data_8GKS # _model_server_result.job_id EbZmgJfHdtF5YyDzUWb8Dg _model_server_result.datetime_utc '2024-11-27 17:03:14' _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 8gks # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 8GKS # _exptl.entry_id 8GKS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _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 90 _cell.angle_gamma 120 _cell.entry_id 8GKS _cell.length_a 157.927 _cell.length_b 157.927 _cell.length_c 206.67 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKS _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,C,D,E,F,I 1 1 B,G,H,J 1 1,2 A,C,D,E,F,I 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 -78.9635 136.768794 -34.445 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N 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 NZ LYS 269 A LYS 280 1_555 F C4A PLP . A PLP 602 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.265 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 H C4A PLP . B PLP 602 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.268 ? # _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 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 8GKS _atom_sites.fract_transf_matrix[1][1] 0.006332 _atom_sites.fract_transf_matrix[1][2] 0.003656 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007312 _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] 0.004839 _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 GLY A 1 601 601 GLY GLY . D 3 Y6U A 1 701 701 Y6U G29 . E 3 Y6U A 1 702 701 Y6U G29 . F 4 PLP A 1 602 280 PLP LLP . G 2 GLY B 1 601 601 GLY GLY . H 4 PLP B 1 602 280 PLP LLP . I 5 HOH A 1 801 75 HOH HOH . I 5 HOH A 2 802 72 HOH HOH . I 5 HOH A 3 803 81 HOH HOH . I 5 HOH A 4 804 93 HOH HOH . I 5 HOH A 5 805 82 HOH HOH . I 5 HOH A 6 806 65 HOH HOH . I 5 HOH A 7 807 94 HOH HOH . I 5 HOH A 8 808 7 HOH HOH . I 5 HOH A 9 809 77 HOH HOH . I 5 HOH A 10 810 103 HOH HOH . I 5 HOH A 11 811 33 HOH HOH . I 5 HOH A 12 812 62 HOH HOH . I 5 HOH A 13 813 58 HOH HOH . I 5 HOH A 14 814 27 HOH HOH . I 5 HOH A 15 815 112 HOH HOH . I 5 HOH A 16 816 110 HOH HOH . I 5 HOH A 17 817 64 HOH HOH . I 5 HOH A 18 818 11 HOH HOH . I 5 HOH A 19 819 80 HOH HOH . I 5 HOH A 20 820 16 HOH HOH . I 5 HOH A 21 821 63 HOH HOH . I 5 HOH A 22 822 8 HOH HOH . I 5 HOH A 23 823 66 HOH HOH . I 5 HOH A 24 824 26 HOH HOH . I 5 HOH A 25 825 76 HOH HOH . I 5 HOH A 26 826 105 HOH HOH . I 5 HOH A 27 827 85 HOH HOH . I 5 HOH A 28 828 120 HOH HOH . I 5 HOH A 29 829 97 HOH HOH . I 5 HOH A 30 830 56 HOH HOH . I 5 HOH A 31 831 24 HOH HOH . I 5 HOH A 32 832 59 HOH HOH . I 5 HOH A 33 833 89 HOH HOH . I 5 HOH A 34 834 52 HOH HOH . I 5 HOH A 35 835 23 HOH HOH . I 5 HOH A 36 836 19 HOH HOH . I 5 HOH A 37 837 74 HOH HOH . I 5 HOH A 38 838 67 HOH HOH . I 5 HOH A 39 839 12 HOH HOH . I 5 HOH A 40 840 69 HOH HOH . I 5 HOH A 41 841 109 HOH HOH . I 5 HOH A 42 842 99 HOH HOH . I 5 HOH A 43 843 100 HOH HOH . I 5 HOH A 44 844 20 HOH HOH . I 5 HOH A 45 845 29 HOH HOH . I 5 HOH A 46 846 60 HOH HOH . I 5 HOH A 47 847 44 HOH HOH . I 5 HOH A 48 848 84 HOH HOH . I 5 HOH A 49 849 5 HOH HOH . I 5 HOH A 50 850 78 HOH HOH . I 5 HOH A 51 851 107 HOH HOH . I 5 HOH A 52 852 43 HOH HOH . I 5 HOH A 53 853 83 HOH HOH . I 5 HOH A 54 854 28 HOH HOH . I 5 HOH A 55 855 102 HOH HOH . I 5 HOH A 56 856 92 HOH HOH . I 5 HOH A 57 857 50 HOH HOH . I 5 HOH A 58 858 111 HOH HOH . I 5 HOH A 59 859 96 HOH HOH . I 5 HOH A 60 860 45 HOH HOH . I 5 HOH A 61 861 35 HOH HOH . I 5 HOH A 62 862 9 HOH HOH . I 5 HOH A 63 863 117 HOH HOH . I 5 HOH A 64 864 98 HOH HOH . I 5 HOH A 65 865 39 HOH HOH . I 5 HOH A 66 866 51 HOH HOH . I 5 HOH A 67 867 41 HOH HOH . I 5 HOH A 68 868 2 HOH HOH . I 5 HOH A 69 869 121 HOH HOH . I 5 HOH A 70 870 48 HOH HOH . I 5 HOH A 71 871 4 HOH HOH . I 5 HOH A 72 872 101 HOH HOH . I 5 HOH A 73 873 18 HOH HOH . I 5 HOH A 74 874 13 HOH HOH . I 5 HOH A 75 875 54 HOH HOH . I 5 HOH A 76 876 115 HOH HOH . I 5 HOH A 77 877 1 HOH HOH . I 5 HOH A 78 878 55 HOH HOH . I 5 HOH A 79 879 42 HOH HOH . I 5 HOH A 80 880 53 HOH HOH . I 5 HOH A 81 881 36 HOH HOH . I 5 HOH A 82 882 79 HOH HOH . I 5 HOH A 83 883 14 HOH HOH . I 5 HOH A 84 884 46 HOH HOH . J 5 HOH B 1 801 3 HOH HOH . J 5 HOH B 2 802 108 HOH HOH . J 5 HOH B 3 803 95 HOH HOH . J 5 HOH B 4 804 68 HOH HOH . J 5 HOH B 5 805 87 HOH HOH . J 5 HOH B 6 806 86 HOH HOH . J 5 HOH B 7 807 61 HOH HOH . J 5 HOH B 8 808 122 HOH HOH . J 5 HOH B 9 809 71 HOH HOH . J 5 HOH B 10 810 73 HOH HOH . J 5 HOH B 11 811 17 HOH HOH . J 5 HOH B 12 812 32 HOH HOH . J 5 HOH B 13 813 57 HOH HOH . J 5 HOH B 14 814 90 HOH HOH . J 5 HOH B 15 815 113 HOH HOH . J 5 HOH B 16 816 30 HOH HOH . J 5 HOH B 17 817 21 HOH HOH . J 5 HOH B 18 818 114 HOH HOH . J 5 HOH B 19 819 106 HOH HOH . J 5 HOH B 20 820 31 HOH HOH . J 5 HOH B 21 821 70 HOH HOH . J 5 HOH B 22 822 6 HOH HOH . J 5 HOH B 23 823 104 HOH HOH . J 5 HOH B 24 824 22 HOH HOH . J 5 HOH B 25 825 88 HOH HOH . J 5 HOH B 26 826 34 HOH HOH . J 5 HOH B 27 827 10 HOH HOH . J 5 HOH B 28 828 91 HOH HOH . J 5 HOH B 29 829 116 HOH HOH . J 5 HOH B 30 830 119 HOH HOH . J 5 HOH B 31 831 40 HOH HOH . J 5 HOH B 32 832 38 HOH HOH . J 5 HOH B 33 833 123 HOH HOH . J 5 HOH B 34 834 25 HOH HOH . J 5 HOH B 35 835 47 HOH HOH . J 5 HOH B 36 836 37 HOH HOH . J 5 HOH B 37 837 49 HOH HOH . J 5 HOH B 38 838 15 HOH HOH . J 5 HOH B 39 839 118 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 . . . H 4 -8.615 74.518 1.676 1 50.45 ? N1 PLP 602 B 1 HETATM 2 C C2 PLP . . . H 4 -7.405 74.651 2.212 1 48.91 ? C2 PLP 602 B 1 HETATM 3 C C2A PLP . . . H 4 -6.516 75.75 1.727 1 45.14 ? C2A PLP 602 B 1 HETATM 4 C C3 PLP . . . H 4 -6.968 73.776 3.212 1 42.52 ? C3 PLP 602 B 1 HETATM 5 O O3 PLP . . . H 4 -5.726 73.967 3.718 1 56.49 ? O3 PLP 602 B 1 HETATM 6 C C4 PLP . . . H 4 -7.822 72.751 3.659 1 32.44 ? C4 PLP 602 B 1 HETATM 7 C C4A PLP . . . H 4 -7.407 71.821 4.707 1 33.6 ? C4A PLP 602 B 1 HETATM 8 C C5 PLP . . . H 4 -9.088 72.63 3.068 1 40.52 ? C5 PLP 602 B 1 HETATM 9 C C6 PLP . . . H 4 -9.434 73.533 2.101 1 40.48 ? C6 PLP 602 B 1 HETATM 10 C C5A PLP . . . H 4 -10.066 71.572 3.495 1 42.59 ? C5A PLP 602 B 1 HETATM 11 O O4P PLP . . . H 4 -9.616 70.219 3.176 1 41.22 ? O4P PLP 602 B 1 HETATM 12 P P PLP . . . H 4 -10.482 68.945 3.661 1 30.25 ? P PLP 602 B 1 HETATM 13 O O1P PLP . . . H 4 -11.815 69.05 2.949 1 32.47 ? O1P PLP 602 B 1 HETATM 14 O O2P PLP . . . H 4 -10.614 69.086 5.165 1 29.69 ? O2P PLP 602 B 1 HETATM 15 O O3P PLP . . . H 4 -9.686 67.722 3.251 1 50.4 ? O3P PLP 602 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #