680 130 HOH HOH . H 5 HOH A 81 681 132 HOH HOH . H 5 HOH A 82 682 134 HOH HOH . H 5 HOH A 83 683 136 HOH HOH . H 5 HOH A 84 684 139 HOH HOH . H 5 HOH A 85 685 141 HOH HOH . H 5 HOH A 86 686 142 HOH HOH . H 5 HOH A 87 687 146 HOH HOH . H 5 HOH A 88 688 147 HOH HOH . H 5 HOH A 89 689 149 HOH HOH . H 5 HOH A 90 690 152 HOH HOH . H 5 HOH A 91 691 153 HOH HOH . H 5 HOH A 92 692 155 HOH HOH . H 5 HOH A 93 693 157 HOH HOH . H 5 HOH A 94 694 159 HOH HOH . H 5 HOH A 95 695 160 HOH HOH . H 5 HOH A 96 696 165 HOH HOH . H 5 HOH A 97 697 167 HOH HOH . H 5 HOH A 98 698 170 HOH HOH . H 5 HOH A 99 699 174 HOH HOH . H 5 HOH A 100 700 175 HOH HOH . H 5 HOH A 101 701 178 HOH HOH . I 5 HOH B 1 1502 1 HOH HOH . I 5 HOH B 2 1503 3 HOH HOH . I 5 HOH B 3 1504 5 HOH HOH . I 5 HOH B 4 1505 9 HOH HOH . I 5 HOH B 5 1506 10 HOH HOH . I 5 HOH B 6 1507 13 HOH HOH . I 5 HOH B 7 1508 16 HOH HOH . I 5 HOH B 8 1509 18 HOH HOH . I 5 HOH B 9 1510 20 HOH HOH . I 5 HOH B 10 1511 22 HOH HOH . I 5 HOH B 11 1512 23 HOH HOH . I 5 HOH B 12 1513 26 HOH HOH . I 5 HOH B 13 1514 29 HOH HOH . I 5 HOH B 14 1515 30 HOH HOH . I 5 HOH B 15 1516 32 HOH HOH . I 5 HOH B 16 1517 33 HOH HOH . I 5 HOH B 17 1518 38 HOH HOH . I 5 HOH B 18 1519 40 HOH HOH . I 5 HOH B 19 1520 41 HOH HOH . I 5 HOH B 20 1521 44 HOH HOH . I 5 HOH B 21 1522 45 HOH HOH . I 5 HOH B 22 1523 49 HOH HOH . I 5 HOH B 23 1524 50 HOH HOH . I 5 HOH B 24 1525 52 HOH HOH . I 5 HOH B 25 1526 53 HOH HOH . I 5 HOH B 26 1527 57 HOH HOH . I 5 HOH B 27 1528 58 HOH HOH . I 5 HOH B 28 1529 63 HOH HOH . I 5 HOH B 29 1530 64 HOH HOH . I 5 HOH B 30 1531 67 HOH HOH . I 5 HOH B 31 1532 68 HOH HOH . I 5 HOH B 32 1533 74 HOH HOH . I 5 HOH B 33 1534 75 HOH HOH . I 5 HOH B 34 1535 76 HOH HOH . I 5 HOH B 35 1536 77 HOH HOH . I 5 HOH B 36 1537 79 HOH HOH . I 5 HOH B 37 1538 83 HOH HOH . I 5 HOH B 38 1539 88 HOH HOH . I 5 HOH B 39 1540 92 HOH HOH . I 5 HOH B 40 1541 95 HOH HOH . I 5 HOH B 41 1542 96 HOH HOH . I 5 HOH B 42 1543 98 HOH HOH . I 5 HOH B 43 1544 100 HOH HOH . I 5 HOH B 44 1545 113 HOH HOH . I 5 HOH B 45 1546 114 HOH HOH . I 5 HOH B 46 1547 116 HOH HOH . I 5 HOH B 47 1548 120 HOH HOH . I 5 HOH B 48 1549 121 HOH HOH . I 5 HOH B 49 1550 122 HOH HOH . I 5 HOH B 50 1551 127 HOH HOH . I 5 HOH B 51 1552 131 HOH HOH . I 5 HOH B 52 1553 133 HOH HOH . I 5 HOH B 53 1554 135 HOH HOH . I 5 HOH B 54 1555 137 HOH HOH . I 5 HOH B 55 1556 138 HOH HOH . I 5 HOH B 56 1557 140 HOH HOH . I 5 HOH B 57 1558 143 HOH HOH . I 5 HOH B 58 1559 144 HOH HOH . I 5 HOH B 59 1560 145 HOH HOH . I 5 HOH B 60 1561 148 HOH HOH . I 5 HOH B 61 1562 150 HOH HOH . I 5 HOH B 62 1563 151 HOH HOH . I 5 HOH B 63 1564 154 HOH HOH . I 5 HOH B 64 1565 156 HOH HOH . I 5 HOH B 65 1566 158 HOH HOH . I 5 HOH B 66 1567 161 HOH HOH . I 5 HOH B 67 1568 162 HOH HOH . I 5 HOH B 68 1569 163 HOH HOH . I 5 HOH B 69 1570 164 HOH HOH . I 5 HOH B 70 1571 166 HOH HOH . I 5 HOH B 71 1572 168 HOH HOH . I 5 HOH B 72 1573 169 HOH HOH . I 5 HOH B 73 1574 171 HOH HOH . I 5 HOH B 74 1575 172 HOH HOH . I 5 HOH B 75 1576 173 HOH HOH . I 5 HOH B 76 1577 176 HOH HOH . I 5 HOH B 77 1578 177 HOH HOH . I 5 HOH B 78 1579 179 HOH HOH . I 5 HOH B 79 1580 180 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 P PB ADP . . . D 3 -20.796 6.396 11.732 1 41.69 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . D 3 -21.254 6.649 10.377 1 41.61 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . D 3 -20.855 7.665 12.506 1 42.5 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . D 3 -19.252 5.757 11.776 1 39.95 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . D 3 -22.796 5.282 13.534 1 39.18 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . D 3 -22.389 6.211 14.554 1 38.98 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . D 3 -23.234 3.882 13.948 1 39.44 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . D 3 -21.605 5.228 12.48 1 41.8 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . D 3 -24.046 5.922 12.737 1 35.66 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . D 3 -24.593 5.231 11.696 1 30.92 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . D 3 -25.341 5.761 10.571 1 29.76 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . D 3 -26.776 6.061 10.691 1 29.56 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . D 3 -24.574 7.014 10.033 1 29.03 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . D 3 -23.502 6.685 9.142 1 32.44 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . D 3 -25.701 7.832 9.459 1 29.7 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . D 3 -25.813 7.638 8.072 1 31.1 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . D 3 -26.959 7.398 10.237 1 29.43 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . D 3 -27.267 8.308 11.41 1 26.85 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . D 3 -26.974 8.283 12.782 1 27.52 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . D 3 -27.411 9.246 13.482 1 28.03 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . D 3 -28.052 10.012 12.584 1 22.9 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . D 3 -28.8 11.28 12.632 1 22.01 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . D 3 -28.947 11.921 13.784 1 18.79 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . D 3 -29.386 11.848 11.409 1 25.15 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . D 3 -29.248 11.192 10.157 1 23.8 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . D 3 -28.541 9.973 10.047 1 22.52 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . D 3 -27.986 9.451 11.25 1 24.21 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #