data_5K1X # _model_server_result.job_id YQr8p01RE7MugtsKIsg79w _model_server_result.datetime_utc '2025-01-11 17:34:10' _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 5k1x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5K1X # _exptl.entry_id 5K1X _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 100.01 _cell.angle_gamma 90 _cell.entry_id 5K1X _cell.length_a 102.017 _cell.length_b 44.14 _cell.length_c 64.309 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K1X _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 _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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -11.178194 0 63.330052 # _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 OE2 GLU 210 A GLU 396 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc2 A OG SER 213 A SER 399 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc3 B O1B ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc4 B O1A ANP . A ANP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc5 B O2G ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc6 B O2B ANP . A ANP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc7 C MG MG . A MG 502 1_555 H O HOH . A HOH 636 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc8 C MG MG . A MG 502 1_555 H O HOH . A HOH 651 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc9 D MG MG . A MG 503 1_555 H O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc10 D MG MG . A MG 503 1_555 H O HOH . A HOH 643 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc11 D MG MG . A MG 503 1_555 H O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc12 D MG MG . A MG 503 1_555 H O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _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 5K1X _atom_sites.fract_transf_matrix[1][1] 0.009802 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001731 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022655 _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] 0.01579 _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 1 ANP ANP . C 3 MG A 1 502 1 MG MG . D 3 MG A 1 503 2 MG MG . E 4 EDO A 1 504 1 EDO EDO . F 5 PEG A 1 505 1 PEG PEG . G 6 CL A 1 506 1 CL CL . H 7 HOH A 1 601 60 HOH HOH . H 7 HOH A 2 602 127 HOH HOH . H 7 HOH A 3 603 15 HOH HOH . H 7 HOH A 4 604 111 HOH HOH . H 7 HOH A 5 605 64 HOH HOH . H 7 HOH A 6 606 134 HOH HOH . H 7 HOH A 7 607 128 HOH HOH . H 7 HOH A 8 608 27 HOH HOH . H 7 HOH A 9 609 55 HOH HOH . H 7 HOH A 10 610 119 HOH HOH . H 7 HOH A 11 611 57 HOH HOH . H 7 HOH A 12 612 19 HOH HOH . H 7 HOH A 13 613 139 HOH HOH . H 7 HOH A 14 614 47 HOH HOH . H 7 HOH A 15 615 58 HOH HOH . H 7 HOH A 16 616 6 HOH HOH . H 7 HOH A 17 617 91 HOH HOH . H 7 HOH A 18 618 20 HOH HOH . H 7 HOH A 19 619 117 HOH HOH . H 7 HOH A 20 620 1 HOH HOH . H 7 HOH A 21 621 68 HOH HOH . H 7 HOH A 22 622 29 HOH HOH . H 7 HOH A 23 623 51 HOH HOH . H 7 HOH A 24 624 72 HOH HOH . H 7 HOH A 25 625 118 HOH HOH . H 7 HOH A 26 626 17 HOH HOH . H 7 HOH A 27 627 14 HOH HOH . H 7 HOH A 28 628 46 HOH HOH . H 7 HOH A 29 629 7 HOH HOH . H 7 HOH A 30 630 34 HOH HOH . H 7 HOH A 31 631 4 HOH HOH . H 7 HOH A 32 632 93 HOH HOH . H 7 HOH A 33 633 124 HOH HOH . H 7 HOH A 34 634 69 HOH HOH . H 7 HOH A 35 635 62 HOH HOH . H 7 HOH A 36 636 130 HOH HOH . H 7 HOH A 37 637 84 HOH HOH . H 7 HOH A 38 638 98 HOH HOH . H 7 HOH A 39 639 80 HOH HOH . H 7 HOH A 40 640 10 HOH HOH . H 7 HOH A 41 641 21 HOH HOH . H 7 HOH A 42 642 22 HOH HOH . H 7 HOH A 43 643 107 HOH HOH . H 7 HOH A 44 644 144 HOH HOH . H 7 HOH A 45 645 103 HOH HOH . H 7 HOH A 46 646 2 HOH HOH . H 7 HOH A 47 647 104 HOH HOH . H 7 HOH A 48 648 38 HOH HOH . H 7 HOH A 49 649 8 HOH HOH . H 7 HOH A 50 650 121 HOH HOH . H 7 HOH A 51 651 70 HOH HOH . H 7 HOH A 52 652 3 HOH HOH . H 7 HOH A 53 653 101 HOH HOH . H 7 HOH A 54 654 18 HOH HOH . H 7 HOH A 55 655 26 HOH HOH . H 7 HOH A 56 656 132 HOH HOH . H 7 HOH A 57 657 83 HOH HOH . H 7 HOH A 58 658 11 HOH HOH . H 7 HOH A 59 659 28 HOH HOH . H 7 HOH A 60 660 67 HOH HOH . H 7 HOH A 61 661 49 HOH HOH . H 7 HOH A 62 662 40 HOH HOH . H 7 HOH A 63 663 65 HOH HOH . H 7 HOH A 64 664 66 HOH HOH . H 7 HOH A 65 665 9 HOH HOH . H 7 HOH A 66 666 63 HOH HOH . H 7 HOH A 67 667 24 HOH HOH . H 7 HOH A 68 668 31 HOH HOH . H 7 HOH A 69 669 44 HOH HOH . H 7 HOH A 70 670 37 HOH HOH . H 7 HOH A 71 671 102 HOH HOH . H 7 HOH A 72 672 42 HOH HOH . H 7 HOH A 73 673 112 HOH HOH . H 7 HOH A 74 674 120 HOH HOH . H 7 HOH A 75 675 33 HOH HOH . H 7 HOH A 76 676 39 HOH HOH . H 7 HOH A 77 677 106 HOH HOH . H 7 HOH A 78 678 75 HOH HOH . H 7 HOH A 79 679 85 HOH HOH . H 7 HOH A 80 680 76 HOH HOH . H 7 HOH A 81 681 23 HOH HOH . H 7 HOH A 82 682 36 HOH HOH . H 7 HOH A 83 683 90 HOH HOH . H 7 HOH A 84 684 5 HOH HOH . H 7 HOH A 85 685 43 HOH HOH . H 7 HOH A 86 686 116 HOH HOH . H 7 HOH A 87 687 122 HOH HOH . H 7 HOH A 88 688 48 HOH HOH . H 7 HOH A 89 689 13 HOH HOH . H 7 HOH A 90 690 97 HOH HOH . H 7 HOH A 91 691 105 HOH HOH . H 7 HOH A 92 692 115 HOH HOH . H 7 HOH A 93 693 12 HOH HOH . H 7 HOH A 94 694 92 HOH HOH . H 7 HOH A 95 695 87 HOH HOH . H 7 HOH A 96 696 74 HOH HOH . H 7 HOH A 97 697 61 HOH HOH . H 7 HOH A 98 698 141 HOH HOH . H 7 HOH A 99 699 135 HOH HOH . H 7 HOH A 100 700 50 HOH HOH . H 7 HOH A 101 701 137 HOH HOH . H 7 HOH A 102 702 86 HOH HOH . H 7 HOH A 103 703 52 HOH HOH . H 7 HOH A 104 704 32 HOH HOH . H 7 HOH A 105 705 142 HOH HOH . H 7 HOH A 106 706 89 HOH HOH . H 7 HOH A 107 707 131 HOH HOH . H 7 HOH A 108 708 133 HOH HOH . H 7 HOH A 109 709 45 HOH HOH . H 7 HOH A 110 710 71 HOH HOH . H 7 HOH A 111 711 54 HOH HOH . H 7 HOH A 112 712 138 HOH HOH . H 7 HOH A 113 713 82 HOH HOH . H 7 HOH A 114 714 110 HOH HOH . H 7 HOH A 115 715 143 HOH HOH . H 7 HOH A 116 716 125 HOH HOH . H 7 HOH A 117 717 95 HOH HOH . H 7 HOH A 118 718 77 HOH HOH . H 7 HOH A 119 719 35 HOH HOH . H 7 HOH A 120 720 53 HOH HOH . H 7 HOH A 121 721 81 HOH HOH . H 7 HOH A 122 722 136 HOH HOH . H 7 HOH A 123 723 88 HOH HOH . H 7 HOH A 124 724 113 HOH HOH . H 7 HOH A 125 725 41 HOH HOH . H 7 HOH A 126 726 126 HOH HOH . H 7 HOH A 127 727 100 HOH HOH . H 7 HOH A 128 728 94 HOH HOH . H 7 HOH A 129 729 30 HOH HOH . H 7 HOH A 130 730 59 HOH HOH . H 7 HOH A 131 731 108 HOH HOH . H 7 HOH A 132 732 96 HOH HOH . H 7 HOH A 133 733 56 HOH HOH . H 7 HOH A 134 734 73 HOH HOH . H 7 HOH A 135 735 79 HOH HOH . H 7 HOH A 136 736 99 HOH HOH . H 7 HOH A 137 737 78 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 -24.047 14.055 23.591 1 36.1 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 -25.06 14.649 22.528 1 36.53 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 -23.297 15.27 24.262 1 35.31 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 -24.79 13.296 24.642 1 36.9 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 -21.896 13.667 21.797 1 34.42 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 -22.509 13.421 20.392 1 31.96 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 -21.744 15.134 22.045 1 32.45 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 -22.942 12.972 22.905 1 35.34 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 -19.53 12.496 20.778 1 33.85 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 -20.235 11.711 19.75 1 30.93 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 -18.796 13.738 20.263 1 33.71 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 -20.499 12.97 21.961 1 34.55 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 -18.506 11.498 21.475 1 33.5 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 -18.595 10.053 21.384 1 31.34 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 -19.203 9.463 22.639 1 28.72 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 -18.506 9.941 23.808 1 28.81 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 -20.661 9.813 22.911 1 27.51 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 -21.566 9.016 22.158 1 27.68 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 -20.776 9.525 24.411 1 26.91 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 -20.975 8.143 24.689 1 26.53 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 -19.393 9.95 24.921 1 27.31 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 -19.399 11.278 25.52 1 26.27 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 -19.346 12.484 24.872 1 25.49 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 -19.39 13.524 25.669 1 25.22 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 -19.502 12.961 26.935 1 25.85 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 -19.594 13.53 28.223 1 26.13 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 -19.587 14.843 28.46 1 26.27 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 -19.689 12.685 29.276 1 25.52 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 -19.697 11.37 29.047 1 25.55 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 -19.612 10.722 27.882 1 26.8 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 -19.521 11.581 26.857 1 26.48 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #