data_3C5Q # _model_server_result.job_id yWp0gze6CisLONCxHAvvdw _model_server_result.datetime_utc '2024-12-17 16:31:16' _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 3c5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":406}' # _entry.id 3C5Q # _exptl.entry_id 3C5Q _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 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 3C5Q _cell.length_a 79.111 _cell.length_b 79.111 _cell.length_c 134.821 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 _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' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 44.940333 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C4A _struct_conn.ptnr1_label_comp_id PLP _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id PLP _struct_conn.ptnr1_auth_seq_id 406 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id NZ _struct_conn.ptnr2_label_comp_id LYS _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LYS _struct_conn.ptnr2_auth_seq_id 407 _struct_conn.ptnr2_symmetry 1_555 _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 1.284 _struct_conn.pdbx_value_order ? # _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 273 n y N1 C6 PLP sing 274 n y C2 C2A PLP sing 275 n n C2 C3 PLP sing 276 n y C2A H2A1 PLP sing 277 n n C2A H2A2 PLP sing 278 n n C2A H2A3 PLP sing 279 n n C3 O3 PLP sing 280 n n C3 C4 PLP doub 281 n y O3 HO3 PLP sing 282 n n C4 C4A PLP sing 283 n n C4 C5 PLP sing 284 n y C4A O4A PLP doub 285 n n C4A H4A PLP sing 286 n n C5 C6 PLP doub 287 n y C5 C5A PLP sing 288 n n C6 H6 PLP sing 289 n n C5A O4P PLP sing 290 n n C5A H5A1 PLP sing 291 n n C5A H5A2 PLP sing 292 n n O4P P PLP sing 293 n n P O1P PLP doub 294 n n P O2P PLP sing 295 n n P O3P PLP sing 296 n n O2P HOP2 PLP sing 297 n n O3P HOP3 PLP sing 298 n n # _atom_sites.entry_id 3C5Q _atom_sites.fract_transf_matrix[1][1] 0.01264 _atom_sites.fract_transf_matrix[1][2] 0.007298 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014596 _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] 0.007417 _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 PLP A 1 406 1 PLP PLP . C 3 LYS A 1 407 2 LYS LYS . D 4 GOL A 1 1003 1003 GOL GOL . E 5 HOH A 1 1004 1 HOH HOH . E 5 HOH A 2 1005 2 HOH HOH . E 5 HOH A 3 1006 3 HOH HOH . E 5 HOH A 4 1007 4 HOH HOH . E 5 HOH A 5 1008 5 HOH HOH . E 5 HOH A 6 1009 6 HOH HOH . E 5 HOH A 7 1010 7 HOH HOH . E 5 HOH A 8 1011 8 HOH HOH . E 5 HOH A 9 1012 9 HOH HOH . E 5 HOH A 10 1013 10 HOH HOH . E 5 HOH A 11 1014 11 HOH HOH . E 5 HOH A 12 1015 12 HOH HOH . E 5 HOH A 13 1016 13 HOH HOH . E 5 HOH A 14 1017 14 HOH HOH . E 5 HOH A 15 1018 15 HOH HOH . E 5 HOH A 16 1019 16 HOH HOH . E 5 HOH A 17 1020 17 HOH HOH . E 5 HOH A 18 1021 18 HOH HOH . E 5 HOH A 19 1022 19 HOH HOH . E 5 HOH A 20 1023 20 HOH HOH . E 5 HOH A 21 1024 21 HOH HOH . E 5 HOH A 22 1025 22 HOH HOH . E 5 HOH A 23 1026 23 HOH HOH . E 5 HOH A 24 1027 24 HOH HOH . E 5 HOH A 25 1028 25 HOH HOH . E 5 HOH A 26 1029 26 HOH HOH . E 5 HOH A 27 1030 27 HOH HOH . E 5 HOH A 28 1031 28 HOH HOH . E 5 HOH A 29 1032 29 HOH HOH . E 5 HOH A 30 1033 30 HOH HOH . E 5 HOH A 31 1034 31 HOH HOH . E 5 HOH A 32 1035 32 HOH HOH . E 5 HOH A 33 1036 33 HOH HOH . E 5 HOH A 34 1037 34 HOH HOH . E 5 HOH A 35 1038 35 HOH HOH . E 5 HOH A 36 1039 36 HOH HOH . E 5 HOH A 37 1040 37 HOH HOH . E 5 HOH A 38 1041 38 HOH HOH . E 5 HOH A 39 1042 39 HOH HOH . E 5 HOH A 40 1043 40 HOH HOH . E 5 HOH A 41 1044 41 HOH HOH . E 5 HOH A 42 1045 42 HOH HOH . E 5 HOH A 43 1046 43 HOH HOH . E 5 HOH A 44 1047 44 HOH HOH . E 5 HOH A 45 1048 45 HOH HOH . E 5 HOH A 46 1049 46 HOH HOH . E 5 HOH A 47 1050 47 HOH HOH . E 5 HOH A 48 1051 48 HOH HOH . E 5 HOH A 49 1052 49 HOH HOH . E 5 HOH A 50 1053 50 HOH HOH . E 5 HOH A 51 1054 51 HOH HOH . E 5 HOH A 52 1055 52 HOH HOH . E 5 HOH A 53 1056 53 HOH HOH . E 5 HOH A 54 1057 54 HOH HOH . E 5 HOH A 55 1058 55 HOH HOH . E 5 HOH A 56 1059 56 HOH HOH . E 5 HOH A 57 1060 57 HOH HOH . E 5 HOH A 58 1061 58 HOH HOH . E 5 HOH A 59 1062 59 HOH HOH . E 5 HOH A 60 1063 60 HOH HOH . E 5 HOH A 61 1064 61 HOH HOH . E 5 HOH A 62 1065 62 HOH HOH . E 5 HOH A 63 1066 63 HOH HOH . E 5 HOH A 64 1067 64 HOH HOH . E 5 HOH A 65 1068 65 HOH HOH . E 5 HOH A 66 1069 66 HOH HOH . E 5 HOH A 67 1070 67 HOH HOH . E 5 HOH A 68 1071 68 HOH HOH . E 5 HOH A 69 1072 69 HOH HOH . E 5 HOH A 70 1073 70 HOH HOH . E 5 HOH A 71 1074 71 HOH HOH . E 5 HOH A 72 1075 72 HOH HOH . E 5 HOH A 73 1076 73 HOH HOH . E 5 HOH A 74 1077 74 HOH HOH . E 5 HOH A 75 1078 75 HOH HOH . E 5 HOH A 76 1079 76 HOH HOH . E 5 HOH A 77 1080 77 HOH HOH . E 5 HOH A 78 1081 78 HOH HOH . E 5 HOH A 79 1082 79 HOH HOH . E 5 HOH A 80 1083 80 HOH HOH . E 5 HOH A 81 1084 81 HOH HOH . E 5 HOH A 82 1085 82 HOH HOH . E 5 HOH A 83 1086 83 HOH HOH . E 5 HOH A 84 1087 84 HOH HOH . E 5 HOH A 85 1088 85 HOH HOH . E 5 HOH A 86 1089 86 HOH HOH . E 5 HOH A 87 1090 87 HOH HOH . E 5 HOH A 88 1091 88 HOH HOH . E 5 HOH A 89 1092 89 HOH HOH . E 5 HOH A 90 1093 90 HOH HOH . E 5 HOH A 91 1094 91 HOH HOH . E 5 HOH A 92 1095 92 HOH HOH . E 5 HOH A 93 1096 93 HOH HOH . E 5 HOH A 94 1097 94 HOH HOH . E 5 HOH A 95 1098 95 HOH HOH . E 5 HOH A 96 1099 96 HOH HOH . E 5 HOH A 97 1100 97 HOH HOH . E 5 HOH A 98 1101 98 HOH HOH . E 5 HOH A 99 1102 99 HOH HOH . E 5 HOH A 100 1103 100 HOH HOH . E 5 HOH A 101 1104 101 HOH HOH . E 5 HOH A 102 1105 102 HOH HOH . E 5 HOH A 103 1106 103 HOH HOH . E 5 HOH A 104 1107 104 HOH HOH . E 5 HOH A 105 1108 105 HOH HOH . E 5 HOH A 106 1109 106 HOH HOH . E 5 HOH A 107 1110 107 HOH HOH . E 5 HOH A 108 1111 108 HOH HOH . E 5 HOH A 109 1112 109 HOH HOH . E 5 HOH A 110 1113 110 HOH HOH . E 5 HOH A 111 1114 111 HOH HOH . E 5 HOH A 112 1115 112 HOH HOH . E 5 HOH A 113 1116 113 HOH HOH . E 5 HOH A 114 1117 114 HOH HOH . E 5 HOH A 115 1118 115 HOH HOH . E 5 HOH A 116 1119 116 HOH HOH . E 5 HOH A 117 1120 117 HOH HOH . E 5 HOH A 118 1121 118 HOH HOH . E 5 HOH A 119 1122 119 HOH HOH . E 5 HOH A 120 1123 120 HOH HOH . E 5 HOH A 121 1124 121 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 . . . B 2 -21.168 15.599 10.134 1 9.44 ? N1 PLP 406 A 1 HETATM 2 C C2 PLP . . . B 2 -20.721 14.35 9.682 1 11.8 ? C2 PLP 406 A 1 HETATM 3 C C2A PLP . . . B 2 -20.617 14.078 8.212 1 6.69 ? C2A PLP 406 A 1 HETATM 4 C C3 PLP . . . B 2 -20.256 13.393 10.669 1 12.54 ? C3 PLP 406 A 1 HETATM 5 O O3 PLP . . . B 2 -19.957 12.109 10.241 1 16.12 ? O3 PLP 406 A 1 HETATM 6 C C4 PLP . . . B 2 -20.192 13.738 12.019 1 14.12 ? C4 PLP 406 A 1 HETATM 7 C C4A PLP . . . B 2 -19.468 12.807 12.96 1 15.36 ? C4A PLP 406 A 1 HETATM 8 C C5 PLP . . . B 2 -20.647 14.987 12.444 1 14.03 ? C5 PLP 406 A 1 HETATM 9 C C6 PLP . . . B 2 -21.145 15.939 11.471 1 13.04 ? C6 PLP 406 A 1 HETATM 10 C C5A PLP . . . B 2 -20.849 15.422 13.855 1 15.51 ? C5A PLP 406 A 1 HETATM 11 O O4P PLP . . . B 2 -19.678 16.062 14.322 1 14.37 ? O4P PLP 406 A 1 HETATM 12 P P PLP . . . B 2 -19.498 16.471 15.728 1 14.75 ? P PLP 406 A 1 HETATM 13 O O1P PLP . . . B 2 -19.622 18.046 15.653 1 14.23 ? O1P PLP 406 A 1 HETATM 14 O O2P PLP . . . B 2 -18.08 15.903 16.027 1 9.88 ? O2P PLP 406 A 1 HETATM 15 O O3P PLP . . . B 2 -20.569 15.921 16.758 1 11.22 ? O3P PLP 406 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #