data_3DAA # _model_server_result.job_id dBF0YH-kGge07B1C881DXg _model_server_result.datetime_utc '2024-12-26 18:57:37' _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 3daa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":285}' # _entry.id 3DAA # _exptl.entry_id 3DAA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 320.236 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" _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 90 _cell.angle_gamma 90 _cell.entry_id 3DAA _cell.length_a 77.1 _cell.length_b 78.3 _cell.length_c 88.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DAA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C11 H17 N2 O7 P' _chem_comp.formula_weight 320.236 _chem_comp.id PDD _chem_comp.mon_nstd_flag . _chem_comp.name "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE" _chem_comp.type 'd-peptide linking' _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 N C4A PDD sing 237 n n N CA PDD sing 238 n n N H PDD sing 239 n n N1 C2 PDD doub 240 n y N1 C6 PDD sing 241 n y C2 C2A PDD sing 242 n n C2 C3 PDD sing 243 n y C2A H2A1 PDD sing 244 n n C2A H2A2 PDD sing 245 n n C2A H2A3 PDD sing 246 n n C3 O3A PDD sing 247 n n C3 C4 PDD doub 248 n y O3A HO3 PDD sing 249 n n C4 C4A PDD sing 250 n n C4 C5 PDD sing 251 n y C4A H4A1 PDD sing 252 n n C4A H4A2 PDD sing 253 n n C5 C5A PDD sing 254 n n C5 C6 PDD doub 255 n y C5A OP4 PDD sing 256 n n C5A H5A1 PDD sing 257 n n C5A H5A2 PDD sing 258 n n OP4 P PDD sing 259 n n P OP1 PDD doub 260 n n P OP2 PDD sing 261 n n P OP3 PDD sing 262 n n OP2 HOP2 PDD sing 263 n n OP3 HOP3 PDD sing 264 n n C6 H6 PDD sing 265 n n CA CB PDD sing 266 n n CA C PDD sing 267 n n CA HA PDD sing 268 n n CB HB1 PDD sing 269 n n CB HB2 PDD sing 270 n n CB HB3 PDD sing 271 n n C O PDD doub 272 n n C OXT PDD sing 273 n n OXT HXT PDD sing 274 n n # _atom_sites.entry_id 3DAA _atom_sites.fract_transf_matrix[1][1] 0.01297 _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] 0.012771 _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] 0.011312 _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 PDD A 1 285 285 PDD PDA . D 2 PDD B 1 285 285 PDD PDA . E 3 HOH A 1 603 603 HOH HOH . E 3 HOH A 2 604 604 HOH HOH . E 3 HOH A 3 607 607 HOH HOH . E 3 HOH A 4 610 610 HOH HOH . E 3 HOH A 5 611 611 HOH HOH . E 3 HOH A 6 613 613 HOH HOH . E 3 HOH A 7 617 617 HOH HOH . E 3 HOH A 8 619 619 HOH HOH . E 3 HOH A 9 624 624 HOH HOH . E 3 HOH A 10 627 627 HOH HOH . E 3 HOH A 11 628 628 HOH HOH . E 3 HOH A 12 632 632 HOH HOH . E 3 HOH A 13 638 638 HOH HOH . E 3 HOH A 14 639 639 HOH HOH . E 3 HOH A 15 641 641 HOH HOH . E 3 HOH A 16 642 642 HOH HOH . E 3 HOH A 17 644 644 HOH HOH . E 3 HOH A 18 649 649 HOH HOH . E 3 HOH A 19 650 650 HOH HOH . E 3 HOH A 20 653 653 HOH HOH . E 3 HOH A 21 654 654 HOH HOH . E 3 HOH A 22 655 655 HOH HOH . E 3 HOH A 23 659 659 HOH HOH . E 3 HOH A 24 661 661 HOH HOH . E 3 HOH A 25 664 664 HOH HOH . E 3 HOH A 26 665 665 HOH HOH . E 3 HOH A 27 666 666 HOH HOH . E 3 HOH A 28 667 667 HOH HOH . E 3 HOH A 29 668 668 HOH HOH . E 3 HOH A 30 669 669 HOH HOH . E 3 HOH A 31 672 672 HOH HOH . E 3 HOH A 32 673 673 HOH HOH . E 3 HOH A 33 674 674 HOH HOH . E 3 HOH A 34 675 675 HOH HOH . E 3 HOH A 35 676 676 HOH HOH . E 3 HOH A 36 677 677 HOH HOH . E 3 HOH A 37 678 678 HOH HOH . E 3 HOH A 38 679 679 HOH HOH . E 3 HOH A 39 680 680 HOH HOH . E 3 HOH A 40 683 683 HOH HOH . E 3 HOH A 41 684 684 HOH HOH . E 3 HOH A 42 685 685 HOH HOH . E 3 HOH A 43 687 687 HOH HOH . E 3 HOH A 44 689 689 HOH HOH . E 3 HOH A 45 690 690 HOH HOH . E 3 HOH A 46 692 692 HOH HOH . E 3 HOH A 47 693 693 HOH HOH . E 3 HOH A 48 695 695 HOH HOH . E 3 HOH A 49 696 696 HOH HOH . E 3 HOH A 50 698 698 HOH HOH . E 3 HOH A 51 699 699 HOH HOH . E 3 HOH A 52 703 703 HOH HOH . E 3 HOH A 53 706 706 HOH HOH . E 3 HOH A 54 708 708 HOH HOH . E 3 HOH A 55 714 714 HOH HOH . E 3 HOH A 56 715 715 HOH HOH . E 3 HOH A 57 718 718 HOH HOH . E 3 HOH A 58 721 721 HOH HOH . E 3 HOH A 59 722 722 HOH HOH . E 3 HOH A 60 723 723 HOH HOH . E 3 HOH A 61 724 724 HOH HOH . E 3 HOH A 62 725 725 HOH HOH . E 3 HOH A 63 726 726 HOH HOH . E 3 HOH A 64 727 727 HOH HOH . E 3 HOH A 65 729 729 HOH HOH . E 3 HOH A 66 730 730 HOH HOH . E 3 HOH A 67 731 731 HOH HOH . E 3 HOH A 68 733 733 HOH HOH . E 3 HOH A 69 734 734 HOH HOH . E 3 HOH A 70 735 735 HOH HOH . E 3 HOH A 71 737 737 HOH HOH . E 3 HOH A 72 738 738 HOH HOH . E 3 HOH A 73 741 741 HOH HOH . E 3 HOH A 74 744 744 HOH HOH . E 3 HOH A 75 748 748 HOH HOH . E 3 HOH A 76 749 749 HOH HOH . E 3 HOH A 77 750 750 HOH HOH . E 3 HOH A 78 753 753 HOH HOH . E 3 HOH A 79 759 759 HOH HOH . E 3 HOH A 80 760 760 HOH HOH . E 3 HOH A 81 761 761 HOH HOH . E 3 HOH A 82 762 762 HOH HOH . E 3 HOH A 83 763 763 HOH HOH . E 3 HOH A 84 765 765 HOH HOH . E 3 HOH A 85 768 768 HOH HOH . E 3 HOH A 86 769 769 HOH HOH . E 3 HOH A 87 771 771 HOH HOH . E 3 HOH A 88 777 777 HOH HOH . E 3 HOH A 89 778 778 HOH HOH . E 3 HOH A 90 780 780 HOH HOH . E 3 HOH A 91 783 783 HOH HOH . E 3 HOH A 92 784 784 HOH HOH . E 3 HOH A 93 785 785 HOH HOH . E 3 HOH A 94 787 787 HOH HOH . E 3 HOH A 95 788 788 HOH HOH . E 3 HOH A 96 789 789 HOH HOH . E 3 HOH A 97 791 791 HOH HOH . E 3 HOH A 98 793 793 HOH HOH . E 3 HOH A 99 797 797 HOH HOH . E 3 HOH A 100 798 798 HOH HOH . E 3 HOH A 101 803 803 HOH HOH . E 3 HOH A 102 806 806 HOH HOH . E 3 HOH A 103 807 807 HOH HOH . E 3 HOH A 104 808 808 HOH HOH . E 3 HOH A 105 809 809 HOH HOH . E 3 HOH A 106 811 811 HOH HOH . E 3 HOH A 107 812 812 HOH HOH . E 3 HOH A 108 814 814 HOH HOH . E 3 HOH A 109 815 815 HOH HOH . E 3 HOH A 110 816 816 HOH HOH . E 3 HOH A 111 818 818 HOH HOH . E 3 HOH A 112 819 819 HOH HOH . E 3 HOH A 113 823 823 HOH HOH . E 3 HOH A 114 825 825 HOH HOH . E 3 HOH A 115 826 826 HOH HOH . E 3 HOH A 116 835 835 HOH HOH . E 3 HOH A 117 839 839 HOH HOH . E 3 HOH A 118 840 840 HOH HOH . E 3 HOH A 119 842 842 HOH HOH . E 3 HOH A 120 843 843 HOH HOH . E 3 HOH A 121 844 844 HOH HOH . E 3 HOH A 122 845 845 HOH HOH . E 3 HOH A 123 846 846 HOH HOH . E 3 HOH A 124 847 847 HOH HOH . E 3 HOH A 125 848 848 HOH HOH . E 3 HOH A 126 849 849 HOH HOH . E 3 HOH A 127 850 850 HOH HOH . E 3 HOH A 128 851 851 HOH HOH . E 3 HOH A 129 852 852 HOH HOH . F 3 HOH B 1 601 601 HOH HOH . F 3 HOH B 2 602 602 HOH HOH . F 3 HOH B 3 605 605 HOH HOH . F 3 HOH B 4 606 606 HOH HOH . F 3 HOH B 5 608 608 HOH HOH . F 3 HOH B 6 609 609 HOH HOH . F 3 HOH B 7 612 612 HOH HOH . F 3 HOH B 8 614 614 HOH HOH . F 3 HOH B 9 615 615 HOH HOH . F 3 HOH B 10 616 616 HOH HOH . F 3 HOH B 11 618 618 HOH HOH . F 3 HOH B 12 620 620 HOH HOH . F 3 HOH B 13 621 621 HOH HOH . F 3 HOH B 14 622 622 HOH HOH . F 3 HOH B 15 623 623 HOH HOH . F 3 HOH B 16 625 625 HOH HOH . F 3 HOH B 17 626 626 HOH HOH . F 3 HOH B 18 629 629 HOH HOH . F 3 HOH B 19 630 630 HOH HOH . F 3 HOH B 20 631 631 HOH HOH . F 3 HOH B 21 633 633 HOH HOH . F 3 HOH B 22 634 634 HOH HOH . F 3 HOH B 23 635 635 HOH HOH . F 3 HOH B 24 636 636 HOH HOH . F 3 HOH B 25 637 637 HOH HOH . F 3 HOH B 26 640 640 HOH HOH . F 3 HOH B 27 643 643 HOH HOH . F 3 HOH B 28 645 645 HOH HOH . F 3 HOH B 29 646 646 HOH HOH . F 3 HOH B 30 647 647 HOH HOH . F 3 HOH B 31 648 648 HOH HOH . F 3 HOH B 32 651 651 HOH HOH . F 3 HOH B 33 652 652 HOH HOH . F 3 HOH B 34 656 656 HOH HOH . F 3 HOH B 35 657 657 HOH HOH . F 3 HOH B 36 658 658 HOH HOH . F 3 HOH B 37 660 660 HOH HOH . F 3 HOH B 38 662 662 HOH HOH . F 3 HOH B 39 663 663 HOH HOH . F 3 HOH B 40 670 670 HOH HOH . F 3 HOH B 41 671 671 HOH HOH . F 3 HOH B 42 681 681 HOH HOH . F 3 HOH B 43 682 682 HOH HOH . F 3 HOH B 44 686 686 HOH HOH . F 3 HOH B 45 688 688 HOH HOH . F 3 HOH B 46 691 691 HOH HOH . F 3 HOH B 47 694 694 HOH HOH . F 3 HOH B 48 697 697 HOH HOH . F 3 HOH B 49 700 700 HOH HOH . F 3 HOH B 50 701 701 HOH HOH . F 3 HOH B 51 702 702 HOH HOH . F 3 HOH B 52 704 704 HOH HOH . F 3 HOH B 53 705 705 HOH HOH . F 3 HOH B 54 707 707 HOH HOH . F 3 HOH B 55 709 709 HOH HOH . F 3 HOH B 56 710 710 HOH HOH . F 3 HOH B 57 711 711 HOH HOH . F 3 HOH B 58 712 712 HOH HOH . F 3 HOH B 59 713 713 HOH HOH . F 3 HOH B 60 716 716 HOH HOH . F 3 HOH B 61 717 717 HOH HOH . F 3 HOH B 62 719 719 HOH HOH . F 3 HOH B 63 720 720 HOH HOH . F 3 HOH B 64 728 728 HOH HOH . F 3 HOH B 65 732 732 HOH HOH . F 3 HOH B 66 736 736 HOH HOH . F 3 HOH B 67 739 739 HOH HOH . F 3 HOH B 68 740 740 HOH HOH . F 3 HOH B 69 742 742 HOH HOH . F 3 HOH B 70 743 743 HOH HOH . F 3 HOH B 71 745 745 HOH HOH . F 3 HOH B 72 746 746 HOH HOH . F 3 HOH B 73 747 747 HOH HOH . F 3 HOH B 74 751 751 HOH HOH . F 3 HOH B 75 752 752 HOH HOH . F 3 HOH B 76 754 754 HOH HOH . F 3 HOH B 77 755 755 HOH HOH . F 3 HOH B 78 756 756 HOH HOH . F 3 HOH B 79 757 757 HOH HOH . F 3 HOH B 80 758 758 HOH HOH . F 3 HOH B 81 764 764 HOH HOH . F 3 HOH B 82 766 766 HOH HOH . F 3 HOH B 83 767 767 HOH HOH . F 3 HOH B 84 770 770 HOH HOH . F 3 HOH B 85 772 772 HOH HOH . F 3 HOH B 86 773 773 HOH HOH . F 3 HOH B 87 774 774 HOH HOH . F 3 HOH B 88 775 775 HOH HOH . F 3 HOH B 89 776 776 HOH HOH . F 3 HOH B 90 779 779 HOH HOH . F 3 HOH B 91 781 781 HOH HOH . F 3 HOH B 92 782 782 HOH HOH . F 3 HOH B 93 786 786 HOH HOH . F 3 HOH B 94 790 790 HOH HOH . F 3 HOH B 95 792 792 HOH HOH . F 3 HOH B 96 794 794 HOH HOH . F 3 HOH B 97 795 795 HOH HOH . F 3 HOH B 98 796 796 HOH HOH . F 3 HOH B 99 799 799 HOH HOH . F 3 HOH B 100 800 800 HOH HOH . F 3 HOH B 101 801 801 HOH HOH . F 3 HOH B 102 802 802 HOH HOH . F 3 HOH B 103 804 804 HOH HOH . F 3 HOH B 104 805 805 HOH HOH . F 3 HOH B 105 810 810 HOH HOH . F 3 HOH B 106 813 813 HOH HOH . F 3 HOH B 107 817 817 HOH HOH . F 3 HOH B 108 820 820 HOH HOH . F 3 HOH B 109 821 821 HOH HOH . F 3 HOH B 110 822 822 HOH HOH . F 3 HOH B 111 824 824 HOH HOH . F 3 HOH B 112 827 827 HOH HOH . F 3 HOH B 113 828 828 HOH HOH . F 3 HOH B 114 829 829 HOH HOH . F 3 HOH B 115 830 830 HOH HOH . F 3 HOH B 116 831 831 HOH HOH . F 3 HOH B 117 832 832 HOH HOH . F 3 HOH B 118 833 833 HOH HOH . F 3 HOH B 119 834 834 HOH HOH . F 3 HOH B 120 836 836 HOH HOH . F 3 HOH B 121 837 837 HOH HOH . F 3 HOH B 122 838 838 HOH HOH . F 3 HOH B 123 841 841 HOH HOH . F 3 HOH B 124 853 853 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 N N PDD . . . D 2 27.215 29.91 11.437 1 24 ? N PDD 285 B 1 HETATM 2 N N1 PDD . . . D 2 27.209 32.625 6.949 1 13.3 ? N1 PDD 285 B 1 HETATM 3 C C2 PDD . . . D 2 27.862 31.493 7.218 1 11.94 ? C2 PDD 285 B 1 HETATM 4 C C2A PDD . . . D 2 28.526 30.799 6.066 1 9.43 ? C2A PDD 285 B 1 HETATM 5 C C3 PDD . . . D 2 27.934 30.949 8.503 1 16.69 ? C3 PDD 285 B 1 HETATM 6 O O3A PDD . . . D 2 28.548 29.721 8.673 1 18.62 ? O3A PDD 285 B 1 HETATM 7 C C4 PDD . . . D 2 27.4 31.666 9.598 1 18.74 ? C4 PDD 285 B 1 HETATM 8 C C4A PDD . . . D 2 27.747 31.202 11.012 1 21.8 ? C4A PDD 285 B 1 HETATM 9 C C5 PDD . . . D 2 26.616 32.816 9.312 1 15.58 ? C5 PDD 285 B 1 HETATM 10 C C5A PDD . . . D 2 25.865 33.604 10.386 1 11.84 ? C5A PDD 285 B 1 HETATM 11 O OP4 PDD . . . D 2 24.582 33.078 10.706 1 11.88 ? OP4 PDD 285 B 1 HETATM 12 P P PDD . . . D 2 24.042 33.322 12.158 1 10.04 ? P PDD 285 B 1 HETATM 13 O OP1 PDD . . . D 2 24.914 32.592 13.129 1 12.31 ? OP1 PDD 285 B 1 HETATM 14 O OP2 PDD . . . D 2 22.632 32.821 12.255 1 10.18 ? OP2 PDD 285 B 1 HETATM 15 O OP3 PDD . . . D 2 24.079 34.784 12.456 1 7.75 ? OP3 PDD 285 B 1 HETATM 16 C C6 PDD . . . D 2 26.601 33.263 7.975 1 15.93 ? C6 PDD 285 B 1 HETATM 17 C CA PDD . . . D 2 27.712 29.261 12.667 1 19.84 ? CA PDD 285 B 1 HETATM 18 C CB PDD . . . D 2 27.961 30.286 13.786 1 22.43 ? CB PDD 285 B 1 HETATM 19 C C PDD . . . D 2 28.956 28.336 12.507 1 21.44 ? C PDD 285 B 1 HETATM 20 O O PDD . . . D 2 29.219 27.655 11.56 1 17.16 ? O PDD 285 B 1 HETATM 21 O OXT PDD . . . D 2 29.756 28.38 13.603 1 18.33 ? OXT PDD 285 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #