data_5QR5 # _model_server_result.job_id 5mwOy1Y6ca-NjKntfV4xWA _model_server_result.datetime_utc '2024-11-07 14:35:06' _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 5qr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5QR5 # _exptl.entry_id 5QR5 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.01 _cell.angle_gamma 90 _cell.entry_id 5QR5 _cell.length_a 125.412 _cell.length_b 108.375 _cell.length_c 75.688 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QR5 _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 _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 E N N # _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 293 n y N1 C6 PLP sing 294 n y C2 C2A PLP sing 295 n n C2 C3 PLP sing 296 n y C2A H2A1 PLP sing 297 n n C2A H2A2 PLP sing 298 n n C2A H2A3 PLP sing 299 n n C3 O3 PLP sing 300 n n C3 C4 PLP doub 301 n y O3 HO3 PLP sing 302 n n C4 C4A PLP sing 303 n n C4 C5 PLP sing 304 n y C4A O4A PLP doub 305 n n C4A H4A PLP sing 306 n n C5 C6 PLP doub 307 n y C5 C5A PLP sing 308 n n C6 H6 PLP sing 309 n n C5A O4P PLP sing 310 n n C5A H5A1 PLP sing 311 n n C5A H5A2 PLP sing 312 n n O4P P PLP sing 313 n n P O1P PLP doub 314 n n P O2P PLP sing 315 n n P O3P PLP sing 316 n n O2P HOP2 PLP sing 317 n n O3P HOP3 PLP sing 318 n n # _atom_sites.entry_id 5QR5 _atom_sites.fract_transf_matrix[1][1] 0.007974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002747 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009227 _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] 0.013974 _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 PLP B 1 601 601 PLP PLP . D 3 NV7 B 1 602 901 NV7 LIG . E 2 PLP A 1 601 601 PLP PLP . F 4 HOH B 1 701 799 HOH HOH . F 4 HOH B 2 702 702 HOH HOH . F 4 HOH B 3 703 701 HOH HOH . F 4 HOH B 4 704 732 HOH HOH . F 4 HOH B 5 705 741 HOH HOH . F 4 HOH B 6 706 704 HOH HOH . F 4 HOH B 7 707 764 HOH HOH . F 4 HOH B 8 708 791 HOH HOH . F 4 HOH B 9 709 717 HOH HOH . F 4 HOH B 10 710 758 HOH HOH . F 4 HOH B 11 711 709 HOH HOH . F 4 HOH B 12 712 714 HOH HOH . F 4 HOH B 13 713 705 HOH HOH . F 4 HOH B 14 714 765 HOH HOH . F 4 HOH B 15 715 795 HOH HOH . F 4 HOH B 16 716 710 HOH HOH . F 4 HOH B 17 717 832 HOH HOH . F 4 HOH B 18 718 716 HOH HOH . F 4 HOH B 19 719 712 HOH HOH . F 4 HOH B 20 720 738 HOH HOH . F 4 HOH B 21 721 712 HOH HOH . F 4 HOH B 22 722 707 HOH HOH . F 4 HOH B 23 723 787 HOH HOH . F 4 HOH B 24 724 762 HOH HOH . F 4 HOH B 25 725 779 HOH HOH . F 4 HOH B 26 726 733 HOH HOH . F 4 HOH B 27 727 750 HOH HOH . F 4 HOH B 28 728 727 HOH HOH . F 4 HOH B 29 729 721 HOH HOH . F 4 HOH B 30 730 723 HOH HOH . F 4 HOH B 31 731 725 HOH HOH . F 4 HOH B 32 732 730 HOH HOH . F 4 HOH B 33 733 770 HOH HOH . F 4 HOH B 34 734 726 HOH HOH . F 4 HOH B 35 735 742 HOH HOH . F 4 HOH B 36 736 729 HOH HOH . F 4 HOH B 37 737 797 HOH HOH . F 4 HOH B 38 738 708 HOH HOH . F 4 HOH B 39 739 810 HOH HOH . F 4 HOH B 40 740 708 HOH HOH . F 4 HOH B 41 741 769 HOH HOH . F 4 HOH B 42 742 720 HOH HOH . F 4 HOH B 43 743 826 HOH HOH . F 4 HOH B 44 744 731 HOH HOH . F 4 HOH B 45 745 713 HOH HOH . F 4 HOH B 46 746 824 HOH HOH . F 4 HOH B 47 747 800 HOH HOH . F 4 HOH B 48 748 719 HOH HOH . F 4 HOH B 49 749 766 HOH HOH . F 4 HOH B 50 750 706 HOH HOH . F 4 HOH B 51 751 827 HOH HOH . F 4 HOH B 52 752 815 HOH HOH . F 4 HOH B 53 753 807 HOH HOH . F 4 HOH B 54 754 748 HOH HOH . F 4 HOH B 55 755 773 HOH HOH . F 4 HOH B 56 756 755 HOH HOH . F 4 HOH B 57 757 764 HOH HOH . F 4 HOH B 58 758 753 HOH HOH . F 4 HOH B 59 759 711 HOH HOH . F 4 HOH B 60 760 760 HOH HOH . F 4 HOH B 61 761 736 HOH HOH . F 4 HOH B 62 762 754 HOH HOH . F 4 HOH B 63 763 780 HOH HOH . F 4 HOH B 64 764 718 HOH HOH . F 4 HOH B 65 765 734 HOH HOH . F 4 HOH B 66 766 806 HOH HOH . F 4 HOH B 67 767 756 HOH HOH . F 4 HOH B 68 768 744 HOH HOH . F 4 HOH B 69 769 749 HOH HOH . F 4 HOH B 70 770 715 HOH HOH . F 4 HOH B 71 771 746 HOH HOH . F 4 HOH B 72 772 787 HOH HOH . F 4 HOH B 73 773 747 HOH HOH . F 4 HOH B 74 774 801 HOH HOH . F 4 HOH B 75 775 752 HOH HOH . F 4 HOH B 76 776 786 HOH HOH . F 4 HOH B 77 777 783 HOH HOH . F 4 HOH B 78 778 745 HOH HOH . F 4 HOH B 79 779 734 HOH HOH . F 4 HOH B 80 780 790 HOH HOH . F 4 HOH B 81 781 740 HOH HOH . F 4 HOH B 82 782 775 HOH HOH . F 4 HOH B 83 783 761 HOH HOH . F 4 HOH B 84 784 728 HOH HOH . F 4 HOH B 85 785 769 HOH HOH . F 4 HOH B 86 786 724 HOH HOH . F 4 HOH B 87 787 792 HOH HOH . F 4 HOH B 88 788 818 HOH HOH . F 4 HOH B 89 789 743 HOH HOH . F 4 HOH B 90 790 784 HOH HOH . F 4 HOH B 91 791 803 HOH HOH . F 4 HOH B 92 792 772 HOH HOH . F 4 HOH B 93 793 739 HOH HOH . F 4 HOH B 94 794 737 HOH HOH . F 4 HOH B 95 795 794 HOH HOH . F 4 HOH B 96 796 771 HOH HOH . F 4 HOH B 97 797 768 HOH HOH . F 4 HOH B 98 798 820 HOH HOH . F 4 HOH B 99 799 789 HOH HOH . F 4 HOH B 100 800 809 HOH HOH . F 4 HOH B 101 801 763 HOH HOH . F 4 HOH B 102 802 751 HOH HOH . F 4 HOH B 103 803 767 HOH HOH . F 4 HOH B 104 804 759 HOH HOH . F 4 HOH B 105 805 782 HOH HOH . F 4 HOH B 106 806 798 HOH HOH . F 4 HOH B 107 807 808 HOH HOH . F 4 HOH B 108 808 774 HOH HOH . F 4 HOH B 109 809 809 HOH HOH . F 4 HOH B 110 810 747 HOH HOH . F 4 HOH B 111 811 813 HOH HOH . F 4 HOH B 112 812 825 HOH HOH . F 4 HOH B 113 813 819 HOH HOH . F 4 HOH B 114 814 778 HOH HOH . F 4 HOH B 115 815 828 HOH HOH . F 4 HOH B 116 816 814 HOH HOH . F 4 HOH B 117 817 788 HOH HOH . F 4 HOH B 118 818 793 HOH HOH . F 4 HOH B 119 819 817 HOH HOH . F 4 HOH B 120 820 823 HOH HOH . F 4 HOH B 121 821 785 HOH HOH . F 4 HOH B 122 822 777 HOH HOH . F 4 HOH B 123 823 745 HOH HOH . F 4 HOH B 124 824 811 HOH HOH . F 4 HOH B 125 825 812 HOH HOH . F 4 HOH B 126 826 805 HOH HOH . F 4 HOH B 127 827 816 HOH HOH . F 4 HOH B 128 828 821 HOH HOH . F 4 HOH B 129 829 834 HOH HOH . F 4 HOH B 130 830 831 HOH HOH . F 4 HOH B 131 831 830 HOH HOH . F 4 HOH B 132 832 833 HOH HOH . F 4 HOH B 133 833 804 HOH HOH . F 4 HOH B 134 834 835 HOH HOH . G 4 HOH A 1 701 731 HOH HOH . G 4 HOH A 2 702 702 HOH HOH . G 4 HOH A 3 703 804 HOH HOH . G 4 HOH A 4 704 705 HOH HOH . G 4 HOH A 5 705 733 HOH HOH . G 4 HOH A 6 706 713 HOH HOH . G 4 HOH A 7 707 710 HOH HOH . G 4 HOH A 8 708 716 HOH HOH . G 4 HOH A 9 709 723 HOH HOH . G 4 HOH A 10 710 729 HOH HOH . G 4 HOH A 11 711 721 HOH HOH . G 4 HOH A 12 712 707 HOH HOH . G 4 HOH A 13 713 781 HOH HOH . G 4 HOH A 14 714 720 HOH HOH . G 4 HOH A 15 715 735 HOH HOH . G 4 HOH A 16 716 703 HOH HOH . G 4 HOH A 17 717 773 HOH HOH . G 4 HOH A 18 718 704 HOH HOH . G 4 HOH A 19 719 722 HOH HOH . G 4 HOH A 20 720 770 HOH HOH . G 4 HOH A 21 721 718 HOH HOH . G 4 HOH A 22 722 724 HOH HOH . G 4 HOH A 23 723 726 HOH HOH . G 4 HOH A 24 724 771 HOH HOH . G 4 HOH A 25 725 783 HOH HOH . G 4 HOH A 26 726 711 HOH HOH . G 4 HOH A 27 727 706 HOH HOH . G 4 HOH A 28 728 791 HOH HOH . G 4 HOH A 29 729 722 HOH HOH . G 4 HOH A 30 730 757 HOH HOH . G 4 HOH A 31 731 738 HOH HOH . G 4 HOH A 32 732 715 HOH HOH . G 4 HOH A 33 733 728 HOH HOH . G 4 HOH A 34 734 744 HOH HOH . G 4 HOH A 35 735 806 HOH HOH . G 4 HOH A 36 736 725 HOH HOH . G 4 HOH A 37 737 782 HOH HOH . G 4 HOH A 38 738 732 HOH HOH . G 4 HOH A 39 739 777 HOH HOH . G 4 HOH A 40 740 752 HOH HOH . G 4 HOH A 41 741 736 HOH HOH . G 4 HOH A 42 742 740 HOH HOH . G 4 HOH A 43 743 779 HOH HOH . G 4 HOH A 44 744 778 HOH HOH . G 4 HOH A 45 745 714 HOH HOH . G 4 HOH A 46 746 758 HOH HOH . G 4 HOH A 47 747 766 HOH HOH . G 4 HOH A 48 748 709 HOH HOH . G 4 HOH A 49 749 717 HOH HOH . G 4 HOH A 50 750 748 HOH HOH . G 4 HOH A 51 751 741 HOH HOH . G 4 HOH A 52 752 737 HOH HOH . G 4 HOH A 53 753 727 HOH HOH . G 4 HOH A 54 754 739 HOH HOH . G 4 HOH A 55 755 743 HOH HOH . G 4 HOH A 56 756 763 HOH HOH . G 4 HOH A 57 757 742 HOH HOH . G 4 HOH A 58 758 762 HOH HOH . G 4 HOH A 59 759 793 HOH HOH . G 4 HOH A 60 760 774 HOH HOH . G 4 HOH A 61 761 759 HOH HOH . G 4 HOH A 62 762 776 HOH HOH . G 4 HOH A 63 763 703 HOH HOH . G 4 HOH A 64 764 730 HOH HOH . G 4 HOH A 65 765 810 HOH HOH . G 4 HOH A 66 766 780 HOH HOH . G 4 HOH A 67 767 735 HOH HOH . G 4 HOH A 68 768 756 HOH HOH . G 4 HOH A 69 769 776 HOH HOH . G 4 HOH A 70 770 746 HOH HOH . G 4 HOH A 71 771 790 HOH HOH . G 4 HOH A 72 772 781 HOH HOH . G 4 HOH A 73 773 797 HOH HOH . G 4 HOH A 74 774 719 HOH HOH . G 4 HOH A 75 775 755 HOH HOH . G 4 HOH A 76 776 754 HOH HOH . G 4 HOH A 77 777 767 HOH HOH . G 4 HOH A 78 778 750 HOH HOH . G 4 HOH A 79 779 796 HOH HOH . G 4 HOH A 80 780 757 HOH HOH . G 4 HOH A 81 781 701 HOH HOH . G 4 HOH A 82 782 784 HOH HOH . G 4 HOH A 83 783 753 HOH HOH . G 4 HOH A 84 784 811 HOH HOH . G 4 HOH A 85 785 786 HOH HOH . G 4 HOH A 86 786 775 HOH HOH . G 4 HOH A 87 787 772 HOH HOH . G 4 HOH A 88 788 765 HOH HOH . G 4 HOH A 89 789 796 HOH HOH . G 4 HOH A 90 790 795 HOH HOH . G 4 HOH A 91 791 751 HOH HOH . G 4 HOH A 92 792 761 HOH HOH . G 4 HOH A 93 793 800 HOH HOH . G 4 HOH A 94 794 798 HOH HOH . G 4 HOH A 95 795 749 HOH HOH . G 4 HOH A 96 796 789 HOH HOH . G 4 HOH A 97 797 768 HOH HOH . G 4 HOH A 98 798 785 HOH HOH . G 4 HOH A 99 799 788 HOH HOH . G 4 HOH A 100 800 792 HOH HOH . G 4 HOH A 101 801 822 HOH HOH . G 4 HOH A 102 802 803 HOH HOH . G 4 HOH A 103 803 802 HOH HOH . G 4 HOH A 104 804 794 HOH HOH . G 4 HOH A 105 805 760 HOH HOH . G 4 HOH A 106 806 802 HOH HOH . G 4 HOH A 107 807 801 HOH HOH . G 4 HOH A 108 808 799 HOH HOH . G 4 HOH A 109 809 829 HOH HOH . G 4 HOH A 110 810 808 HOH HOH . G 4 HOH A 111 811 807 HOH HOH . G 4 HOH A 112 812 805 HOH HOH . G 4 HOH A 113 813 836 HOH HOH . G 4 HOH A 114 814 812 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 . . . C 2 28.574 -31.882 -0.024 1 24 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . C 2 29.572 -32.136 -0.883 1 27.83 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . C 2 29.355 -33.109 -1.995 1 27.24 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . C 2 30.853 -31.563 -0.711 1 27.97 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . C 2 31.859 -31.891 -1.569 1 22.16 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . C 2 31.092 -30.663 0.343 1 28.08 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . C 2 32.471 -30.136 0.43 1 33.11 ? C4A PLP 601 B 1 HETATM 8 O O4A PLP . . . C 2 32.879 -29.187 1.055 1 41.81 ? O4A PLP 601 B 1 HETATM 9 C C5 PLP . . . C 2 30.009 -30.371 1.199 1 25.55 ? C5 PLP 601 B 1 HETATM 10 C C6 PLP . . . C 2 28.796 -30.986 0.973 1 28.12 ? C6 PLP 601 B 1 HETATM 11 C C5A PLP . . . C 2 30.151 -29.418 2.357 1 24.43 ? C5A PLP 601 B 1 HETATM 12 O O4P PLP . . . C 2 29.946 -28.013 1.977 1 19.4 ? O4P PLP 601 B 1 HETATM 13 P P PLP . . . C 2 30.956 -27.007 2.86 1 24.76 ? P PLP 601 B 1 HETATM 14 O O1P PLP . . . C 2 32.334 -26.908 2.196 1 26.81 ? O1P PLP 601 B 1 HETATM 15 O O2P PLP . . . C 2 31.154 -27.544 4.312 1 21.69 ? O2P PLP 601 B 1 HETATM 16 O O3P PLP . . . C 2 30.26 -25.596 2.766 1 24.21 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #