data_8GKT # _model_server_result.job_id 14Ta53AMvXCab5AA4DDOSw _model_server_result.datetime_utc '2024-11-28 10:04:47' _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 8gkt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 8GKT # _exptl.entry_id 8GKT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 306.209 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _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 90 _cell.angle_gamma 120 _cell.entry_id 8GKT _cell.length_a 158.196 _cell.length_b 158.196 _cell.length_c 207.279 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKT _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.098 137.001755 -34.5465 # 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 'C10 H15 N2 O7 P' _chem_comp.formula_weight 306.209 _chem_comp.id PLG _chem_comp.mon_nstd_flag . _chem_comp.name N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE # 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 PLG doub 260 n y N1 C6 PLG sing 261 n y C2 C2A PLG sing 262 n n C2 C3 PLG sing 263 n y C2A H2A1 PLG sing 264 n n C2A H2A2 PLG sing 265 n n C2A H2A3 PLG sing 266 n n C3 O3 PLG sing 267 n n C3 C4 PLG doub 268 n y O3 HO3 PLG sing 269 n n C4 C4A PLG sing 270 n n C4 C5 PLG sing 271 n y C4A N PLG sing 272 n n C4A H4A1 PLG sing 273 n n C4A H4A2 PLG sing 274 n n C5 C6 PLG doub 275 n y C5 C5A PLG sing 276 n n C6 H6 PLG sing 277 n n C5A OP4 PLG sing 278 n n C5A H5A1 PLG sing 279 n n C5A H5A2 PLG sing 280 n n OP4 P PLG sing 281 n n P OP1 PLG doub 282 n n P OP2 PLG sing 283 n n P OP3 PLG sing 284 n n OP2 HOP2 PLG sing 285 n n OP3 HOP3 PLG sing 286 n n C O PLG doub 287 n n C OXT PLG sing 288 n n C CA PLG sing 289 n n OXT HXT PLG sing 290 n n CA N PLG sing 291 n n CA HA2 PLG sing 292 n n CA HA1 PLG sing 293 n n N H PLG sing 294 n n # _atom_sites.entry_id 8GKT _atom_sites.fract_transf_matrix[1][1] 0.006321 _atom_sites.fract_transf_matrix[1][2] 0.00365 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007299 _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] 0.004824 _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 PLG A 1 601 601 PLG PLG . D 3 Y7L A 1 602 701 Y7L G32 . E 2 PLG B 1 601 601 PLG PLG . F 3 Y7L B 1 602 701 Y7L G32 . G 4 HOH A 1 701 161 HOH HOH . G 4 HOH A 2 702 53 HOH HOH . G 4 HOH A 3 703 155 HOH HOH . G 4 HOH A 4 704 167 HOH HOH . G 4 HOH A 5 705 130 HOH HOH . G 4 HOH A 6 706 75 HOH HOH . G 4 HOH A 7 707 29 HOH HOH . G 4 HOH A 8 708 45 HOH HOH . G 4 HOH A 9 709 108 HOH HOH . G 4 HOH A 10 710 157 HOH HOH . G 4 HOH A 11 711 159 HOH HOH . G 4 HOH A 12 712 140 HOH HOH . G 4 HOH A 13 713 78 HOH HOH . G 4 HOH A 14 714 107 HOH HOH . G 4 HOH A 15 715 80 HOH HOH . G 4 HOH A 16 716 76 HOH HOH . G 4 HOH A 17 717 50 HOH HOH . G 4 HOH A 18 718 43 HOH HOH . G 4 HOH A 19 719 85 HOH HOH . G 4 HOH A 20 720 62 HOH HOH . G 4 HOH A 21 721 119 HOH HOH . G 4 HOH A 22 722 94 HOH HOH . G 4 HOH A 23 723 114 HOH HOH . G 4 HOH A 24 724 38 HOH HOH . G 4 HOH A 25 725 31 HOH HOH . G 4 HOH A 26 726 69 HOH HOH . G 4 HOH A 27 727 25 HOH HOH . G 4 HOH A 28 728 56 HOH HOH . G 4 HOH A 29 729 14 HOH HOH . G 4 HOH A 30 730 143 HOH HOH . G 4 HOH A 31 731 66 HOH HOH . G 4 HOH A 32 732 5 HOH HOH . G 4 HOH A 33 733 103 HOH HOH . G 4 HOH A 34 734 96 HOH HOH . G 4 HOH A 35 735 142 HOH HOH . G 4 HOH A 36 736 88 HOH HOH . G 4 HOH A 37 737 52 HOH HOH . G 4 HOH A 38 738 9 HOH HOH . G 4 HOH A 39 739 11 HOH HOH . G 4 HOH A 40 740 118 HOH HOH . G 4 HOH A 41 741 18 HOH HOH . G 4 HOH A 42 742 37 HOH HOH . G 4 HOH A 43 743 22 HOH HOH . G 4 HOH A 44 744 40 HOH HOH . G 4 HOH A 45 745 67 HOH HOH . G 4 HOH A 46 746 89 HOH HOH . G 4 HOH A 47 747 95 HOH HOH . G 4 HOH A 48 748 168 HOH HOH . G 4 HOH A 49 749 41 HOH HOH . G 4 HOH A 50 750 27 HOH HOH . G 4 HOH A 51 751 124 HOH HOH . G 4 HOH A 52 752 58 HOH HOH . G 4 HOH A 53 753 160 HOH HOH . G 4 HOH A 54 754 158 HOH HOH . G 4 HOH A 55 755 19 HOH HOH . G 4 HOH A 56 756 7 HOH HOH . G 4 HOH A 57 757 46 HOH HOH . G 4 HOH A 58 758 86 HOH HOH . G 4 HOH A 59 759 21 HOH HOH . G 4 HOH A 60 760 55 HOH HOH . G 4 HOH A 61 761 131 HOH HOH . G 4 HOH A 62 762 44 HOH HOH . G 4 HOH A 63 763 83 HOH HOH . G 4 HOH A 64 764 73 HOH HOH . G 4 HOH A 65 765 60 HOH HOH . G 4 HOH A 66 766 12 HOH HOH . G 4 HOH A 67 767 151 HOH HOH . G 4 HOH A 68 768 17 HOH HOH . G 4 HOH A 69 769 13 HOH HOH . G 4 HOH A 70 770 166 HOH HOH . G 4 HOH A 71 771 116 HOH HOH . G 4 HOH A 72 772 23 HOH HOH . G 4 HOH A 73 773 3 HOH HOH . G 4 HOH A 74 774 30 HOH HOH . G 4 HOH A 75 775 49 HOH HOH . G 4 HOH A 76 776 81 HOH HOH . G 4 HOH A 77 777 129 HOH HOH . G 4 HOH A 78 778 63 HOH HOH . G 4 HOH A 79 779 70 HOH HOH . G 4 HOH A 80 780 162 HOH HOH . G 4 HOH A 81 781 128 HOH HOH . G 4 HOH A 82 782 35 HOH HOH . G 4 HOH A 83 783 165 HOH HOH . G 4 HOH A 84 784 147 HOH HOH . G 4 HOH A 85 785 153 HOH HOH . G 4 HOH A 86 786 139 HOH HOH . G 4 HOH A 87 787 97 HOH HOH . G 4 HOH A 88 788 79 HOH HOH . G 4 HOH A 89 789 133 HOH HOH . G 4 HOH A 90 790 48 HOH HOH . G 4 HOH A 91 791 156 HOH HOH . G 4 HOH A 92 792 16 HOH HOH . G 4 HOH A 93 793 10 HOH HOH . G 4 HOH A 94 794 105 HOH HOH . G 4 HOH A 95 795 71 HOH HOH . G 4 HOH A 96 796 170 HOH HOH . G 4 HOH A 97 797 39 HOH HOH . G 4 HOH A 98 798 146 HOH HOH . G 4 HOH A 99 799 134 HOH HOH . G 4 HOH A 100 800 135 HOH HOH . G 4 HOH A 101 801 68 HOH HOH . G 4 HOH A 102 802 4 HOH HOH . G 4 HOH A 103 803 28 HOH HOH . G 4 HOH A 104 804 102 HOH HOH . G 4 HOH A 105 805 136 HOH HOH . G 4 HOH A 106 806 74 HOH HOH . G 4 HOH A 107 807 106 HOH HOH . G 4 HOH A 108 808 122 HOH HOH . G 4 HOH A 109 809 137 HOH HOH . G 4 HOH A 110 810 109 HOH HOH . G 4 HOH A 111 811 90 HOH HOH . G 4 HOH A 112 812 91 HOH HOH . G 4 HOH A 113 813 111 HOH HOH . G 4 HOH A 114 814 98 HOH HOH . G 4 HOH A 115 815 42 HOH HOH . G 4 HOH A 116 816 144 HOH HOH . G 4 HOH A 117 817 65 HOH HOH . G 4 HOH A 118 818 138 HOH HOH . G 4 HOH A 119 819 57 HOH HOH . H 4 HOH B 1 701 61 HOH HOH . H 4 HOH B 2 702 120 HOH HOH . H 4 HOH B 3 703 100 HOH HOH . H 4 HOH B 4 704 164 HOH HOH . H 4 HOH B 5 705 82 HOH HOH . H 4 HOH B 6 706 64 HOH HOH . H 4 HOH B 7 707 93 HOH HOH . H 4 HOH B 8 708 127 HOH HOH . H 4 HOH B 9 709 87 HOH HOH . H 4 HOH B 10 710 47 HOH HOH . H 4 HOH B 11 711 92 HOH HOH . H 4 HOH B 12 712 152 HOH HOH . H 4 HOH B 13 713 20 HOH HOH . H 4 HOH B 14 714 59 HOH HOH . H 4 HOH B 15 715 77 HOH HOH . H 4 HOH B 16 716 123 HOH HOH . H 4 HOH B 17 717 110 HOH HOH . H 4 HOH B 18 718 115 HOH HOH . H 4 HOH B 19 719 15 HOH HOH . H 4 HOH B 20 720 126 HOH HOH . H 4 HOH B 21 721 8 HOH HOH . H 4 HOH B 22 722 33 HOH HOH . H 4 HOH B 23 723 36 HOH HOH . H 4 HOH B 24 724 24 HOH HOH . H 4 HOH B 25 725 6 HOH HOH . H 4 HOH B 26 726 169 HOH HOH . H 4 HOH B 27 727 112 HOH HOH . H 4 HOH B 28 728 99 HOH HOH . H 4 HOH B 29 729 104 HOH HOH . H 4 HOH B 30 730 148 HOH HOH . H 4 HOH B 31 731 34 HOH HOH . H 4 HOH B 32 732 72 HOH HOH . H 4 HOH B 33 733 51 HOH HOH . H 4 HOH B 34 734 154 HOH HOH . H 4 HOH B 35 735 121 HOH HOH . H 4 HOH B 36 736 113 HOH HOH . H 4 HOH B 37 737 163 HOH HOH . H 4 HOH B 38 738 32 HOH HOH . H 4 HOH B 39 739 132 HOH HOH . H 4 HOH B 40 740 150 HOH HOH . H 4 HOH B 41 741 54 HOH HOH . H 4 HOH B 42 742 26 HOH HOH . H 4 HOH B 43 743 101 HOH HOH . H 4 HOH B 44 744 125 HOH HOH . H 4 HOH B 45 745 84 HOH HOH . H 4 HOH B 46 746 117 HOH HOH . H 4 HOH B 47 747 141 HOH HOH . H 4 HOH B 48 748 145 HOH HOH . H 4 HOH B 49 749 149 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 PLG . . . E 2 -9.026 74.85 2.406 0.93 48.18 ? N1 PLG 601 B 1 HETATM 2 C C2 PLG . . . E 2 -7.683 74.767 2.553 0.93 56.06 ? C2 PLG 601 B 1 HETATM 3 C C2A PLG . . . E 2 -6.848 76.019 2.543 0.93 53.82 ? C2A PLG 601 B 1 HETATM 4 C C3 PLG . . . E 2 -7.037 73.443 2.724 0.93 61.17 ? C3 PLG 601 B 1 HETATM 5 O O3 PLG . . . E 2 -5.69 73.329 2.872 0.93 65.13 ? O3 PLG 601 B 1 HETATM 6 C C4 PLG . . . E 2 -7.914 72.251 2.725 0.93 61.5 ? C4 PLG 601 B 1 HETATM 7 C C4A PLG . . . E 2 -7.353 70.86 2.885 0.93 66.67 ? C4A PLG 601 B 1 HETATM 8 C C5 PLG . . . E 2 -9.366 72.477 2.547 0.93 46.91 ? C5 PLG 601 B 1 HETATM 9 C C6 PLG . . . E 2 -9.838 73.779 2.402 0.93 49.21 ? C6 PLG 601 B 1 HETATM 10 C C5A PLG . . . E 2 -10.322 71.306 2.534 0.93 53.6 ? C5A PLG 601 B 1 HETATM 11 O OP4 PLG . . . E 2 -10.43 70.695 3.817 0.93 47.13 ? OP4 PLG 601 B 1 HETATM 12 P P PLG . . . E 2 -10.933 69.172 3.901 0.93 41.89 ? P PLG 601 B 1 HETATM 13 O OP1 PLG . . . E 2 -11.225 68.929 5.362 0.93 52.97 ? OP1 PLG 601 B 1 HETATM 14 O OP2 PLG . . . E 2 -12.158 69.169 3.023 0.93 48.92 ? OP2 PLG 601 B 1 HETATM 15 O OP3 PLG . . . E 2 -9.778 68.375 3.34 0.93 43.07 ? OP3 PLG 601 B 1 HETATM 16 C C PLG . . . E 2 -3.744 69.852 2.844 0.93 59.96 ? C PLG 601 B 1 HETATM 17 O O PLG . . . E 2 -3.334 71.034 2.869 0.93 54.61 ? O PLG 601 B 1 HETATM 18 O OXT PLG . . . E 2 -3.002 68.864 3.034 0.93 64.44 ? OXT PLG 601 B 1 HETATM 19 C CA PLG . . . E 2 -5.208 69.611 2.576 0.93 50.66 ? CA PLG 601 B 1 HETATM 20 N N PLG . . . E 2 -5.931 70.864 2.61 0.93 63.09 ? N PLG 601 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #