data_2HDK
#
_model_server_result.job_id            zmYsf1-nyXh71Sg6ktWfvw 
_model_server_result.datetime_utc      '2024-10-11 15:17:16' 
_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          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              66 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           15 
#