data_6KFZ # _model_server_result.job_id aiwdFnO1LTwRfkoSkt04Rg _model_server_result.datetime_utc '2024-10-10 17:09:34' _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 6kfz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6KFZ # _exptl.entry_id 6KFZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 352.301 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE _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 6KFZ _cell.length_a 92.8 _cell.length_b 92.8 _cell.length_c 128.6 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KFZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 _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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -85.733333 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A C HIS 363 A HIS 360 1_555 A N CSS 364 A CSS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 A C CSS 364 A CSS 361 1_555 A N ALA 365 A ALA 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? # _chem_comp.formula 'C11 H17 N2 O7 P S' _chem_comp.formula_weight 352.301 _chem_comp.id C6P _chem_comp.mon_nstd_flag . _chem_comp.name N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 4-((1-CARBOXY-2-THIOL-ETHYLAMINO)-METHYL)-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM # 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 N CA C6P sing 70 n n N C4A C6P sing 71 n n N HN C6P sing 72 n n C O C6P doub 73 n n C CA C6P sing 74 n n C OXT C6P sing 75 n n P OP2 C6P doub 76 n n P OP1 C6P sing 77 n n P OP3 C6P sing 78 n n P OP4 C6P sing 79 n n OP3 HOP3 C6P sing 80 n n OP1 HOP1 C6P sing 81 n n OP4 C5M C6P sing 82 n n C5M C5 C6P sing 83 n n C5M H5M1 C6P sing 84 n n C5M H5M2 C6P sing 85 n n C5 C4 C6P sing 86 n y C5 C6 C6P doub 87 n y C6 N1 C6P sing 88 n y C6 H6 C6P sing 89 n n N1 C2 C6P doub 90 n y C2 C3 C6P sing 91 n y C2 C2A C6P sing 92 n n C2A H2A1 C6P sing 93 n n C2A H2A2 C6P sing 94 n n C2A H2A3 C6P sing 95 n n C3 C4 C6P doub 96 n y C3 O3 C6P sing 97 n n O3 HO3 C6P sing 98 n n C4 C4A C6P sing 99 n n C4A H4A1 C6P sing 100 n n C4A H4A2 C6P sing 101 n n CA CB C6P sing 102 n n CA HA C6P sing 103 n n OXT HOXT C6P sing 104 n n CB SG C6P sing 105 n n CB HB1 C6P sing 106 n n CB HB2 C6P sing 107 n n SG HSG C6P sing 108 n n # _atom_sites.entry_id 6KFZ _atom_sites.fract_transf_matrix[1][1] 0.010776 _atom_sites.fract_transf_matrix[1][2] 0.006221 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012443 _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] 0.007776 _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 C6P A 1 601 601 C6P C6P . C 3 PEG A 1 602 1 PEG PEG . D 3 PEG A 1 603 2 PEG PEG . E 3 PEG A 1 604 3 PEG PEG . F 4 HOH A 1 701 210 HOH HOH . F 4 HOH A 2 702 175 HOH HOH . F 4 HOH A 3 703 165 HOH HOH . F 4 HOH A 4 704 99 HOH HOH . F 4 HOH A 5 705 49 HOH HOH . F 4 HOH A 6 706 102 HOH HOH . F 4 HOH A 7 707 110 HOH HOH . F 4 HOH A 8 708 89 HOH HOH . F 4 HOH A 9 709 63 HOH HOH . F 4 HOH A 10 710 31 HOH HOH . F 4 HOH A 11 711 124 HOH HOH . F 4 HOH A 12 712 34 HOH HOH . F 4 HOH A 13 713 80 HOH HOH . F 4 HOH A 14 714 14 HOH HOH . F 4 HOH A 15 715 65 HOH HOH . F 4 HOH A 16 716 156 HOH HOH . F 4 HOH A 17 717 3 HOH HOH . F 4 HOH A 18 718 204 HOH HOH . F 4 HOH A 19 719 161 HOH HOH . F 4 HOH A 20 720 19 HOH HOH . F 4 HOH A 21 721 104 HOH HOH . F 4 HOH A 22 722 51 HOH HOH . F 4 HOH A 23 723 50 HOH HOH . F 4 HOH A 24 724 87 HOH HOH . F 4 HOH A 25 725 54 HOH HOH . F 4 HOH A 26 726 177 HOH HOH . F 4 HOH A 27 727 185 HOH HOH . F 4 HOH A 28 728 148 HOH HOH . F 4 HOH A 29 729 196 HOH HOH . F 4 HOH A 30 730 45 HOH HOH . F 4 HOH A 31 731 113 HOH HOH . F 4 HOH A 32 732 26 HOH HOH . F 4 HOH A 33 733 79 HOH HOH . F 4 HOH A 34 734 115 HOH HOH . F 4 HOH A 35 735 4 HOH HOH . F 4 HOH A 36 736 71 HOH HOH . F 4 HOH A 37 737 106 HOH HOH . F 4 HOH A 38 738 172 HOH HOH . F 4 HOH A 39 739 132 HOH HOH . F 4 HOH A 40 740 149 HOH HOH . F 4 HOH A 41 741 37 HOH HOH . F 4 HOH A 42 742 73 HOH HOH . F 4 HOH A 43 743 7 HOH HOH . F 4 HOH A 44 744 160 HOH HOH . F 4 HOH A 45 745 101 HOH HOH . F 4 HOH A 46 746 16 HOH HOH . F 4 HOH A 47 747 27 HOH HOH . F 4 HOH A 48 748 118 HOH HOH . F 4 HOH A 49 749 141 HOH HOH . F 4 HOH A 50 750 32 HOH HOH . F 4 HOH A 51 751 128 HOH HOH . F 4 HOH A 52 752 11 HOH HOH . F 4 HOH A 53 753 181 HOH HOH . F 4 HOH A 54 754 43 HOH HOH . F 4 HOH A 55 755 47 HOH HOH . F 4 HOH A 56 756 138 HOH HOH . F 4 HOH A 57 757 114 HOH HOH . F 4 HOH A 58 758 57 HOH HOH . F 4 HOH A 59 759 111 HOH HOH . F 4 HOH A 60 760 76 HOH HOH . F 4 HOH A 61 761 127 HOH HOH . F 4 HOH A 62 762 126 HOH HOH . F 4 HOH A 63 763 58 HOH HOH . F 4 HOH A 64 764 173 HOH HOH . F 4 HOH A 65 765 55 HOH HOH . F 4 HOH A 66 766 42 HOH HOH . F 4 HOH A 67 767 91 HOH HOH . F 4 HOH A 68 768 59 HOH HOH . F 4 HOH A 69 769 24 HOH HOH . F 4 HOH A 70 770 60 HOH HOH . F 4 HOH A 71 771 171 HOH HOH . F 4 HOH A 72 772 112 HOH HOH . F 4 HOH A 73 773 12 HOH HOH . F 4 HOH A 74 774 199 HOH HOH . F 4 HOH A 75 775 83 HOH HOH . F 4 HOH A 76 776 48 HOH HOH . F 4 HOH A 77 777 86 HOH HOH . F 4 HOH A 78 778 8 HOH HOH . F 4 HOH A 79 779 77 HOH HOH . F 4 HOH A 80 780 84 HOH HOH . F 4 HOH A 81 781 39 HOH HOH . F 4 HOH A 82 782 20 HOH HOH . F 4 HOH A 83 783 56 HOH HOH . F 4 HOH A 84 784 61 HOH HOH . F 4 HOH A 85 785 167 HOH HOH . F 4 HOH A 86 786 30 HOH HOH . F 4 HOH A 87 787 78 HOH HOH . F 4 HOH A 88 788 195 HOH HOH . F 4 HOH A 89 789 147 HOH HOH . F 4 HOH A 90 790 69 HOH HOH . F 4 HOH A 91 791 103 HOH HOH . F 4 HOH A 92 792 17 HOH HOH . F 4 HOH A 93 793 82 HOH HOH . F 4 HOH A 94 794 36 HOH HOH . F 4 HOH A 95 795 2 HOH HOH . F 4 HOH A 96 796 203 HOH HOH . F 4 HOH A 97 797 18 HOH HOH . F 4 HOH A 98 798 191 HOH HOH . F 4 HOH A 99 799 33 HOH HOH . F 4 HOH A 100 800 162 HOH HOH . F 4 HOH A 101 801 140 HOH HOH . F 4 HOH A 102 802 46 HOH HOH . F 4 HOH A 103 803 64 HOH HOH . F 4 HOH A 104 804 139 HOH HOH . F 4 HOH A 105 805 74 HOH HOH . F 4 HOH A 106 806 66 HOH HOH . F 4 HOH A 107 807 123 HOH HOH . F 4 HOH A 108 808 125 HOH HOH . F 4 HOH A 109 809 13 HOH HOH . F 4 HOH A 110 810 40 HOH HOH . F 4 HOH A 111 811 53 HOH HOH . F 4 HOH A 112 812 9 HOH HOH . F 4 HOH A 113 813 23 HOH HOH . F 4 HOH A 114 814 15 HOH HOH . F 4 HOH A 115 815 1 HOH HOH . F 4 HOH A 116 816 200 HOH HOH . F 4 HOH A 117 817 109 HOH HOH . F 4 HOH A 118 818 187 HOH HOH . F 4 HOH A 119 819 44 HOH HOH . F 4 HOH A 120 820 28 HOH HOH . F 4 HOH A 121 821 5 HOH HOH . F 4 HOH A 122 822 72 HOH HOH . F 4 HOH A 123 823 6 HOH HOH . F 4 HOH A 124 824 92 HOH HOH . F 4 HOH A 125 825 68 HOH HOH . F 4 HOH A 126 826 105 HOH HOH . F 4 HOH A 127 827 178 HOH HOH . F 4 HOH A 128 828 95 HOH HOH . F 4 HOH A 129 829 88 HOH HOH . F 4 HOH A 130 830 186 HOH HOH . F 4 HOH A 131 831 183 HOH HOH . F 4 HOH A 132 832 22 HOH HOH . F 4 HOH A 133 833 41 HOH HOH . F 4 HOH A 134 834 75 HOH HOH . F 4 HOH A 135 835 119 HOH HOH . F 4 HOH A 136 836 21 HOH HOH . F 4 HOH A 137 837 25 HOH HOH . F 4 HOH A 138 838 129 HOH HOH . F 4 HOH A 139 839 163 HOH HOH . F 4 HOH A 140 840 116 HOH HOH . F 4 HOH A 141 841 10 HOH HOH . F 4 HOH A 142 842 157 HOH HOH . F 4 HOH A 143 843 202 HOH HOH . F 4 HOH A 144 844 90 HOH HOH . F 4 HOH A 145 845 35 HOH HOH . F 4 HOH A 146 846 100 HOH HOH . F 4 HOH A 147 847 94 HOH HOH . F 4 HOH A 148 848 93 HOH HOH . F 4 HOH A 149 849 98 HOH HOH . F 4 HOH A 150 850 38 HOH HOH . F 4 HOH A 151 851 145 HOH HOH . F 4 HOH A 152 852 176 HOH HOH . F 4 HOH A 153 853 164 HOH HOH . F 4 HOH A 154 854 155 HOH HOH . F 4 HOH A 155 855 152 HOH HOH . F 4 HOH A 156 856 122 HOH HOH . F 4 HOH A 157 857 170 HOH HOH . F 4 HOH A 158 858 121 HOH HOH . F 4 HOH A 159 859 96 HOH HOH . F 4 HOH A 160 860 180 HOH HOH . F 4 HOH A 161 861 144 HOH HOH . F 4 HOH A 162 862 192 HOH HOH . F 4 HOH A 163 863 70 HOH HOH . F 4 HOH A 164 864 207 HOH HOH . F 4 HOH A 165 865 193 HOH HOH . F 4 HOH A 166 866 198 HOH HOH . F 4 HOH A 167 867 179 HOH HOH . F 4 HOH A 168 868 108 HOH HOH . F 4 HOH A 169 869 117 HOH HOH . F 4 HOH A 170 870 201 HOH HOH . F 4 HOH A 171 871 52 HOH HOH . F 4 HOH A 172 872 184 HOH HOH . F 4 HOH A 173 873 194 HOH HOH . F 4 HOH A 174 874 150 HOH HOH . F 4 HOH A 175 875 137 HOH HOH . F 4 HOH A 176 876 168 HOH HOH . F 4 HOH A 177 877 182 HOH HOH . F 4 HOH A 178 878 29 HOH HOH . F 4 HOH A 179 879 189 HOH HOH . F 4 HOH A 180 880 62 HOH HOH . F 4 HOH A 181 881 190 HOH HOH . F 4 HOH A 182 882 205 HOH HOH . F 4 HOH A 183 883 154 HOH HOH . F 4 HOH A 184 884 206 HOH HOH . F 4 HOH A 185 885 158 HOH HOH . F 4 HOH A 186 886 151 HOH HOH . F 4 HOH A 187 887 146 HOH HOH . F 4 HOH A 188 888 67 HOH HOH . F 4 HOH A 189 889 85 HOH HOH . F 4 HOH A 190 890 97 HOH HOH . F 4 HOH A 191 891 208 HOH HOH . F 4 HOH A 192 892 174 HOH HOH . F 4 HOH A 193 893 159 HOH HOH . F 4 HOH A 194 894 81 HOH HOH . F 4 HOH A 195 895 197 HOH HOH . F 4 HOH A 196 896 130 HOH HOH . F 4 HOH A 197 897 153 HOH HOH . F 4 HOH A 198 898 143 HOH HOH . F 4 HOH A 199 899 107 HOH HOH . F 4 HOH A 200 900 131 HOH HOH . F 4 HOH A 201 901 142 HOH HOH . F 4 HOH A 202 902 166 HOH HOH . F 4 HOH A 203 903 120 HOH HOH . F 4 HOH A 204 904 136 HOH HOH . F 4 HOH A 205 905 169 HOH HOH . F 4 HOH A 206 906 209 HOH HOH . F 4 HOH A 207 907 188 HOH HOH . F 4 HOH A 208 908 133 HOH HOH . F 4 HOH A 209 909 135 HOH HOH . F 4 HOH A 210 910 134 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 N C6P . . . B 2 36.893 -32.963 -36.971 1 31.22 ? N C6P 601 A 1 HETATM 2 C C C6P . . . B 2 39.213 -33.48 -37.648 1 34.6 ? C C6P 601 A 1 HETATM 3 O O C6P . . . B 2 40.088 -33.915 -38.46 1 33.68 ? O C6P 601 A 1 HETATM 4 P P C6P . . . B 2 32.013 -35.19 -38.266 1 27.59 ? P C6P 601 A 1 HETATM 5 O OP3 C6P . . . B 2 32.068 -36.601 -37.766 1 27.47 ? OP3 C6P 601 A 1 HETATM 6 O OP1 C6P . . . B 2 32.872 -34.756 -39.436 1 27.93 ? OP1 C6P 601 A 1 HETATM 7 O OP2 C6P . . . B 2 30.571 -34.723 -38.559 1 28.69 ? OP2 C6P 601 A 1 HETATM 8 O OP4 C6P . . . B 2 32.531 -34.341 -36.916 1 26.94 ? OP4 C6P 601 A 1 HETATM 9 C C5M C6P . . . B 2 32.659 -32.917 -37.201 1 26.67 ? C5M C6P 601 A 1 HETATM 10 C C5 C6P . . . B 2 33.407 -32.344 -35.95 1 27.92 ? C5 C6P 601 A 1 HETATM 11 C C6 C6P . . . B 2 32.731 -31.502 -35.101 1 29.91 ? C6 C6P 601 A 1 HETATM 12 N N1 C6P . . . B 2 33.41 -30.996 -33.978 1 30 ? N1 C6P 601 A 1 HETATM 13 C C2 C6P . . . B 2 34.693 -31.24 -33.757 1 30.47 ? C2 C6P 601 A 1 HETATM 14 C C2A C6P . . . B 2 35.435 -30.645 -32.492 1 30.86 ? C2A C6P 601 A 1 HETATM 15 C C3 C6P . . . B 2 35.385 -32.085 -34.645 1 33.25 ? C3 C6P 601 A 1 HETATM 16 O O3 C6P . . . B 2 36.742 -32.372 -34.41 1 31.37 ? O3 C6P 601 A 1 HETATM 17 C C4 C6P . . . B 2 34.732 -32.633 -35.722 1 30.09 ? C4 C6P 601 A 1 HETATM 18 C C4A C6P . . . B 2 35.549 -33.525 -36.677 1 33.51 ? C4A C6P 601 A 1 HETATM 19 C CA C6P . . . B 2 37.751 -33.817 -37.731 1 33.25 ? CA C6P 601 A 1 HETATM 20 O OXT C6P . . . B 2 39.543 -32.655 -36.757 1 34.06 ? OXT C6P 601 A 1 HETATM 21 C CB C6P . . . B 2 37.359 -34.06 -39.11 1 31.03 ? CB C6P 601 A 1 HETATM 22 S SG C6P . . . B 2 37.09 -32.415 -40.012 1 33.69 ? SG C6P 601 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #