data_2HDK # _model_server_result.job_id r-j2lHABiQh_CkHolae0uA _model_server_result.datetime_utc '2024-12-12 00:58:08' _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 2hdk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 2HDK # _exptl.entry_id 2HDK _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 96.16 _cell.angle_gamma 90 _cell.entry_id 2HDK _cell.length_a 59.48 _cell.length_b 112.187 _cell.length_c 60.265 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HDK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,H _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 # 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 202 A LYS 202 1_555 C C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale2 E C4A PLP . B PLP 401 1_555 B NZ LYS 202 B LYS 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? # _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' # _atom_sites.entry_id 2HDK _atom_sites.fract_transf_matrix[1][1] 0.016812 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001815 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008914 _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] 0.01669 _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 A 1 400 400 PLP PLP . D 3 ACY A 1 1001 1001 ACY ACY . E 2 PLP B 1 401 401 PLP PLP . F 4 COI B 1 900 900 COI COI . G 5 HOH A 1 1002 1 HOH HOH . G 5 HOH A 2 1003 3 HOH HOH . G 5 HOH A 3 1004 4 HOH HOH . G 5 HOH A 4 1005 5 HOH HOH . G 5 HOH A 5 1006 7 HOH HOH . G 5 HOH A 6 1007 8 HOH HOH . G 5 HOH A 7 1008 9 HOH HOH . G 5 HOH A 8 1009 14 HOH HOH . G 5 HOH A 9 1010 15 HOH HOH . G 5 HOH A 10 1011 16 HOH HOH . G 5 HOH A 11 1012 18 HOH HOH . G 5 HOH A 12 1013 19 HOH HOH . G 5 HOH A 13 1014 20 HOH HOH . G 5 HOH A 14 1015 21 HOH HOH . G 5 HOH A 15 1016 25 HOH HOH . G 5 HOH A 16 1017 26 HOH HOH . G 5 HOH A 17 1018 28 HOH HOH . G 5 HOH A 18 1019 30 HOH HOH . G 5 HOH A 19 1020 32 HOH HOH . G 5 HOH A 20 1021 34 HOH HOH . G 5 HOH A 21 1022 36 HOH HOH . G 5 HOH A 22 1023 37 HOH HOH . G 5 HOH A 23 1024 39 HOH HOH . G 5 HOH A 24 1025 41 HOH HOH . G 5 HOH A 25 1026 42 HOH HOH . G 5 HOH A 26 1027 45 HOH HOH . G 5 HOH A 27 1028 46 HOH HOH . G 5 HOH A 28 1029 49 HOH HOH . G 5 HOH A 29 1030 51 HOH HOH . G 5 HOH A 30 1031 54 HOH HOH . G 5 HOH A 31 1032 55 HOH HOH . G 5 HOH A 32 1033 57 HOH HOH . G 5 HOH A 33 1034 58 HOH HOH . G 5 HOH A 34 1035 62 HOH HOH . G 5 HOH A 35 1036 68 HOH HOH . G 5 HOH A 36 1037 71 HOH HOH . G 5 HOH A 37 1038 72 HOH HOH . G 5 HOH A 38 1039 74 HOH HOH . G 5 HOH A 39 1040 76 HOH HOH . G 5 HOH A 40 1041 79 HOH HOH . G 5 HOH A 41 1042 80 HOH HOH . G 5 HOH A 42 1043 82 HOH HOH . G 5 HOH A 43 1044 85 HOH HOH . G 5 HOH A 44 1045 88 HOH HOH . G 5 HOH A 45 1046 89 HOH HOH . G 5 HOH A 46 1047 90 HOH HOH . G 5 HOH A 47 1048 94 HOH HOH . G 5 HOH A 48 1049 97 HOH HOH . G 5 HOH A 49 1050 99 HOH HOH . G 5 HOH A 50 1051 101 HOH HOH . G 5 HOH A 51 1052 102 HOH HOH . G 5 HOH A 52 1053 103 HOH HOH . G 5 HOH A 53 1054 105 HOH HOH . G 5 HOH A 54 1055 106 HOH HOH . G 5 HOH A 55 1056 108 HOH HOH . G 5 HOH A 56 1057 109 HOH HOH . G 5 HOH A 57 1058 111 HOH HOH . G 5 HOH A 58 1059 112 HOH HOH . G 5 HOH A 59 1060 113 HOH HOH . G 5 HOH A 60 1061 116 HOH HOH . G 5 HOH A 61 1062 117 HOH HOH . G 5 HOH A 62 1063 118 HOH HOH . G 5 HOH A 63 1064 119 HOH HOH . G 5 HOH A 64 1065 120 HOH HOH . G 5 HOH A 65 1066 123 HOH HOH . G 5 HOH A 66 1067 124 HOH HOH . G 5 HOH A 67 1068 126 HOH HOH . G 5 HOH A 68 1069 127 HOH HOH . G 5 HOH A 69 1070 130 HOH HOH . G 5 HOH A 70 1071 131 HOH HOH . G 5 HOH A 71 1072 135 HOH HOH . G 5 HOH A 72 1073 136 HOH HOH . G 5 HOH A 73 1074 140 HOH HOH . G 5 HOH A 74 1075 145 HOH HOH . H 5 HOH B 1 2 2 HOH HOH . H 5 HOH B 2 6 6 HOH HOH . H 5 HOH B 3 10 10 HOH HOH . H 5 HOH B 4 11 11 HOH HOH . H 5 HOH B 5 12 12 HOH HOH . H 5 HOH B 6 13 13 HOH HOH . H 5 HOH B 7 17 17 HOH HOH . H 5 HOH B 8 22 22 HOH HOH . H 5 HOH B 9 23 23 HOH HOH . H 5 HOH B 10 24 24 HOH HOH . H 5 HOH B 11 27 27 HOH HOH . H 5 HOH B 12 29 29 HOH HOH . H 5 HOH B 13 31 31 HOH HOH . H 5 HOH B 14 33 33 HOH HOH . H 5 HOH B 15 35 35 HOH HOH . H 5 HOH B 16 38 38 HOH HOH . H 5 HOH B 17 40 40 HOH HOH . H 5 HOH B 18 43 43 HOH HOH . H 5 HOH B 19 44 44 HOH HOH . H 5 HOH B 20 47 47 HOH HOH . H 5 HOH B 21 48 48 HOH HOH . H 5 HOH B 22 50 50 HOH HOH . H 5 HOH B 23 52 52 HOH HOH . H 5 HOH B 24 53 53 HOH HOH . H 5 HOH B 25 56 56 HOH HOH . H 5 HOH B 26 59 59 HOH HOH . H 5 HOH B 27 60 60 HOH HOH . H 5 HOH B 28 61 61 HOH HOH . H 5 HOH B 29 63 63 HOH HOH . H 5 HOH B 30 64 64 HOH HOH . H 5 HOH B 31 65 65 HOH HOH . H 5 HOH B 32 66 66 HOH HOH . H 5 HOH B 33 67 67 HOH HOH . H 5 HOH B 34 69 69 HOH HOH . H 5 HOH B 35 70 70 HOH HOH . H 5 HOH B 36 73 73 HOH HOH . H 5 HOH B 37 75 75 HOH HOH . H 5 HOH B 38 77 77 HOH HOH . H 5 HOH B 39 78 78 HOH HOH . H 5 HOH B 40 81 81 HOH HOH . H 5 HOH B 41 83 83 HOH HOH . H 5 HOH B 42 84 84 HOH HOH . H 5 HOH B 43 86 86 HOH HOH . H 5 HOH B 44 87 87 HOH HOH . H 5 HOH B 45 91 91 HOH HOH . H 5 HOH B 46 92 92 HOH HOH . H 5 HOH B 47 93 93 HOH HOH . H 5 HOH B 48 95 95 HOH HOH . H 5 HOH B 49 96 96 HOH HOH . H 5 HOH B 50 98 98 HOH HOH . H 5 HOH B 51 100 100 HOH HOH . H 5 HOH B 52 104 104 HOH HOH . H 5 HOH B 53 107 107 HOH HOH . H 5 HOH B 54 110 110 HOH HOH . H 5 HOH B 55 114 114 HOH HOH . H 5 HOH B 56 115 115 HOH HOH . H 5 HOH B 57 121 121 HOH HOH . H 5 HOH B 58 122 122 HOH HOH . H 5 HOH B 59 125 125 HOH HOH . H 5 HOH B 60 128 128 HOH HOH . H 5 HOH B 61 129 129 HOH HOH . H 5 HOH B 62 132 132 HOH HOH . H 5 HOH B 63 133 133 HOH HOH . H 5 HOH B 64 134 134 HOH HOH . H 5 HOH B 65 138 138 HOH HOH . H 5 HOH B 66 142 142 HOH HOH . H 5 HOH B 67 144 144 HOH HOH . H 5 HOH B 68 146 146 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 -4.834 -5.227 1.762 1 15.95 ? N1 PLP 400 A 1 HETATM 2 C C2 PLP . . . C 2 -4.306 -5.047 3.006 1 18.18 ? C2 PLP 400 A 1 HETATM 3 C C2A PLP . . . C 2 -3.591 -3.721 3.322 1 17.64 ? C2A PLP 400 A 1 HETATM 4 C C3 PLP . . . C 2 -4.424 -6.081 3.945 1 18.21 ? C3 PLP 400 A 1 HETATM 5 O O3 PLP . . . C 2 -3.913 -5.905 5.149 1 19.83 ? O3 PLP 400 A 1 HETATM 6 C C4 PLP . . . C 2 -5.068 -7.287 3.62 1 18.34 ? C4 PLP 400 A 1 HETATM 7 C C4A PLP . . . C 2 -5.171 -8.43 4.67 1 20.44 ? C4A PLP 400 A 1 HETATM 8 C C5 PLP . . . C 2 -5.598 -7.403 2.334 1 18.53 ? C5 PLP 400 A 1 HETATM 9 C C6 PLP . . . C 2 -5.469 -6.363 1.427 1 18.55 ? C6 PLP 400 A 1 HETATM 10 C C5A PLP . . . C 2 -6.353 -8.564 1.857 1 19.63 ? C5A PLP 400 A 1 HETATM 11 O O4P PLP . . . C 2 -5.728 -9.789 1.954 1 19.98 ? O4P PLP 400 A 1 HETATM 12 P P PLP . . . C 2 -6.645 -11.014 2.087 1 19.52 ? P PLP 400 A 1 HETATM 13 O O1P PLP . . . C 2 -7.416 -10.999 3.314 1 17.75 ? O1P PLP 400 A 1 HETATM 14 O O2P PLP . . . C 2 -5.614 -12.163 2.198 1 19.1 ? O2P PLP 400 A 1 HETATM 15 O O3P PLP . . . C 2 -7.295 -11.151 0.748 1 17.38 ? O3P PLP 400 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #