data_5QR8 # _model_server_result.job_id mZYwy0oUGq8TyVRY2sC68Q _model_server_result.datetime_utc '2024-11-22 14:30:02' _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 5qr8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5QR8 # _exptl.entry_id 5QR8 _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 109.11 _cell.angle_gamma 90 _cell.entry_id 5QR8 _cell.length_a 125.33 _cell.length_b 108.28 _cell.length_c 75.64 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QR8 _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 292 n y N1 C6 PLP sing 293 n y C2 C2A PLP sing 294 n n C2 C3 PLP sing 295 n y C2A H2A1 PLP sing 296 n n C2A H2A2 PLP sing 297 n n C2A H2A3 PLP sing 298 n n C3 O3 PLP sing 299 n n C3 C4 PLP doub 300 n y O3 HO3 PLP sing 301 n n C4 C4A PLP sing 302 n n C4 C5 PLP sing 303 n y C4A O4A PLP doub 304 n n C4A H4A PLP sing 305 n n C5 C6 PLP doub 306 n y C5 C5A PLP sing 307 n n C6 H6 PLP sing 308 n n C5A O4P PLP sing 309 n n C5A H5A1 PLP sing 310 n n C5A H5A2 PLP sing 311 n n O4P P PLP sing 312 n n P O1P PLP doub 313 n n P O2P PLP sing 314 n n P O3P PLP sing 315 n n O2P HOP2 PLP sing 316 n n O3P HOP3 PLP sing 317 n n # _atom_sites.entry_id 5QR8 _atom_sites.fract_transf_matrix[1][1] 0.007979 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002765 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009235 _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] 0.013992 _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 NVD B 1 602 901 NVD 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 3 703 827 HOH HOH . F 4 HOH B 4 704 701 HOH HOH . F 4 HOH B 5 705 791 HOH HOH . F 4 HOH B 6 706 712 HOH HOH . F 4 HOH B 7 707 714 HOH HOH . F 4 HOH B 8 708 717 HOH HOH . F 4 HOH B 9 709 733 HOH HOH . F 4 HOH B 10 710 706 HOH HOH . F 4 HOH B 11 711 727 HOH HOH . F 4 HOH B 12 712 764 HOH HOH . F 4 HOH B 13 713 765 HOH HOH . F 4 HOH B 14 714 741 HOH HOH . F 4 HOH B 15 715 758 HOH HOH . F 4 HOH B 16 716 723 HOH HOH . F 4 HOH B 17 717 720 HOH HOH . F 4 HOH B 18 718 729 HOH HOH . F 4 HOH B 19 719 762 HOH HOH . F 4 HOH B 20 720 738 HOH HOH . F 4 HOH B 21 721 818 HOH HOH . F 4 HOH B 22 722 795 HOH HOH . F 4 HOH B 23 723 713 HOH HOH . F 4 HOH B 24 724 709 HOH HOH . F 4 HOH B 25 725 749 HOH HOH . F 4 HOH B 26 726 787 HOH HOH . F 4 HOH B 27 727 730 HOH HOH . F 4 HOH B 28 728 704 HOH HOH . F 4 HOH B 29 729 716 HOH HOH . F 4 HOH B 30 730 705 HOH HOH . F 4 HOH B 31 731 726 HOH HOH . F 4 HOH B 32 732 770 HOH HOH . F 4 HOH B 33 733 768 HOH HOH . F 4 HOH B 34 734 742 HOH HOH . F 4 HOH B 35 735 780 HOH HOH . F 4 HOH B 36 736 779 HOH HOH . F 4 HOH B 37 737 725 HOH HOH . F 4 HOH B 38 738 708 HOH HOH . F 4 HOH B 39 739 731 HOH HOH . F 4 HOH B 40 740 810 HOH HOH . F 4 HOH B 41 741 721 HOH HOH . F 4 HOH B 42 742 744 HOH HOH . F 4 HOH B 43 743 732 HOH HOH . F 4 HOH B 44 744 748 HOH HOH . F 4 HOH B 45 745 797 HOH HOH . F 4 HOH B 46 746 806 HOH HOH . F 4 HOH B 47 747 753 HOH HOH . F 4 HOH B 48 748 715 HOH HOH . F 4 HOH B 49 749 710 HOH HOH . F 4 HOH B 50 750 725 HOH HOH . F 4 HOH B 51 751 787 HOH HOH . F 4 HOH B 52 752 711 HOH HOH . F 4 HOH B 53 753 772 HOH HOH . F 4 HOH B 54 754 708 HOH HOH . F 4 HOH B 55 755 746 HOH HOH . F 4 HOH B 56 756 734 HOH HOH . F 4 HOH B 57 757 750 HOH HOH . F 4 HOH B 58 758 773 HOH HOH . F 4 HOH B 59 759 800 HOH HOH . F 4 HOH B 60 760 756 HOH HOH . F 4 HOH B 61 761 790 HOH HOH . F 4 HOH B 62 762 718 HOH HOH . F 4 HOH B 63 763 735 HOH HOH . F 4 HOH B 64 764 769 HOH HOH . F 4 HOH B 65 765 719 HOH HOH . F 4 HOH B 66 766 766 HOH HOH . F 4 HOH B 67 767 815 HOH HOH . F 4 HOH B 68 768 752 HOH HOH . F 4 HOH B 69 769 794 HOH HOH . F 4 HOH B 70 770 807 HOH HOH . F 4 HOH B 71 771 764 HOH HOH . F 4 HOH B 72 772 805 HOH HOH . F 4 HOH B 73 773 760 HOH HOH . F 4 HOH B 74 774 826 HOH HOH . F 4 HOH B 75 775 739 HOH HOH . F 4 HOH B 76 776 754 HOH HOH . F 4 HOH B 77 777 809 HOH HOH . F 4 HOH B 78 778 751 HOH HOH . F 4 HOH B 79 779 737 HOH HOH . F 4 HOH B 80 780 761 HOH HOH . F 4 HOH B 81 781 724 HOH HOH . F 4 HOH B 82 782 740 HOH HOH . F 4 HOH B 83 783 747 HOH HOH . F 4 HOH B 84 784 755 HOH HOH . F 4 HOH B 85 785 736 HOH HOH . F 4 HOH B 86 786 776 HOH HOH . F 4 HOH B 87 787 775 HOH HOH . F 4 HOH B 88 788 786 HOH HOH . F 4 HOH B 89 789 782 HOH HOH . F 4 HOH B 90 790 803 HOH HOH . F 4 HOH B 91 791 792 HOH HOH . F 4 HOH B 92 792 767 HOH HOH . F 4 HOH B 93 793 771 HOH HOH . F 4 HOH B 94 794 743 HOH HOH . F 4 HOH B 95 795 759 HOH HOH . F 4 HOH B 96 796 784 HOH HOH . F 4 HOH B 97 797 814 HOH HOH . F 4 HOH B 98 798 745 HOH HOH . F 4 HOH B 99 799 798 HOH HOH . F 4 HOH B 100 800 801 HOH HOH . F 4 HOH B 101 801 820 HOH HOH . F 4 HOH B 102 802 763 HOH HOH . F 4 HOH B 103 803 821 HOH HOH . F 4 HOH B 104 804 809 HOH HOH . F 4 HOH B 105 805 778 HOH HOH . F 4 HOH B 106 806 789 HOH HOH . F 4 HOH B 107 807 808 HOH HOH . F 4 HOH B 108 808 747 HOH HOH . F 4 HOH B 109 809 802 HOH HOH . F 4 HOH B 110 810 830 HOH HOH . F 4 HOH B 111 811 785 HOH HOH . F 4 HOH B 112 812 774 HOH HOH . F 4 HOH B 113 813 777 HOH HOH . F 4 HOH B 114 814 825 HOH HOH . F 4 HOH B 115 815 793 HOH HOH . F 4 HOH B 116 816 823 HOH HOH . F 4 HOH B 117 817 832 HOH HOH . F 4 HOH B 118 818 817 HOH HOH . F 4 HOH B 119 819 728 HOH HOH . F 4 HOH B 120 820 811 HOH HOH . F 4 HOH B 121 821 813 HOH HOH . F 4 HOH B 122 822 788 HOH HOH . F 4 HOH B 123 823 828 HOH HOH . F 4 HOH B 124 824 819 HOH HOH . F 4 HOH B 125 825 812 HOH HOH . F 4 HOH B 126 826 816 HOH HOH . F 4 HOH B 127 827 834 HOH HOH . F 4 HOH B 128 828 831 HOH HOH . F 4 HOH B 129 829 833 HOH HOH . F 4 HOH B 130 830 824 HOH HOH . F 4 HOH B 131 831 804 HOH HOH . F 4 HOH B 132 832 835 HOH HOH . G 4 HOH A 1 701 707 HOH HOH . G 4 HOH A 2 702 720 HOH HOH . G 4 HOH A 3 703 713 HOH HOH . G 4 HOH A 4 704 705 HOH HOH . G 4 HOH A 5 705 722 HOH HOH . G 4 HOH A 6 706 716 HOH HOH . G 4 HOH A 7 707 702 HOH HOH . G 4 HOH A 8 708 729 HOH HOH . G 4 HOH A 9 709 710 HOH HOH . G 4 HOH A 10 710 781 HOH HOH . G 4 HOH A 11 711 733 HOH HOH . G 4 HOH A 12 712 731 HOH HOH . G 4 HOH A 13 713 707 HOH HOH . G 4 HOH A 14 714 735 HOH HOH . G 4 HOH A 15 715 791 HOH HOH . G 4 HOH A 16 716 757 HOH HOH . G 4 HOH A 17 717 740 HOH HOH . G 4 HOH A 18 718 721 HOH HOH . G 4 HOH A 19 719 773 HOH HOH . G 4 HOH A 20 720 722 HOH HOH . G 4 HOH A 21 721 709 HOH HOH . G 4 HOH A 22 722 726 HOH HOH . G 4 HOH A 23 723 712 HOH HOH . G 4 HOH A 24 724 730 HOH HOH . G 4 HOH A 25 725 756 HOH HOH . G 4 HOH A 26 726 732 HOH HOH . G 4 HOH A 27 727 738 HOH HOH . G 4 HOH A 28 728 704 HOH HOH . G 4 HOH A 29 729 748 HOH HOH . G 4 HOH A 30 730 718 HOH HOH . G 4 HOH A 31 731 717 HOH HOH . G 4 HOH A 32 732 727 HOH HOH . G 4 HOH A 33 733 804 HOH HOH . G 4 HOH A 34 734 711 HOH HOH . G 4 HOH A 35 735 742 HOH HOH . G 4 HOH A 36 736 793 HOH HOH . G 4 HOH A 37 737 703 HOH HOH . G 4 HOH A 38 738 766 HOH HOH . G 4 HOH A 39 739 723 HOH HOH . G 4 HOH A 40 740 724 HOH HOH . G 4 HOH A 41 741 759 HOH HOH . G 4 HOH A 42 742 714 HOH HOH . G 4 HOH A 43 743 778 HOH HOH . G 4 HOH A 44 744 797 HOH HOH . G 4 HOH A 45 745 728 HOH HOH . G 4 HOH A 46 746 703 HOH HOH . G 4 HOH A 47 747 779 HOH HOH . G 4 HOH A 48 748 757 HOH HOH . G 4 HOH A 49 749 783 HOH HOH . G 4 HOH A 50 750 744 HOH HOH . G 4 HOH A 51 751 780 HOH HOH . G 4 HOH A 52 752 734 HOH HOH . G 4 HOH A 53 753 790 HOH HOH . G 4 HOH A 54 754 745 HOH HOH . G 4 HOH A 55 755 771 HOH HOH . G 4 HOH A 56 756 736 HOH HOH . G 4 HOH A 57 757 706 HOH HOH . G 4 HOH A 58 758 701 HOH HOH . G 4 HOH A 59 759 743 HOH HOH . G 4 HOH A 60 760 796 HOH HOH . G 4 HOH A 61 761 753 HOH HOH . G 4 HOH A 62 762 774 HOH HOH . G 4 HOH A 63 763 741 HOH HOH . G 4 HOH A 64 764 781 HOH HOH . G 4 HOH A 65 765 811 HOH HOH . G 4 HOH A 66 766 746 HOH HOH . G 4 HOH A 67 767 715 HOH HOH . G 4 HOH A 68 768 758 HOH HOH . G 4 HOH A 69 769 782 HOH HOH . G 4 HOH A 70 770 719 HOH HOH . G 4 HOH A 71 771 798 HOH HOH . G 4 HOH A 72 772 739 HOH HOH . G 4 HOH A 73 773 737 HOH HOH . G 4 HOH A 74 774 754 HOH HOH . G 4 HOH A 75 775 767 HOH HOH . G 4 HOH A 76 776 752 HOH HOH . G 4 HOH A 77 777 755 HOH HOH . G 4 HOH A 78 778 763 HOH HOH . G 4 HOH A 79 779 762 HOH HOH . G 4 HOH A 80 780 765 HOH HOH . G 4 HOH A 81 781 784 HOH HOH . G 4 HOH A 82 782 786 HOH HOH . G 4 HOH A 83 783 776 HOH HOH . G 4 HOH A 84 784 810 HOH HOH . G 4 HOH A 85 785 789 HOH HOH . G 4 HOH A 86 786 777 HOH HOH . G 4 HOH A 87 787 750 HOH HOH . G 4 HOH A 88 788 751 HOH HOH . G 4 HOH A 89 789 795 HOH HOH . G 4 HOH A 90 790 768 HOH HOH . G 4 HOH A 91 791 772 HOH HOH . G 4 HOH A 92 792 769 HOH HOH . G 4 HOH A 93 793 749 HOH HOH . G 4 HOH A 94 794 775 HOH HOH . G 4 HOH A 95 795 796 HOH HOH . G 4 HOH A 96 796 770 HOH HOH . G 4 HOH A 97 797 800 HOH HOH . G 4 HOH A 98 798 783 HOH HOH . G 4 HOH A 99 799 785 HOH HOH . G 4 HOH A 100 800 822 HOH HOH . G 4 HOH A 101 801 794 HOH HOH . G 4 HOH A 102 802 792 HOH HOH . G 4 HOH A 103 803 803 HOH HOH . G 4 HOH A 104 804 788 HOH HOH . G 4 HOH A 105 805 806 HOH HOH . G 4 HOH A 106 806 807 HOH HOH . G 4 HOH A 107 807 799 HOH HOH . G 4 HOH A 108 808 801 HOH HOH . G 4 HOH A 109 809 761 HOH HOH . G 4 HOH A 110 810 829 HOH HOH . G 4 HOH A 111 811 802 HOH HOH . G 4 HOH A 112 812 760 HOH HOH . G 4 HOH A 113 813 808 HOH HOH . G 4 HOH A 114 814 805 HOH HOH . G 4 HOH A 115 815 836 HOH HOH . G 4 HOH A 116 816 812 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 28.541 -31.796 -0.073 1 34.65 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . C 2 29.525 -32.084 -0.935 1 38.85 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . C 2 29.249 -33.007 -2.08 1 38.45 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . C 2 30.821 -31.531 -0.76 1 38.2 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . C 2 31.804 -31.866 -1.614 1 31.07 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . C 2 31.102 -30.665 0.316 1 37.95 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . C 2 32.506 -30.195 0.407 1 44.35 ? C4A PLP 601 B 1 HETATM 8 O O4A PLP . . . C 2 32.959 -29.191 0.929 1 49.1 ? O4A PLP 601 B 1 HETATM 9 C C5 PLP . . . C 2 30.036 -30.371 1.189 1 35.73 ? C5 PLP 601 B 1 HETATM 10 C C6 PLP . . . C 2 28.81 -30.957 0.959 1 38.76 ? C6 PLP 601 B 1 HETATM 11 C C5A PLP . . . C 2 30.202 -29.463 2.385 1 38.31 ? C5A PLP 601 B 1 HETATM 12 O O4P PLP . . . C 2 29.952 -28.043 2.083 1 32 ? O4P PLP 601 B 1 HETATM 13 P P PLP . . . C 2 30.901 -26.957 2.883 1 38.61 ? P PLP 601 B 1 HETATM 14 O O1P PLP . . . C 2 32.277 -26.898 2.218 1 44.22 ? O1P PLP 601 B 1 HETATM 15 O O2P PLP . . . C 2 31.065 -27.448 4.342 1 32.36 ? O2P PLP 601 B 1 HETATM 16 O O3P PLP . . . C 2 30.087 -25.65 2.691 1 35.96 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #