data_8OR9 # _model_server_result.job_id FqADQF2E7I-U67KOyvWYFA _model_server_result.datetime_utc '2024-10-19 13:18:27' _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 8or9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8OR9 # _exptl.entry_id 8OR9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 8OR9 _cell.length_a 107.17 _cell.length_b 107.17 _cell.length_c 218.981 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OR9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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' 10_554 -y,-x,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -36.496833 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 303 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 303 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 1.429 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 290 n y N1 C6 PLP sing 291 n y C2 C2A PLP sing 292 n n C2 C3 PLP sing 293 n y C2A H2A1 PLP sing 294 n n C2A H2A2 PLP sing 295 n n C2A H2A3 PLP sing 296 n n C3 O3 PLP sing 297 n n C3 C4 PLP doub 298 n y O3 HO3 PLP sing 299 n n C4 C4A PLP sing 300 n n C4 C5 PLP sing 301 n y C4A O4A PLP doub 302 n n C4A H4A PLP sing 303 n n C5 C6 PLP doub 304 n y C5 C5A PLP sing 305 n n C6 H6 PLP sing 306 n n C5A O4P PLP sing 307 n n C5A H5A1 PLP sing 308 n n C5A H5A2 PLP sing 309 n n O4P P PLP sing 310 n n P O1P PLP doub 311 n n P O2P PLP sing 312 n n P O3P PLP sing 313 n n O2P HOP2 PLP sing 314 n n O3P HOP3 PLP sing 315 n n # _atom_sites.entry_id 8OR9 _atom_sites.fract_transf_matrix[1][1] 0.009331 _atom_sites.fract_transf_matrix[1][2] 0.005387 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010774 _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] 0.004567 _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 PLP A 1 501 501 PLP PLP . C 3 PG4 A 1 502 601 PG4 PG4 . D 4 HOH A 1 601 962 HOH HOH . D 4 HOH A 2 602 721 HOH HOH . D 4 HOH A 3 603 980 HOH HOH . D 4 HOH A 4 604 946 HOH HOH . D 4 HOH A 5 605 909 HOH HOH . D 4 HOH A 6 606 805 HOH HOH . D 4 HOH A 7 607 872 HOH HOH . D 4 HOH A 8 608 799 HOH HOH . D 4 HOH A 9 609 707 HOH HOH . D 4 HOH A 10 610 828 HOH HOH . D 4 HOH A 11 611 851 HOH HOH . D 4 HOH A 12 612 749 HOH HOH . D 4 HOH A 13 613 868 HOH HOH . D 4 HOH A 14 614 712 HOH HOH . D 4 HOH A 15 615 744 HOH HOH . D 4 HOH A 16 616 832 HOH HOH . D 4 HOH A 17 617 821 HOH HOH . D 4 HOH A 18 618 719 HOH HOH . D 4 HOH A 19 619 935 HOH HOH . D 4 HOH A 20 620 704 HOH HOH . D 4 HOH A 21 621 790 HOH HOH . D 4 HOH A 22 622 857 HOH HOH . D 4 HOH A 23 623 977 HOH HOH . D 4 HOH A 24 624 772 HOH HOH . D 4 HOH A 25 625 731 HOH HOH . D 4 HOH A 26 626 824 HOH HOH . D 4 HOH A 27 627 817 HOH HOH . D 4 HOH A 28 628 792 HOH HOH . D 4 HOH A 29 629 842 HOH HOH . D 4 HOH A 30 630 964 HOH HOH . D 4 HOH A 31 631 701 HOH HOH . D 4 HOH A 32 632 714 HOH HOH . D 4 HOH A 33 633 959 HOH HOH . D 4 HOH A 34 634 813 HOH HOH . D 4 HOH A 35 635 729 HOH HOH . D 4 HOH A 36 636 864 HOH HOH . D 4 HOH A 37 637 710 HOH HOH . D 4 HOH A 38 638 818 HOH HOH . D 4 HOH A 39 639 850 HOH HOH . D 4 HOH A 40 640 815 HOH HOH . D 4 HOH A 41 641 732 HOH HOH . D 4 HOH A 42 642 795 HOH HOH . D 4 HOH A 43 643 982 HOH HOH . D 4 HOH A 44 644 798 HOH HOH . D 4 HOH A 45 645 849 HOH HOH . D 4 HOH A 46 646 770 HOH HOH . D 4 HOH A 47 647 708 HOH HOH . D 4 HOH A 48 648 728 HOH HOH . D 4 HOH A 49 649 886 HOH HOH . D 4 HOH A 50 650 703 HOH HOH . D 4 HOH A 51 651 948 HOH HOH . D 4 HOH A 52 652 903 HOH HOH . D 4 HOH A 53 653 914 HOH HOH . D 4 HOH A 54 654 733 HOH HOH . D 4 HOH A 55 655 736 HOH HOH . D 4 HOH A 56 656 970 HOH HOH . D 4 HOH A 57 657 775 HOH HOH . D 4 HOH A 58 658 910 HOH HOH . D 4 HOH A 59 659 804 HOH HOH . D 4 HOH A 60 660 885 HOH HOH . D 4 HOH A 61 661 802 HOH HOH . D 4 HOH A 62 662 950 HOH HOH . D 4 HOH A 63 663 752 HOH HOH . D 4 HOH A 64 664 963 HOH HOH . D 4 HOH A 65 665 769 HOH HOH . D 4 HOH A 66 666 730 HOH HOH . D 4 HOH A 67 667 741 HOH HOH . D 4 HOH A 68 668 734 HOH HOH . D 4 HOH A 69 669 739 HOH HOH . D 4 HOH A 70 670 794 HOH HOH . D 4 HOH A 71 671 908 HOH HOH . D 4 HOH A 72 672 843 HOH HOH . D 4 HOH A 73 673 781 HOH HOH . D 4 HOH A 74 674 715 HOH HOH . D 4 HOH A 75 675 911 HOH HOH . D 4 HOH A 76 676 906 HOH HOH . D 4 HOH A 77 677 737 HOH HOH . D 4 HOH A 78 678 954 HOH HOH . D 4 HOH A 79 679 759 HOH HOH . D 4 HOH A 80 680 952 HOH HOH . D 4 HOH A 81 681 905 HOH HOH . D 4 HOH A 82 682 913 HOH HOH . D 4 HOH A 83 683 944 HOH HOH . D 4 HOH A 84 684 702 HOH HOH . D 4 HOH A 85 685 812 HOH HOH . D 4 HOH A 86 686 918 HOH HOH . D 4 HOH A 87 687 738 HOH HOH . D 4 HOH A 88 688 705 HOH HOH . D 4 HOH A 89 689 765 HOH HOH . D 4 HOH A 90 690 825 HOH HOH . D 4 HOH A 91 691 725 HOH HOH . D 4 HOH A 92 692 856 HOH HOH . D 4 HOH A 93 693 830 HOH HOH . D 4 HOH A 94 694 754 HOH HOH . D 4 HOH A 95 695 750 HOH HOH . D 4 HOH A 96 696 801 HOH HOH . D 4 HOH A 97 697 782 HOH HOH . D 4 HOH A 98 698 826 HOH HOH . D 4 HOH A 99 699 722 HOH HOH . D 4 HOH A 100 700 947 HOH HOH . D 4 HOH A 101 701 764 HOH HOH . D 4 HOH A 102 702 768 HOH HOH . D 4 HOH A 103 703 968 HOH HOH . D 4 HOH A 104 704 761 HOH HOH . D 4 HOH A 105 705 973 HOH HOH . D 4 HOH A 106 706 835 HOH HOH . D 4 HOH A 107 707 760 HOH HOH . D 4 HOH A 108 708 720 HOH HOH . D 4 HOH A 109 709 773 HOH HOH . D 4 HOH A 110 710 757 HOH HOH . D 4 HOH A 111 711 941 HOH HOH . D 4 HOH A 112 712 717 HOH HOH . D 4 HOH A 113 713 783 HOH HOH . D 4 HOH A 114 714 847 HOH HOH . D 4 HOH A 115 715 916 HOH HOH . D 4 HOH A 116 716 865 HOH HOH . D 4 HOH A 117 717 912 HOH HOH . D 4 HOH A 118 718 767 HOH HOH . D 4 HOH A 119 719 892 HOH HOH . D 4 HOH A 120 720 902 HOH HOH . D 4 HOH A 121 721 943 HOH HOH . D 4 HOH A 122 722 895 HOH HOH . D 4 HOH A 123 723 934 HOH HOH . D 4 HOH A 124 724 924 HOH HOH . D 4 HOH A 125 725 711 HOH HOH . D 4 HOH A 126 726 844 HOH HOH . D 4 HOH A 127 727 777 HOH HOH . D 4 HOH A 128 728 840 HOH HOH . D 4 HOH A 129 729 740 HOH HOH . D 4 HOH A 130 730 814 HOH HOH . D 4 HOH A 131 731 727 HOH HOH . D 4 HOH A 132 732 893 HOH HOH . D 4 HOH A 133 733 706 HOH HOH . D 4 HOH A 134 734 748 HOH HOH . D 4 HOH A 135 735 803 HOH HOH . D 4 HOH A 136 736 723 HOH HOH . D 4 HOH A 137 737 986 HOH HOH . D 4 HOH A 138 738 784 HOH HOH . D 4 HOH A 139 739 899 HOH HOH . D 4 HOH A 140 740 718 HOH HOH . D 4 HOH A 141 741 958 HOH HOH . D 4 HOH A 142 742 806 HOH HOH . D 4 HOH A 143 743 861 HOH HOH . D 4 HOH A 144 744 870 HOH HOH . D 4 HOH A 145 745 742 HOH HOH . D 4 HOH A 146 746 920 HOH HOH . D 4 HOH A 147 747 845 HOH HOH . D 4 HOH A 148 748 890 HOH HOH . D 4 HOH A 149 749 713 HOH HOH . D 4 HOH A 150 750 836 HOH HOH . D 4 HOH A 151 751 915 HOH HOH . D 4 HOH A 152 752 822 HOH HOH . D 4 HOH A 153 753 945 HOH HOH . D 4 HOH A 154 754 785 HOH HOH . D 4 HOH A 155 755 882 HOH HOH . D 4 HOH A 156 756 938 HOH HOH . D 4 HOH A 157 757 852 HOH HOH . D 4 HOH A 158 758 867 HOH HOH . D 4 HOH A 159 759 921 HOH HOH . D 4 HOH A 160 760 829 HOH HOH . D 4 HOH A 161 761 974 HOH HOH . D 4 HOH A 162 762 884 HOH HOH . D 4 HOH A 163 763 762 HOH HOH . D 4 HOH A 164 764 758 HOH HOH . D 4 HOH A 165 765 860 HOH HOH . D 4 HOH A 166 766 808 HOH HOH . D 4 HOH A 167 767 745 HOH HOH . D 4 HOH A 168 768 735 HOH HOH . D 4 HOH A 169 769 880 HOH HOH . D 4 HOH A 170 770 926 HOH HOH . D 4 HOH A 171 771 925 HOH HOH . D 4 HOH A 172 772 810 HOH HOH . D 4 HOH A 173 773 969 HOH HOH . D 4 HOH A 174 774 771 HOH HOH . D 4 HOH A 175 775 791 HOH HOH . D 4 HOH A 176 776 904 HOH HOH . D 4 HOH A 177 777 716 HOH HOH . D 4 HOH A 178 778 756 HOH HOH . D 4 HOH A 179 779 887 HOH HOH . D 4 HOH A 180 780 877 HOH HOH . D 4 HOH A 181 781 961 HOH HOH . D 4 HOH A 182 782 846 HOH HOH . D 4 HOH A 183 783 819 HOH HOH . D 4 HOH A 184 784 837 HOH HOH . D 4 HOH A 185 785 747 HOH HOH . D 4 HOH A 186 786 753 HOH HOH . D 4 HOH A 187 787 709 HOH HOH . D 4 HOH A 188 788 897 HOH HOH . D 4 HOH A 189 789 796 HOH HOH . D 4 HOH A 190 790 778 HOH HOH . D 4 HOH A 191 791 816 HOH HOH . D 4 HOH A 192 792 971 HOH HOH . D 4 HOH A 193 793 967 HOH HOH . D 4 HOH A 194 794 929 HOH HOH . D 4 HOH A 195 795 942 HOH HOH . D 4 HOH A 196 796 901 HOH HOH . D 4 HOH A 197 797 951 HOH HOH . D 4 HOH A 198 798 956 HOH HOH . D 4 HOH A 199 799 917 HOH HOH . D 4 HOH A 200 800 869 HOH HOH . D 4 HOH A 201 801 776 HOH HOH . D 4 HOH A 202 802 797 HOH HOH . D 4 HOH A 203 803 927 HOH HOH . D 4 HOH A 204 804 875 HOH HOH . D 4 HOH A 205 805 955 HOH HOH . D 4 HOH A 206 806 862 HOH HOH . D 4 HOH A 207 807 833 HOH HOH . D 4 HOH A 208 808 726 HOH HOH . D 4 HOH A 209 809 841 HOH HOH . D 4 HOH A 210 810 966 HOH HOH . D 4 HOH A 211 811 789 HOH HOH . D 4 HOH A 212 812 755 HOH HOH . D 4 HOH A 213 813 724 HOH HOH . D 4 HOH A 214 814 940 HOH HOH . D 4 HOH A 215 815 848 HOH HOH . D 4 HOH A 216 816 928 HOH HOH . D 4 HOH A 217 817 919 HOH HOH . D 4 HOH A 218 818 871 HOH HOH . D 4 HOH A 219 819 978 HOH HOH . D 4 HOH A 220 820 898 HOH HOH . D 4 HOH A 221 821 949 HOH HOH . D 4 HOH A 222 822 863 HOH HOH . D 4 HOH A 223 823 780 HOH HOH . D 4 HOH A 224 824 939 HOH HOH . D 4 HOH A 225 825 831 HOH HOH . D 4 HOH A 226 826 936 HOH HOH . D 4 HOH A 227 827 807 HOH HOH . D 4 HOH A 228 828 751 HOH HOH . D 4 HOH A 229 829 984 HOH HOH . D 4 HOH A 230 830 823 HOH HOH . D 4 HOH A 231 831 931 HOH HOH . D 4 HOH A 232 832 766 HOH HOH . D 4 HOH A 233 833 834 HOH HOH . D 4 HOH A 234 834 933 HOH HOH . D 4 HOH A 235 835 793 HOH HOH . D 4 HOH A 236 836 988 HOH HOH . D 4 HOH A 237 837 930 HOH HOH . D 4 HOH A 238 838 983 HOH HOH . D 4 HOH A 239 839 937 HOH HOH . D 4 HOH A 240 840 876 HOH HOH . D 4 HOH A 241 841 981 HOH HOH . D 4 HOH A 242 842 820 HOH HOH . D 4 HOH A 243 843 985 HOH HOH . D 4 HOH A 244 844 827 HOH HOH . D 4 HOH A 245 845 788 HOH HOH . D 4 HOH A 246 846 979 HOH HOH . D 4 HOH A 247 847 858 HOH HOH . D 4 HOH A 248 848 987 HOH HOH . D 4 HOH A 249 849 976 HOH HOH . D 4 HOH A 250 850 960 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 N1 PLP . . . B 2 40.309 -36.961 -8.905 1 16.77 ? N1 PLP 501 A 1 HETATM 2 C C2 PLP . . . B 2 39.17 -37.302 -8.285 1 20.69 ? C2 PLP 501 A 1 HETATM 3 C C2A PLP . . . B 2 39.208 -38.042 -7.105 1 20.33 ? C2A PLP 501 A 1 HETATM 4 C C3 PLP . . . B 2 37.958 -36.903 -8.837 1 20.04 ? C3 PLP 501 A 1 HETATM 5 O O3 PLP . . . B 2 36.804 -37.256 -8.205 1 18.53 ? O3 PLP 501 A 1 HETATM 6 C C4 PLP . . . B 2 37.886 -36.165 -10.011 1 16.25 ? C4 PLP 501 A 1 HETATM 7 C C4A PLP . . . B 2 36.669 -35.772 -10.553 1 20.52 ? C4A PLP 501 A 1 HETATM 8 C C5 PLP . . . B 2 39.069 -35.816 -10.644 1 19.22 ? C5 PLP 501 A 1 HETATM 9 C C6 PLP . . . B 2 40.284 -36.212 -10.093 1 17.36 ? C6 PLP 501 A 1 HETATM 10 C C5A PLP . . . B 2 39.016 -35.083 -11.822 1 17.2 ? C5A PLP 501 A 1 HETATM 11 O O4P PLP . . . B 2 39.137 -33.692 -11.547 1 20.48 ? O4P PLP 501 A 1 HETATM 12 P P PLP . . . B 2 38.759 -32.628 -12.688 1 18.09 ? P PLP 501 A 1 HETATM 13 O O1P PLP . . . B 2 37.659 -33.152 -13.524 1 21.17 ? O1P PLP 501 A 1 HETATM 14 O O2P PLP . . . B 2 40.127 -32.638 -13.521 1 16.44 ? O2P PLP 501 A 1 HETATM 15 O O3P PLP . . . B 2 38.615 -31.304 -12.037 1 17.94 ? O3P PLP 501 A 1 # _model_server_stats.io_time_ms 82 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 377 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 15 #