data_8KE5 # _model_server_result.job_id dA_-ELiWJjncB_vZr-v5dw _model_server_result.datetime_utc '2025-01-11 06:54:41' _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 8ke5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 8KE5 # _exptl.entry_id 8KE5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 8KE5 _cell.length_a 104.685 _cell.length_b 104.685 _cell.length_c 71.338 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KE5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall 'P 64' _symmetry.space_group_name_H-M 'P 64' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_685 -x+1,-y+3,z -1 0 0 0 -1 0 0 0 1 -52.3425 271.979608 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 219 A GLU 396 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc2 A OG SER 222 A SER 399 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc3 B MG MG . A MG 501 1_555 D O1B ANP . A ANP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc4 B MG MG . A MG 501 1_555 D O1A ANP . A ANP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc5 B MG MG . A MG 501 1_555 F O HOH . A HOH 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc6 C MG MG . A MG 502 1_555 D O2B ANP . A ANP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc7 C MG MG . A MG 502 1_555 D O2G ANP . A ANP 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc8 C MG MG . A MG 502 1_555 F O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc9 C MG MG . A MG 502 1_555 F O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc10 C MG MG . A MG 502 1_555 F O HOH . A HOH 645 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc11 C MG MG . A MG 502 1_555 F O HOH . A HOH 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 8KE5 _atom_sites.fract_transf_matrix[1][1] 0.009552 _atom_sites.fract_transf_matrix[1][2] 0.005515 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01103 _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] 0.014018 _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 MG A 1 501 501 MG MG . C 2 MG A 1 502 502 MG MG . D 3 ANP A 1 503 503 ANP ANP . E 4 FXL A 1 504 504 FXL FXL . F 5 HOH A 1 601 601 HOH HOH . F 5 HOH A 2 602 602 HOH HOH . F 5 HOH A 3 603 603 HOH HOH . F 5 HOH A 4 604 604 HOH HOH . F 5 HOH A 5 605 605 HOH HOH . F 5 HOH A 6 606 606 HOH HOH . F 5 HOH A 7 607 607 HOH HOH . F 5 HOH A 8 608 608 HOH HOH . F 5 HOH A 9 609 609 HOH HOH . F 5 HOH A 10 610 610 HOH HOH . F 5 HOH A 11 611 611 HOH HOH . F 5 HOH A 12 612 612 HOH HOH . F 5 HOH A 13 613 613 HOH HOH . F 5 HOH A 14 614 614 HOH HOH . F 5 HOH A 15 615 615 HOH HOH . F 5 HOH A 16 616 616 HOH HOH . F 5 HOH A 17 617 617 HOH HOH . F 5 HOH A 18 618 618 HOH HOH . F 5 HOH A 19 619 619 HOH HOH . F 5 HOH A 20 620 620 HOH HOH . F 5 HOH A 21 621 621 HOH HOH . F 5 HOH A 22 622 622 HOH HOH . F 5 HOH A 23 623 623 HOH HOH . F 5 HOH A 24 624 624 HOH HOH . F 5 HOH A 25 625 625 HOH HOH . F 5 HOH A 26 626 626 HOH HOH . F 5 HOH A 27 627 627 HOH HOH . F 5 HOH A 28 628 628 HOH HOH . F 5 HOH A 29 629 629 HOH HOH . F 5 HOH A 30 630 630 HOH HOH . F 5 HOH A 31 631 631 HOH HOH . F 5 HOH A 32 632 632 HOH HOH . F 5 HOH A 33 633 633 HOH HOH . F 5 HOH A 34 634 634 HOH HOH . F 5 HOH A 35 635 635 HOH HOH . F 5 HOH A 36 636 636 HOH HOH . F 5 HOH A 37 637 637 HOH HOH . F 5 HOH A 38 638 638 HOH HOH . F 5 HOH A 39 639 639 HOH HOH . F 5 HOH A 40 640 640 HOH HOH . F 5 HOH A 41 641 641 HOH HOH . F 5 HOH A 42 642 642 HOH HOH . F 5 HOH A 43 643 643 HOH HOH . F 5 HOH A 44 644 644 HOH HOH . F 5 HOH A 45 645 645 HOH HOH . F 5 HOH A 46 646 646 HOH HOH . F 5 HOH A 47 647 648 HOH HOH . F 5 HOH A 48 648 647 HOH HOH . F 5 HOH A 49 649 649 HOH HOH . F 5 HOH A 50 650 650 HOH HOH . F 5 HOH A 51 651 651 HOH HOH . F 5 HOH A 52 652 652 HOH HOH . F 5 HOH A 53 653 653 HOH HOH . F 5 HOH A 54 654 654 HOH HOH . F 5 HOH A 55 655 655 HOH HOH . F 5 HOH A 56 656 656 HOH HOH . F 5 HOH A 57 657 657 HOH HOH . F 5 HOH A 58 658 658 HOH HOH . F 5 HOH A 59 659 659 HOH HOH . F 5 HOH A 60 660 660 HOH HOH . F 5 HOH A 61 661 661 HOH HOH . F 5 HOH A 62 662 662 HOH HOH . F 5 HOH A 63 663 663 HOH HOH . F 5 HOH A 64 664 664 HOH HOH . F 5 HOH A 65 665 665 HOH HOH . F 5 HOH A 66 666 666 HOH HOH . F 5 HOH A 67 667 667 HOH HOH . F 5 HOH A 68 668 668 HOH HOH . F 5 HOH A 69 669 669 HOH HOH . F 5 HOH A 70 670 670 HOH HOH . F 5 HOH A 71 671 671 HOH HOH . F 5 HOH A 72 672 672 HOH HOH . F 5 HOH A 73 673 673 HOH HOH . F 5 HOH A 74 674 674 HOH HOH . F 5 HOH A 75 675 675 HOH HOH . F 5 HOH A 76 676 676 HOH HOH . F 5 HOH A 77 677 677 HOH HOH . F 5 HOH A 78 678 678 HOH HOH . F 5 HOH A 79 679 679 HOH HOH . F 5 HOH A 80 680 680 HOH HOH . F 5 HOH A 81 681 681 HOH HOH . F 5 HOH A 82 682 682 HOH HOH . F 5 HOH A 83 683 683 HOH HOH . F 5 HOH A 84 684 684 HOH HOH . F 5 HOH A 85 685 685 HOH HOH . F 5 HOH A 86 686 686 HOH HOH . F 5 HOH A 87 687 687 HOH HOH . F 5 HOH A 88 688 688 HOH HOH . F 5 HOH A 89 689 689 HOH HOH . F 5 HOH A 90 690 690 HOH HOH . F 5 HOH A 91 691 691 HOH HOH . F 5 HOH A 92 692 692 HOH HOH . F 5 HOH A 93 693 693 HOH HOH . F 5 HOH A 94 694 694 HOH HOH . F 5 HOH A 95 695 695 HOH HOH . F 5 HOH A 96 696 696 HOH HOH . F 5 HOH A 97 697 697 HOH HOH . F 5 HOH A 98 698 698 HOH HOH . F 5 HOH A 99 699 699 HOH HOH . F 5 HOH A 100 700 700 HOH HOH . F 5 HOH A 101 701 701 HOH HOH . F 5 HOH A 102 702 702 HOH HOH . F 5 HOH A 103 703 703 HOH HOH . F 5 HOH A 104 704 704 HOH HOH . F 5 HOH A 105 705 705 HOH HOH . F 5 HOH A 106 706 706 HOH HOH . F 5 HOH A 107 707 707 HOH HOH . F 5 HOH A 108 708 708 HOH HOH . F 5 HOH A 109 709 709 HOH HOH . F 5 HOH A 110 710 710 HOH HOH . F 5 HOH A 111 711 711 HOH HOH . F 5 HOH A 112 712 712 HOH HOH . F 5 HOH A 113 713 713 HOH HOH . F 5 HOH A 114 714 714 HOH HOH . F 5 HOH A 115 715 715 HOH HOH . F 5 HOH A 116 716 716 HOH HOH . F 5 HOH A 117 717 717 HOH HOH . F 5 HOH A 118 718 718 HOH HOH . F 5 HOH A 119 719 719 HOH HOH . F 5 HOH A 120 720 720 HOH HOH . F 5 HOH A 121 721 721 HOH HOH . F 5 HOH A 122 722 722 HOH HOH . F 5 HOH A 123 723 723 HOH HOH . F 5 HOH A 124 724 724 HOH HOH . F 5 HOH A 125 725 725 HOH HOH . F 5 HOH A 126 726 726 HOH HOH . F 5 HOH A 127 727 727 HOH HOH . F 5 HOH A 128 728 728 HOH HOH . F 5 HOH A 129 729 729 HOH HOH . F 5 HOH A 130 730 730 HOH HOH . F 5 HOH A 131 731 731 HOH HOH . F 5 HOH A 132 732 732 HOH HOH . F 5 HOH A 133 733 733 HOH HOH . F 5 HOH A 134 734 734 HOH HOH . F 5 HOH A 135 735 735 HOH HOH . F 5 HOH A 136 736 736 HOH HOH . F 5 HOH A 137 737 737 HOH HOH . F 5 HOH A 138 738 738 HOH HOH . F 5 HOH A 139 739 739 HOH HOH . F 5 HOH A 140 740 740 HOH HOH . F 5 HOH A 141 741 741 HOH HOH . F 5 HOH A 142 742 742 HOH HOH . F 5 HOH A 143 743 743 HOH HOH . F 5 HOH A 144 744 744 HOH HOH . F 5 HOH A 145 745 745 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 PG ANP . . . D 3 -9.247 147.153 15.342 1 19.79 ? PG ANP 503 A 1 HETATM 2 O O1G ANP . . . D 3 -9.774 148.172 14.363 1 18.52 ? O1G ANP 503 A 1 HETATM 3 O O2G ANP . . . D 3 -10.221 146.79 16.436 1 16.65 ? O2G ANP 503 A 1 HETATM 4 O O3G ANP . . . D 3 -7.851 147.446 15.833 1 20.44 ? O3G ANP 503 A 1 HETATM 5 P PB ANP . . . D 3 -8.877 144.134 15.142 1 19.01 ? PB ANP 503 A 1 HETATM 6 O O1B ANP . . . D 3 -7.439 143.709 14.993 1 19.53 ? O1B ANP 503 A 1 HETATM 7 O O2B ANP . . . D 3 -9.483 144.182 16.522 1 17.23 ? O2B ANP 503 A 1 HETATM 8 N N3B ANP . . . D 3 -9.084 145.698 14.389 1 15.87 ? N3B ANP 503 A 1 HETATM 9 P PA ANP . . . D 3 -9.294 141.671 13.806 1 17.92 ? PA ANP 503 A 1 HETATM 10 O O1A ANP . . . D 3 -8.032 141.801 12.992 1 19.38 -1 O1A ANP 503 A 1 HETATM 11 O O2A ANP . . . D 3 -9.347 140.745 14.995 1 17.95 ? O2A ANP 503 A 1 HETATM 12 O O3A ANP . . . D 3 -9.779 143.128 14.274 1 16.5 ? O3A ANP 503 A 1 HETATM 13 O O5' ANP . . . D 3 -10.512 141.312 12.819 1 15.34 ? O5' ANP 503 A 1 HETATM 14 C C5' ANP . . . D 3 -10.301 141.126 11.424 1 15.37 ? C5' ANP 503 A 1 HETATM 15 C C4' ANP . . . D 3 -11.066 142.211 10.675 1 17.14 ? C4' ANP 503 A 1 HETATM 16 O O4' ANP . . . D 3 -12.404 142.332 11.167 1 16.85 ? O4' ANP 503 A 1 HETATM 17 C C3' ANP . . . D 3 -10.421 143.578 10.854 1 19.65 ? C3' ANP 503 A 1 HETATM 18 O O3' ANP . . . D 3 -9.455 143.838 9.827 1 22.13 ? O3' ANP 503 A 1 HETATM 19 C C2' ANP . . . D 3 -11.586 144.555 10.849 1 22.51 ? C2' ANP 503 A 1 HETATM 20 O O2' ANP . . . D 3 -11.777 145.179 9.574 1 19.3 ? O2' ANP 503 A 1 HETATM 21 C C1' ANP . . . D 3 -12.81 143.705 11.14 1 18.64 ? C1' ANP 503 A 1 HETATM 22 N N9 ANP . . . D 3 -13.382 144.094 12.453 1 18.42 ? N9 ANP 503 A 1 HETATM 23 C C8 ANP . . . D 3 -12.841 143.809 13.652 1 16.25 ? C8 ANP 503 A 1 HETATM 24 N N7 ANP . . . D 3 -13.588 144.317 14.663 1 15.21 ? N7 ANP 503 A 1 HETATM 25 C C5 ANP . . . D 3 -14.624 144.969 14.108 1 15.23 ? C5 ANP 503 A 1 HETATM 26 C C6 ANP . . . D 3 -15.787 145.738 14.607 1 17.13 ? C6 ANP 503 A 1 HETATM 27 N N6 ANP . . . D 3 -15.991 145.913 15.934 1 18.19 ? N6 ANP 503 A 1 HETATM 28 N N1 ANP . . . D 3 -16.634 146.258 13.693 1 19.67 ? N1 ANP 503 A 1 HETATM 29 C C2 ANP . . . D 3 -16.44 146.089 12.373 1 20.17 ? C2 ANP 503 A 1 HETATM 30 N N3 ANP . . . D 3 -15.408 145.403 11.85 1 16.15 ? N3 ANP 503 A 1 HETATM 31 C C4 ANP . . . D 3 -14.48 144.828 12.651 1 18.4 ? C4 ANP 503 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #