data_5QRD # _model_server_result.job_id 7EOIrEog284RnczECfjxyg _model_server_result.datetime_utc '2024-10-20 00:40:52' _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 5qrd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5QRD # _exptl.entry_id 5QRD _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 109.15 _cell.angle_gamma 90 _cell.entry_id 5QRD _cell.length_a 127.972 _cell.length_b 108.831 _cell.length_c 76.076 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QRD _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 285 n y N1 C6 PLP sing 286 n y C2 C2A PLP sing 287 n n C2 C3 PLP sing 288 n y C2A H2A1 PLP sing 289 n n C2A H2A2 PLP sing 290 n n C2A H2A3 PLP sing 291 n n C3 O3 PLP sing 292 n n C3 C4 PLP doub 293 n y O3 HO3 PLP sing 294 n n C4 C4A PLP sing 295 n n C4 C5 PLP sing 296 n y C4A O4A PLP doub 297 n n C4A H4A PLP sing 298 n n C5 C6 PLP doub 299 n y C5 C5A PLP sing 300 n n C6 H6 PLP sing 301 n n C5A O4P PLP sing 302 n n C5A H5A1 PLP sing 303 n n C5A H5A2 PLP sing 304 n n O4P P PLP sing 305 n n P O1P PLP doub 306 n n P O2P PLP sing 307 n n P O3P PLP sing 308 n n O2P HOP2 PLP sing 309 n n O3P HOP3 PLP sing 310 n n # _atom_sites.entry_id 5QRD _atom_sites.fract_transf_matrix[1][1] 0.007814 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002713 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009189 _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] 0.013914 _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 J4Q B 1 602 901 J4Q LIG . E 2 PLP A 1 601 601 PLP PLP . F 4 HOH B 1 701 702 HOH HOH . F 4 HOH B 2 702 799 HOH HOH . F 4 HOH B 3 703 732 HOH HOH . F 4 HOH B 4 704 717 HOH HOH . F 4 HOH B 5 705 815 HOH HOH . F 4 HOH B 6 706 758 HOH HOH . F 4 HOH B 7 707 714 HOH HOH . F 4 HOH B 8 708 709 HOH HOH . F 4 HOH B 9 709 795 HOH HOH . F 4 HOH B 10 710 701 HOH HOH . F 4 HOH B 11 711 765 HOH HOH . F 4 HOH B 12 712 712 HOH HOH . F 4 HOH B 13 713 727 HOH HOH . F 4 HOH B 14 714 725 HOH HOH . F 4 HOH B 15 715 791 HOH HOH . F 4 HOH B 16 716 762 HOH HOH . F 4 HOH B 17 717 768 HOH HOH . F 4 HOH B 18 718 729 HOH HOH . F 4 HOH B 19 719 704 HOH HOH . F 4 HOH B 20 720 773 HOH HOH . F 4 HOH B 21 721 731 HOH HOH . F 4 HOH B 22 722 706 HOH HOH . F 4 HOH B 23 723 713 HOH HOH . F 4 HOH B 24 724 797 HOH HOH . F 4 HOH B 25 725 769 HOH HOH . F 4 HOH B 26 726 726 HOH HOH . F 4 HOH B 27 727 716 HOH HOH . F 4 HOH B 28 728 741 HOH HOH . F 4 HOH B 29 729 748 HOH HOH . F 4 HOH B 30 730 711 HOH HOH . F 4 HOH B 31 731 715 HOH HOH . F 4 HOH B 32 732 712 HOH HOH . F 4 HOH B 33 733 728 HOH HOH . F 4 HOH B 34 734 733 HOH HOH . F 4 HOH B 35 735 772 HOH HOH . F 4 HOH B 36 736 756 HOH HOH . F 4 HOH B 37 737 708 HOH HOH . F 4 HOH B 38 738 779 HOH HOH . F 4 HOH B 39 739 719 HOH HOH . F 4 HOH B 40 740 736 HOH HOH . F 4 HOH B 41 741 764 HOH HOH . F 4 HOH B 42 742 755 HOH HOH . F 4 HOH B 43 743 801 HOH HOH . F 4 HOH B 44 744 724 HOH HOH . F 4 HOH B 45 745 730 HOH HOH . F 4 HOH B 46 746 742 HOH HOH . F 4 HOH B 47 747 721 HOH HOH . F 4 HOH B 48 748 786 HOH HOH . F 4 HOH B 49 749 806 HOH HOH . F 4 HOH B 50 750 720 HOH HOH . F 4 HOH B 51 751 723 HOH HOH . F 4 HOH B 52 752 760 HOH HOH . F 4 HOH B 53 753 767 HOH HOH . F 4 HOH B 54 754 718 HOH HOH . F 4 HOH B 55 755 790 HOH HOH . F 4 HOH B 56 756 780 HOH HOH . F 4 HOH B 57 757 787 HOH HOH . F 4 HOH B 58 758 710 HOH HOH . F 4 HOH B 59 759 744 HOH HOH . F 4 HOH B 60 760 783 HOH HOH . F 4 HOH B 61 761 787 HOH HOH . F 4 HOH B 62 762 749 HOH HOH . F 4 HOH B 63 763 750 HOH HOH . F 4 HOH B 64 764 754 HOH HOH . F 4 HOH B 65 765 766 HOH HOH . F 4 HOH B 66 766 810 HOH HOH . F 4 HOH B 67 767 747 HOH HOH . F 4 HOH B 68 768 746 HOH HOH . F 4 HOH B 69 769 735 HOH HOH . F 4 HOH B 70 770 740 HOH HOH . F 4 HOH B 71 771 753 HOH HOH . F 4 HOH B 72 772 807 HOH HOH . F 4 HOH B 73 773 739 HOH HOH . F 4 HOH B 74 774 826 HOH HOH . F 4 HOH B 75 775 734 HOH HOH . F 4 HOH B 76 776 745 HOH HOH . F 4 HOH B 77 777 775 HOH HOH . F 4 HOH B 78 778 764 HOH HOH . F 4 HOH B 79 779 769 HOH HOH . F 4 HOH B 80 780 771 HOH HOH . F 4 HOH B 81 781 778 HOH HOH . F 4 HOH B 82 782 808 HOH HOH . F 4 HOH B 83 783 759 HOH HOH . F 4 HOH B 84 784 743 HOH HOH . F 4 HOH B 85 785 751 HOH HOH . F 4 HOH B 86 786 770 HOH HOH . F 4 HOH B 87 787 792 HOH HOH . F 4 HOH B 88 788 761 HOH HOH . F 4 HOH B 89 789 782 HOH HOH . F 4 HOH B 90 790 763 HOH HOH . F 4 HOH B 91 791 785 HOH HOH . F 4 HOH B 92 792 809 HOH HOH . F 4 HOH B 93 793 803 HOH HOH . F 4 HOH B 94 794 800 HOH HOH . F 4 HOH B 95 795 737 HOH HOH . F 4 HOH B 96 796 752 HOH HOH . F 4 HOH B 97 797 820 HOH HOH . F 4 HOH B 98 798 789 HOH HOH . F 4 HOH B 99 799 812 HOH HOH . F 4 HOH B 100 800 747 HOH HOH . F 4 HOH B 101 801 784 HOH HOH . F 4 HOH B 102 802 798 HOH HOH . F 4 HOH B 103 803 813 HOH HOH . F 4 HOH B 104 804 777 HOH HOH . F 4 HOH B 105 805 802 HOH HOH . F 4 HOH B 106 806 827 HOH HOH . F 4 HOH B 107 807 811 HOH HOH . F 4 HOH B 108 808 788 HOH HOH . F 4 HOH B 109 809 825 HOH HOH . F 4 HOH B 110 810 774 HOH HOH . F 4 HOH B 111 811 814 HOH HOH . F 4 HOH B 112 812 705 HOH HOH . F 4 HOH B 113 813 816 HOH HOH . F 4 HOH B 114 814 824 HOH HOH . F 4 HOH B 115 815 819 HOH HOH . F 4 HOH B 116 816 831 HOH HOH . F 4 HOH B 117 817 828 HOH HOH . F 4 HOH B 118 818 823 HOH HOH . F 4 HOH B 119 819 805 HOH HOH . F 4 HOH B 120 820 793 HOH HOH . F 4 HOH B 121 821 821 HOH HOH . F 4 HOH B 122 822 794 HOH HOH . F 4 HOH B 123 823 817 HOH HOH . F 4 HOH B 124 824 834 HOH HOH . F 4 HOH B 125 825 818 HOH HOH . F 4 HOH B 126 826 830 HOH HOH . F 4 HOH B 127 827 833 HOH HOH . F 4 HOH B 128 828 832 HOH HOH . F 4 HOH B 129 829 804 HOH HOH . F 4 HOH B 130 830 835 HOH HOH . G 4 HOH A 1 701 748 HOH HOH . G 4 HOH A 2 702 731 HOH HOH . G 4 HOH A 3 703 716 HOH HOH . G 4 HOH A 4 704 710 HOH HOH . G 4 HOH A 5 705 757 HOH HOH . G 4 HOH A 6 706 723 HOH HOH . G 4 HOH A 7 707 802 HOH HOH . G 4 HOH A 8 708 703 HOH HOH . G 4 HOH A 9 709 779 HOH HOH . G 4 HOH A 10 710 713 HOH HOH . G 4 HOH A 11 711 742 HOH HOH . G 4 HOH A 12 712 759 HOH HOH . G 4 HOH A 13 713 733 HOH HOH . G 4 HOH A 14 714 729 HOH HOH . G 4 HOH A 15 715 707 HOH HOH . G 4 HOH A 16 716 714 HOH HOH . G 4 HOH A 17 717 711 HOH HOH . G 4 HOH A 18 718 702 HOH HOH . G 4 HOH A 19 719 780 HOH HOH . G 4 HOH A 20 720 744 HOH HOH . G 4 HOH A 21 721 704 HOH HOH . G 4 HOH A 22 722 735 HOH HOH . G 4 HOH A 23 723 720 HOH HOH . G 4 HOH A 24 724 725 HOH HOH . G 4 HOH A 25 725 707 HOH HOH . G 4 HOH A 26 726 721 HOH HOH . G 4 HOH A 27 727 722 HOH HOH . G 4 HOH A 28 728 756 HOH HOH . G 4 HOH A 29 729 791 HOH HOH . G 4 HOH A 30 730 718 HOH HOH . G 4 HOH A 31 731 722 HOH HOH . G 4 HOH A 32 732 738 HOH HOH . G 4 HOH A 33 733 703 HOH HOH . G 4 HOH A 34 734 705 HOH HOH . G 4 HOH A 35 735 809 HOH HOH . G 4 HOH A 36 736 783 HOH HOH . G 4 HOH A 37 737 804 HOH HOH . G 4 HOH A 38 738 740 HOH HOH . G 4 HOH A 39 739 734 HOH HOH . G 4 HOH A 40 740 737 HOH HOH . G 4 HOH A 41 741 724 HOH HOH . G 4 HOH A 42 742 701 HOH HOH . G 4 HOH A 43 743 732 HOH HOH . G 4 HOH A 44 744 777 HOH HOH . G 4 HOH A 45 745 709 HOH HOH . G 4 HOH A 46 746 774 HOH HOH . G 4 HOH A 47 747 778 HOH HOH . G 4 HOH A 48 748 728 HOH HOH . G 4 HOH A 49 749 727 HOH HOH . G 4 HOH A 50 750 717 HOH HOH . G 4 HOH A 51 751 739 HOH HOH . G 4 HOH A 52 752 773 HOH HOH . G 4 HOH A 53 753 741 HOH HOH . G 4 HOH A 54 754 752 HOH HOH . G 4 HOH A 55 755 726 HOH HOH . G 4 HOH A 56 756 719 HOH HOH . G 4 HOH A 57 757 706 HOH HOH . G 4 HOH A 58 758 766 HOH HOH . G 4 HOH A 59 759 708 HOH HOH . G 4 HOH A 60 760 796 HOH HOH . G 4 HOH A 61 761 772 HOH HOH . G 4 HOH A 62 762 758 HOH HOH . G 4 HOH A 63 763 797 HOH HOH . G 4 HOH A 64 764 760 HOH HOH . G 4 HOH A 65 765 736 HOH HOH . G 4 HOH A 66 766 755 HOH HOH . G 4 HOH A 67 767 762 HOH HOH . G 4 HOH A 68 768 776 HOH HOH . G 4 HOH A 69 769 746 HOH HOH . G 4 HOH A 70 770 753 HOH HOH . G 4 HOH A 71 771 790 HOH HOH . G 4 HOH A 72 772 788 HOH HOH . G 4 HOH A 73 773 767 HOH HOH . G 4 HOH A 74 774 738 HOH HOH . G 4 HOH A 75 775 763 HOH HOH . G 4 HOH A 76 776 730 HOH HOH . G 4 HOH A 77 777 750 HOH HOH . G 4 HOH A 78 778 795 HOH HOH . G 4 HOH A 79 779 757 HOH HOH . G 4 HOH A 80 780 810 HOH HOH . G 4 HOH A 81 781 745 HOH HOH . G 4 HOH A 82 782 765 HOH HOH . G 4 HOH A 83 783 781 HOH HOH . G 4 HOH A 84 784 770 HOH HOH . G 4 HOH A 85 785 811 HOH HOH . G 4 HOH A 86 786 751 HOH HOH . G 4 HOH A 87 787 776 HOH HOH . G 4 HOH A 88 788 806 HOH HOH . G 4 HOH A 89 789 798 HOH HOH . G 4 HOH A 90 790 793 HOH HOH . G 4 HOH A 91 791 789 HOH HOH . G 4 HOH A 92 792 794 HOH HOH . G 4 HOH A 93 793 715 HOH HOH . G 4 HOH A 94 794 768 HOH HOH . G 4 HOH A 95 795 784 HOH HOH . G 4 HOH A 96 796 754 HOH HOH . G 4 HOH A 97 797 775 HOH HOH . G 4 HOH A 98 798 792 HOH HOH . G 4 HOH A 99 799 782 HOH HOH . G 4 HOH A 100 800 800 HOH HOH . G 4 HOH A 101 801 749 HOH HOH . G 4 HOH A 102 802 786 HOH HOH . G 4 HOH A 103 803 796 HOH HOH . G 4 HOH A 104 804 785 HOH HOH . G 4 HOH A 105 805 743 HOH HOH . G 4 HOH A 106 806 761 HOH HOH . G 4 HOH A 107 807 801 HOH HOH . G 4 HOH A 108 808 829 HOH HOH . G 4 HOH A 109 809 822 HOH HOH . G 4 HOH A 110 810 799 HOH HOH . G 4 HOH A 111 811 807 HOH HOH . G 4 HOH A 112 812 805 HOH HOH . G 4 HOH A 113 813 771 HOH HOH . G 4 HOH A 114 814 781 HOH HOH . G 4 HOH A 115 815 812 HOH HOH . G 4 HOH A 116 816 803 HOH HOH . G 4 HOH A 117 817 836 HOH HOH . G 4 HOH A 118 818 808 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 29.039 -32.002 0.125 1 28.53 ? N1 PLP 601 B 1 HETATM 2 C C2 PLP . . . C 2 30.025 -32.282 -0.732 1 34.61 ? C2 PLP 601 B 1 HETATM 3 C C2A PLP . . . C 2 29.778 -33.231 -1.864 1 32.48 ? C2A PLP 601 B 1 HETATM 4 C C3 PLP . . . C 2 31.311 -31.71 -0.569 1 34.21 ? C3 PLP 601 B 1 HETATM 5 O O3 PLP . . . C 2 32.273 -32.04 -1.469 1 29.31 ? O3 PLP 601 B 1 HETATM 6 C C4 PLP . . . C 2 31.57 -30.809 0.488 1 32.13 ? C4 PLP 601 B 1 HETATM 7 C C4A PLP . . . C 2 32.95 -30.283 0.57 1 34.66 ? C4A PLP 601 B 1 HETATM 8 O O4A PLP . . . C 2 33.378 -29.329 1.192 1 42.87 ? O4A PLP 601 B 1 HETATM 9 C C5 PLP . . . C 2 30.496 -30.521 1.362 1 28.62 ? C5 PLP 601 B 1 HETATM 10 C C6 PLP . . . C 2 29.287 -31.135 1.141 1 31.83 ? C6 PLP 601 B 1 HETATM 11 C C5A PLP . . . C 2 30.623 -29.575 2.532 1 27 ? C5A PLP 601 B 1 HETATM 12 O O4P PLP . . . C 2 30.405 -28.154 2.189 1 24.46 ? O4P PLP 601 B 1 HETATM 13 P P PLP . . . C 2 31.466 -27.115 2.982 1 32.82 ? P PLP 601 B 1 HETATM 14 O O1P PLP . . . C 2 32.841 -27.135 2.258 1 34.18 ? O1P PLP 601 B 1 HETATM 15 O O2P PLP . . . C 2 31.716 -27.626 4.373 1 25.23 ? O2P PLP 601 B 1 HETATM 16 O O3P PLP . . . C 2 30.815 -25.686 2.874 1 26.28 ? O3P PLP 601 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #