data_8KE3 # _model_server_result.job_id IMlXYenP7WuFzmWngrGM4A _model_server_result.datetime_utc '2024-11-15 11:39:14' _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 8ke3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8KE3 # _exptl.entry_id 8KE3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _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 8KE3 _cell.length_a 104.67 _cell.length_b 104.67 _cell.length_c 71.813 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KE3 _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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -52.335 90.646879 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OE1 GLU 219 A GLU 396 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc2 A OE2 GLU 219 A GLU 396 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc3 A OG SER 222 A SER 399 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 B O1B ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc5 B O2A ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc6 B O2G ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc7 B O2B ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc8 C MG MG . A MG 502 1_555 F O HOH . A HOH 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc9 D MG MG . A MG 503 1_555 F O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc10 D MG MG . A MG 503 1_555 F O HOH . A HOH 640 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc11 D MG MG . A MG 503 1_555 F O HOH . A HOH 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc12 D MG MG . A MG 503 1_555 F O HOH . A HOH 663 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? # _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 8KE3 _atom_sites.fract_transf_matrix[1][1] 0.009554 _atom_sites.fract_transf_matrix[1][2] 0.005516 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011032 _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] 0.013925 _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 ANP A 1 501 501 ANP ANP . C 3 MG A 1 502 502 MG MG . D 3 MG A 1 503 503 MG MG . E 4 FXC A 1 504 504 FXC FXC . 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 47 647 647 HOH HOH . F 5 HOH A 48 648 648 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 . # 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 . . . B 2 -24.994 25.062 -3.828 1 22.65 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 -23.716 24.947 -4.593 1 22.06 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 -24.829 26.129 -2.68 1 19.07 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 -25.355 23.655 -3.204 1 23.1 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 -27.514 26.285 -4.148 1 21.72 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 -28.627 25.315 -3.936 1 24.99 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 -27.082 26.877 -2.777 1 22.86 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 -26.217 25.53 -4.9 1 28.64 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 -29.456 27.808 -5.394 1 19.76 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 -30.169 28.163 -4.147 1 19.38 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 -30.089 26.641 -6.153 1 18.61 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 -27.947 27.428 -5.114 1 22.26 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 -29.348 29.099 -6.3 1 19.33 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 -29.466 29.032 -7.736 1 24.11 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 -28.1 29.08 -8.38 1 17.47 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 -27.361 30.215 -7.888 1 16.88 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 -27.188 27.891 -8.112 1 16.09 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 -27.489 26.803 -8.979 1 16.85 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 -25.804 28.481 -8.395 1 16.91 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 -25.472 28.432 -9.778 1 18.55 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 -25.971 29.939 -7.943 1 17.04 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 -25.387 30.221 -6.636 1 19.25 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 -25.953 29.991 -5.409 1 17.1 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 -25.195 30.339 -4.396 1 17.17 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 -24.047 30.83 -5 1 17.2 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 -22.847 31.363 -4.476 1 14.43 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 -22.601 31.493 -3.171 1 15.96 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 -21.89 31.766 -5.36 1 18.5 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 -22.132 31.638 -6.671 1 15.29 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 -23.225 31.151 -7.273 1 16.27 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 -24.151 30.762 -6.381 1 18.82 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 49 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 361 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #