data_5QRB # _model_server_result.job_id XRlhZwVhg58q4HfdszWb7A _model_server_result.datetime_utc '2024-11-08 05:39:35' _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 5qrb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5QRB # _exptl.entry_id 5QRB _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 109.22 _cell.angle_gamma 90 _cell.entry_id 5QRB _cell.length_a 125.403 _cell.length_b 108.16 _cell.length_c 75.698 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QRB _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 296 n y N1 C6 PLP sing 297 n y C2 C2A PLP sing 298 n n C2 C3 PLP sing 299 n y C2A H2A1 PLP sing 300 n n C2A H2A2 PLP sing 301 n n C2A H2A3 PLP sing 302 n n C3 O3 PLP sing 303 n n C3 C4 PLP doub 304 n y O3 HO3 PLP sing 305 n n C4 C4A PLP sing 306 n n C4 C5 PLP sing 307 n y C4A O4A PLP doub 308 n n C4A H4A PLP sing 309 n n C5 C6 PLP doub 310 n y C5 C5A PLP sing 311 n n C6 H6 PLP sing 312 n n C5A O4P PLP sing 313 n n C5A H5A1 PLP sing 314 n n C5A H5A2 PLP sing 315 n n O4P P PLP sing 316 n n P O1P PLP doub 317 n n P O2P PLP sing 318 n n P O3P PLP sing 319 n n O2P HOP2 PLP sing 320 n n O3P HOP3 PLP sing 321 n n # _atom_sites.entry_id 5QRB _atom_sites.fract_transf_matrix[1][1] 0.007974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002779 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009246 _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] 0.01399 _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 NVY B 1 602 901 NVY LIG . E 2 PLP A 1 601 601 PLP PLP . F 4 HOH B 1 701 702 HOH HOH . F 4 HOH B 2 702 732 HOH HOH . F 4 HOH B 3 703 765 HOH HOH . F 4 HOH B 4 704 799 HOH HOH . F 4 HOH B 5 705 827 HOH HOH . F 4 HOH B 6 706 701 HOH HOH . F 4 HOH B 7 707 738 HOH HOH . F 4 HOH B 8 708 791 HOH HOH . F 4 HOH B 9 709 717 HOH HOH . F 4 HOH B 10 710 709 HOH HOH . F 4 HOH B 11 711 764 HOH HOH . F 4 HOH B 12 712 795 HOH HOH . F 4 HOH B 13 713 733 HOH HOH . F 4 HOH B 14 714 712 HOH HOH . F 4 HOH B 15 715 714 HOH HOH . F 4 HOH B 16 716 810 HOH HOH . F 4 HOH B 17 717 727 HOH HOH . F 4 HOH B 18 718 758 HOH HOH . F 4 HOH B 19 719 704 HOH HOH . F 4 HOH B 20 720 741 HOH HOH . F 4 HOH B 21 721 706 HOH HOH . F 4 HOH B 22 722 729 HOH HOH . F 4 HOH B 23 723 780 HOH HOH . F 4 HOH B 24 724 749 HOH HOH . F 4 HOH B 25 725 710 HOH HOH . F 4 HOH B 26 726 725 HOH HOH . F 4 HOH B 27 727 716 HOH HOH . F 4 HOH B 28 728 769 HOH HOH . F 4 HOH B 29 729 726 HOH HOH . F 4 HOH B 30 730 723 HOH HOH . F 4 HOH B 31 731 787 HOH HOH . F 4 HOH B 32 732 742 HOH HOH . F 4 HOH B 33 733 705 HOH HOH . F 4 HOH B 34 734 713 HOH HOH . F 4 HOH B 35 735 707 HOH HOH . F 4 HOH B 36 736 818 HOH HOH . F 4 HOH B 37 737 731 HOH HOH . F 4 HOH B 38 738 708 HOH HOH . F 4 HOH B 39 739 721 HOH HOH . F 4 HOH B 40 740 720 HOH HOH . F 4 HOH B 41 741 779 HOH HOH . F 4 HOH B 42 742 730 HOH HOH . F 4 HOH B 43 743 753 HOH HOH . F 4 HOH B 44 744 748 HOH HOH . F 4 HOH B 45 745 767 HOH HOH . F 4 HOH B 46 746 797 HOH HOH . F 4 HOH B 47 747 762 HOH HOH . F 4 HOH B 48 748 832 HOH HOH . F 4 HOH B 49 749 787 HOH HOH . F 4 HOH B 50 750 770 HOH HOH . F 4 HOH B 51 751 750 HOH HOH . F 4 HOH B 52 752 711 HOH HOH . F 4 HOH B 53 753 806 HOH HOH . F 4 HOH B 54 754 719 HOH HOH . F 4 HOH B 55 755 766 HOH HOH . F 4 HOH B 56 756 715 HOH HOH . F 4 HOH B 57 757 756 HOH HOH . F 4 HOH B 58 758 746 HOH HOH . F 4 HOH B 59 759 772 HOH HOH . F 4 HOH B 60 760 708 HOH HOH . F 4 HOH B 61 761 728 HOH HOH . F 4 HOH B 62 762 704 HOH HOH . F 4 HOH B 63 763 815 HOH HOH . F 4 HOH B 64 764 736 HOH HOH . F 4 HOH B 65 765 755 HOH HOH . F 4 HOH B 66 766 760 HOH HOH . F 4 HOH B 67 767 773 HOH HOH . F 4 HOH B 68 768 790 HOH HOH . F 4 HOH B 69 769 768 HOH HOH . F 4 HOH B 70 770 809 HOH HOH . F 4 HOH B 71 771 769 HOH HOH . F 4 HOH B 72 772 734 HOH HOH . F 4 HOH B 73 773 801 HOH HOH . F 4 HOH B 74 774 747 HOH HOH . F 4 HOH B 75 775 764 HOH HOH . F 4 HOH B 76 776 718 HOH HOH . F 4 HOH B 77 777 783 HOH HOH . F 4 HOH B 78 778 775 HOH HOH . F 4 HOH B 79 779 763 HOH HOH . F 4 HOH B 80 780 737 HOH HOH . F 4 HOH B 81 781 794 HOH HOH . F 4 HOH B 82 782 735 HOH HOH . F 4 HOH B 83 783 759 HOH HOH . F 4 HOH B 84 784 807 HOH HOH . F 4 HOH B 85 785 776 HOH HOH . F 4 HOH B 86 786 751 HOH HOH . F 4 HOH B 87 787 786 HOH HOH . F 4 HOH B 88 788 757 HOH HOH . F 4 HOH B 89 789 826 HOH HOH . F 4 HOH B 90 790 761 HOH HOH . F 4 HOH B 91 791 739 HOH HOH . F 4 HOH B 92 792 771 HOH HOH . F 4 HOH B 93 793 752 HOH HOH . F 4 HOH B 94 794 743 HOH HOH . F 4 HOH B 95 795 740 HOH HOH . F 4 HOH B 96 796 809 HOH HOH . F 4 HOH B 97 797 763 HOH HOH . F 4 HOH B 98 798 754 HOH HOH . F 4 HOH B 99 799 824 HOH HOH . F 4 HOH B 100 800 805 HOH HOH . F 4 HOH B 101 801 744 HOH HOH . F 4 HOH B 102 802 808 HOH HOH . F 4 HOH B 103 803 724 HOH HOH . F 4 HOH B 104 804 792 HOH HOH . F 4 HOH B 105 805 820 HOH HOH . F 4 HOH B 106 806 774 HOH HOH . F 4 HOH B 107 807 745 HOH HOH . F 4 HOH B 108 808 784 HOH HOH . F 4 HOH B 109 809 819 HOH HOH . F 4 HOH B 110 810 777 HOH HOH . F 4 HOH B 111 811 800 HOH HOH . F 4 HOH B 112 812 798 HOH HOH . F 4 HOH B 113 813 789 HOH HOH . F 4 HOH B 114 814 825 HOH HOH . F 4 HOH B 115 815 747 HOH HOH . F 4 HOH B 116 816 814 HOH HOH . F 4 HOH B 117 817 788 HOH HOH . F 4 HOH B 118 818 817 HOH HOH . F 4 HOH B 119 819 802 HOH HOH . F 4 HOH B 120 820 821 HOH HOH . F 4 HOH B 121 821 778 HOH HOH . F 4 HOH B 122 822 782 HOH HOH . F 4 HOH B 123 823 803 HOH HOH . F 4 HOH B 124 824 785 HOH HOH . F 4 HOH B 125 825 813 HOH HOH . F 4 HOH B 126 826 823 HOH HOH . F 4 HOH B 127 827 811 HOH HOH . F 4 HOH B 128 828 793 HOH HOH . F 4 HOH B 129 829 828 HOH HOH . F 4 HOH B 130 830 816 HOH HOH . F 4 HOH B 131 831 812 HOH HOH . F 4 HOH B 132 832 834 HOH HOH . F 4 HOH B 133 833 831 HOH HOH . F 4 HOH B 134 834 833 HOH HOH . F 4 HOH B 135 835 804 HOH HOH . F 4 HOH B 136 836 835 HOH HOH . G 4 HOH A 1 701 731 HOH HOH . G 4 HOH A 2 702 733 HOH HOH . G 4 HOH A 3 703 702 HOH HOH . G 4 HOH A 4 704 716 HOH HOH . G 4 HOH A 5 705 707 HOH HOH . G 4 HOH A 6 706 720 HOH HOH . G 4 HOH A 7 707 703 HOH HOH . G 4 HOH A 8 708 713 HOH HOH . G 4 HOH A 9 709 710 HOH HOH . G 4 HOH A 10 710 729 HOH HOH . G 4 HOH A 11 711 705 HOH HOH . G 4 HOH A 12 712 723 HOH HOH . G 4 HOH A 13 713 773 HOH HOH . G 4 HOH A 14 714 740 HOH HOH . G 4 HOH A 15 715 718 HOH HOH . G 4 HOH A 16 716 722 HOH HOH . G 4 HOH A 17 717 738 HOH HOH . G 4 HOH A 18 718 735 HOH HOH . G 4 HOH A 19 719 726 HOH HOH . G 4 HOH A 20 720 721 HOH HOH . G 4 HOH A 21 721 757 HOH HOH . G 4 HOH A 22 722 724 HOH HOH . G 4 HOH A 23 723 712 HOH HOH . G 4 HOH A 24 724 791 HOH HOH . G 4 HOH A 25 725 711 HOH HOH . G 4 HOH A 26 726 781 HOH HOH . G 4 HOH A 27 727 732 HOH HOH . G 4 HOH A 28 728 790 HOH HOH . G 4 HOH A 29 729 766 HOH HOH . G 4 HOH A 30 730 742 HOH HOH . G 4 HOH A 31 731 771 HOH HOH . G 4 HOH A 32 732 804 HOH HOH . G 4 HOH A 33 733 727 HOH HOH . G 4 HOH A 34 734 722 HOH HOH . G 4 HOH A 35 735 717 HOH HOH . G 4 HOH A 36 736 748 HOH HOH . G 4 HOH A 37 737 752 HOH HOH . G 4 HOH A 38 738 714 HOH HOH . G 4 HOH A 39 739 728 HOH HOH . G 4 HOH A 40 740 754 HOH HOH . G 4 HOH A 41 741 725 HOH HOH . G 4 HOH A 42 742 759 HOH HOH . G 4 HOH A 43 743 734 HOH HOH . G 4 HOH A 44 744 779 HOH HOH . G 4 HOH A 45 745 780 HOH HOH . G 4 HOH A 46 746 774 HOH HOH . G 4 HOH A 47 747 736 HOH HOH . G 4 HOH A 48 748 741 HOH HOH . G 4 HOH A 49 749 715 HOH HOH . G 4 HOH A 50 750 782 HOH HOH . G 4 HOH A 51 751 797 HOH HOH . G 4 HOH A 52 752 730 HOH HOH . G 4 HOH A 53 753 743 HOH HOH . G 4 HOH A 54 754 744 HOH HOH . G 4 HOH A 55 755 706 HOH HOH . G 4 HOH A 56 756 709 HOH HOH . G 4 HOH A 57 757 739 HOH HOH . G 4 HOH A 58 758 781 HOH HOH . G 4 HOH A 59 759 746 HOH HOH . G 4 HOH A 60 760 756 HOH HOH . G 4 HOH A 61 761 701 HOH HOH . G 4 HOH A 62 762 703 HOH HOH . G 4 HOH A 63 763 778 HOH HOH . G 4 HOH A 64 764 765 HOH HOH . G 4 HOH A 65 765 793 HOH HOH . G 4 HOH A 66 766 783 HOH HOH . G 4 HOH A 67 767 776 HOH HOH . G 4 HOH A 68 768 811 HOH HOH . G 4 HOH A 69 769 755 HOH HOH . G 4 HOH A 70 770 745 HOH HOH . G 4 HOH A 71 771 737 HOH HOH . G 4 HOH A 72 772 758 HOH HOH . G 4 HOH A 73 773 762 HOH HOH . G 4 HOH A 74 774 719 HOH HOH . G 4 HOH A 75 775 767 HOH HOH . G 4 HOH A 76 776 753 HOH HOH . G 4 HOH A 77 777 798 HOH HOH . G 4 HOH A 78 778 777 HOH HOH . G 4 HOH A 79 779 796 HOH HOH . G 4 HOH A 80 780 772 HOH HOH . G 4 HOH A 81 781 749 HOH HOH . G 4 HOH A 82 782 784 HOH HOH . G 4 HOH A 83 783 775 HOH HOH . G 4 HOH A 84 784 750 HOH HOH . G 4 HOH A 85 785 796 HOH HOH . G 4 HOH A 86 786 786 HOH HOH . G 4 HOH A 87 787 751 HOH HOH . G 4 HOH A 88 788 795 HOH HOH . G 4 HOH A 89 789 768 HOH HOH . G 4 HOH A 90 790 789 HOH HOH . G 4 HOH A 91 791 806 HOH HOH . G 4 HOH A 92 792 800 HOH HOH . G 4 HOH A 93 793 803 HOH HOH . G 4 HOH A 94 794 822 HOH HOH . G 4 HOH A 95 795 802 HOH HOH . G 4 HOH A 96 796 770 HOH HOH . G 4 HOH A 97 797 760 HOH HOH . G 4 HOH A 98 798 761 HOH HOH . G 4 HOH A 99 799 788 HOH HOH . G 4 HOH A 100 800 794 HOH HOH . G 4 HOH A 101 801 785 HOH HOH . G 4 HOH A 102 802 792 HOH HOH . G 4 HOH A 103 803 801 HOH HOH . G 4 HOH A 104 804 807 HOH HOH . G 4 HOH A 105 805 808 HOH HOH . G 4 HOH A 106 806 799 HOH HOH . G 4 HOH A 107 807 829 HOH HOH . G 4 HOH A 108 808 830 HOH HOH . G 4 HOH A 109 809 812 HOH HOH . G 4 HOH A 110 810 805 HOH HOH . G 4 HOH A 111 811 836 HOH HOH . G 4 HOH A 112 812 810 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 28.586 -31.804 0.032 1 28.12 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . C 2 29.577 -32.076 -0.83 1 29.93 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . C 2 29.323 -33.027 -1.955 1 27.94 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . C 2 30.861 -31.491 -0.673 1 29.5 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . C 2 31.854 -31.811 -1.543 1 22.64 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . C 2 31.11 -30.603 0.392 1 31.37 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . C 2 32.482 -30.071 0.472 1 34.77 ? C4A PLP 601 B 1 HETATM 8 O O4A PLP . . . C 2 32.88 -29.097 1.059 1 41.73 ? O4A PLP 601 B 1 HETATM 9 C C5 PLP . . . C 2 30.038 -30.318 1.267 1 29.43 ? C5 PLP 601 B 1 HETATM 10 C C6 PLP . . . C 2 28.827 -30.938 1.049 1 31.55 ? C6 PLP 601 B 1 HETATM 11 C C5A PLP . . . C 2 30.177 -29.371 2.434 1 29.74 ? C5A PLP 601 B 1 HETATM 12 O O4P PLP . . . C 2 29.941 -27.956 2.086 1 22.85 ? O4P PLP 601 B 1 HETATM 13 P P PLP . . . C 2 30.922 -26.901 2.933 1 31.32 ? P PLP 601 B 1 HETATM 14 O O1P PLP . . . C 2 32.306 -26.821 2.286 1 32.31 ? O1P PLP 601 B 1 HETATM 15 O O2P PLP . . . C 2 31.101 -27.455 4.361 1 26.53 ? O2P PLP 601 B 1 HETATM 16 O O3P PLP . . . C 2 30.178 -25.514 2.835 1 26.2 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 16 #