data_5DDS
#
_model_server_result.job_id            yNSMhy97vqFmuLhdWWpIvw 
_model_server_result.datetime_utc      '2024-11-29 13:08:04' 
_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          5dds 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":601}' 
#
_entry.id    5DDS 
#
_exptl.entry_id    5DDS 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         106.71 
_cell.angle_beta          109.16 
_cell.angle_gamma         95.03 
_cell.entry_id            5DDS 
_cell.length_a            84.078 
_cell.length_b            84.21 
_cell.length_c            88.949 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DDS 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,L,M 1 1 
C,D,I,J,K,N,O 2 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 J 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 344 A LYS 344 1_555 E C4A PLP . A PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale2 B NZ LYS 344 B LYS 344 1_555 G C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? 
covale ? covale3 C NZ LYS 344 C LYS 344 1_555 I C4A PLP . C PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
covale ? covale4 D NZ LYS 344 D LYS 344 1_555 J C4A PLP . D PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? 
#
_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                     5DDS 
_atom_sites.fract_transf_matrix[1][1]    0.011894 
_atom_sites.fract_transf_matrix[1][2]    0.001047 
_atom_sites.fract_transf_matrix[1][3]    0.004762 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011921 
_atom_sites.fract_transf_matrix[2][3]    0.004254 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.012637 
_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
E 2 PLP A 1 601 524 PLP PLP . 
F 3 GOL A 1 602 2 GOL GOL . 
G 2 PLP B 1 601 524 PLP PLP . 
H 3 GOL B 1 602 1 GOL GOL . 
I 2 PLP C 1 601 524 PLP PLP . 
J 2 PLP D 1 601 524 PLP PLP . 
K 4 ACY D 1 602 1 ACY ACY . 
L 5 HOH A 1 701 44 HOH HOH . 
L 5 HOH A 2 702 17 HOH HOH . 
L 5 HOH A 3 703 127 HOH HOH . 
L 5 HOH A 4 704 163 HOH HOH . 
L 5 HOH A 5 705 165 HOH HOH . 
L 5 HOH A 6 706 149 HOH HOH . 
L 5 HOH A 7 707 166 HOH HOH . 
L 5 HOH A 8 708 32 HOH HOH . 
L 5 HOH A 9 709 162 HOH HOH . 
L 5 HOH A 10 710 156 HOH HOH . 
L 5 HOH A 11 711 164 HOH HOH . 
L 5 HOH A 12 712 155 HOH HOH . 
L 5 HOH A 13 713 31 HOH HOH . 
L 5 HOH A 14 714 63 HOH HOH . 
L 5 HOH A 15 715 139 HOH HOH . 
L 5 HOH A 16 716 70 HOH HOH . 
L 5 HOH A 17 717 19 HOH HOH . 
L 5 HOH A 18 718 34 HOH HOH . 
L 5 HOH A 19 719 42 HOH HOH . 
L 5 HOH A 20 720 40 HOH HOH . 
L 5 HOH A 21 721 115 HOH HOH . 
L 5 HOH A 22 722 7 HOH HOH . 
L 5 HOH A 23 723 74 HOH HOH . 
L 5 HOH A 24 724 1 HOH HOH . 
L 5 HOH A 25 725 38 HOH HOH . 
L 5 HOH A 26 726 146 HOH HOH . 
L 5 HOH A 27 727 148 HOH HOH . 
L 5 HOH A 28 728 99 HOH HOH . 
L 5 HOH A 29 729 78 HOH HOH . 
L 5 HOH A 30 730 67 HOH HOH . 
L 5 HOH A 31 731 109 HOH HOH . 
L 5 HOH A 32 732 141 HOH HOH . 
L 5 HOH A 33 733 167 HOH HOH . 
M 5 HOH B 1 701 3 HOH HOH . 
M 5 HOH B 2 702 59 HOH HOH . 
M 5 HOH B 3 703 101 HOH HOH . 
M 5 HOH B 4 704 147 HOH HOH . 
M 5 HOH B 5 705 66 HOH HOH . 
M 5 HOH B 6 706 106 HOH HOH . 
M 5 HOH B 7 707 128 HOH HOH . 
M 5 HOH B 8 708 64 HOH HOH . 
M 5 HOH B 9 709 85 HOH HOH . 
M 5 HOH B 10 710 25 HOH HOH . 
M 5 HOH B 11 711 91 HOH HOH . 
M 5 HOH B 12 712 69 HOH HOH . 
M 5 HOH B 13 713 150 HOH HOH . 
M 5 HOH B 14 714 20 HOH HOH . 
M 5 HOH B 15 715 60 HOH HOH . 
M 5 HOH B 16 716 140 HOH HOH . 
M 5 HOH B 17 717 116 HOH HOH . 
M 5 HOH B 18 718 13 HOH HOH . 
M 5 HOH B 19 719 61 HOH HOH . 
M 5 HOH B 20 720 75 HOH HOH . 
M 5 HOH B 21 721 52 HOH HOH . 
M 5 HOH B 22 722 73 HOH HOH . 
M 5 HOH B 23 723 4 HOH HOH . 
M 5 HOH B 24 724 47 HOH HOH . 
M 5 HOH B 25 725 36 HOH HOH . 
M 5 HOH B 26 726 117 HOH HOH . 
M 5 HOH B 27 727 120 HOH HOH . 
M 5 HOH B 28 728 87 HOH HOH . 
M 5 HOH B 29 729 104 HOH HOH . 
M 5 HOH B 30 730 54 HOH HOH . 
M 5 HOH B 31 731 86 HOH HOH . 
M 5 HOH B 32 732 129 HOH HOH . 
N 5 HOH C 1 701 105 HOH HOH . 
N 5 HOH C 2 702 41 HOH HOH . 
N 5 HOH C 3 703 113 HOH HOH . 
N 5 HOH C 4 704 110 HOH HOH . 
N 5 HOH C 5 705 151 HOH HOH . 
N 5 HOH C 6 706 126 HOH HOH . 
N 5 HOH C 7 707 76 HOH HOH . 
N 5 HOH C 8 708 82 HOH HOH . 
N 5 HOH C 9 709 49 HOH HOH . 
N 5 HOH C 10 710 27 HOH HOH . 
N 5 HOH C 11 711 14 HOH HOH . 
N 5 HOH C 12 712 10 HOH HOH . 
N 5 HOH C 13 713 107 HOH HOH . 
N 5 HOH C 14 714 50 HOH HOH . 
N 5 HOH C 15 715 77 HOH HOH . 
N 5 HOH C 16 716 122 HOH HOH . 
N 5 HOH C 17 717 48 HOH HOH . 
N 5 HOH C 18 718 92 HOH HOH . 
N 5 HOH C 19 719 100 HOH HOH . 
N 5 HOH C 20 720 53 HOH HOH . 
O 5 HOH D 1 701 5 HOH HOH . 
O 5 HOH D 2 702 26 HOH HOH . 
O 5 HOH D 3 703 119 HOH HOH . 
O 5 HOH D 4 704 56 HOH HOH . 
O 5 HOH D 5 705 22 HOH HOH . 
O 5 HOH D 6 706 6 HOH HOH . 
O 5 HOH D 7 707 29 HOH HOH . 
O 5 HOH D 8 708 35 HOH HOH . 
O 5 HOH D 9 709 15 HOH HOH . 
O 5 HOH D 10 710 30 HOH HOH . 
O 5 HOH D 11 711 23 HOH HOH . 
O 5 HOH D 12 712 65 HOH HOH . 
O 5 HOH D 13 713 12 HOH HOH . 
O 5 HOH D 14 714 33 HOH HOH . 
O 5 HOH D 15 715 84 HOH HOH . 
O 5 HOH D 16 716 152 HOH HOH . 
O 5 HOH D 17 717 62 HOH HOH . 
O 5 HOH D 18 718 8 HOH HOH . 
O 5 HOH D 19 719 88 HOH HOH . 
O 5 HOH D 20 720 2 HOH HOH . 
O 5 HOH D 21 721 124 HOH HOH . 
O 5 HOH D 22 722 153 HOH HOH . 
O 5 HOH D 23 723 108 HOH HOH . 
O 5 HOH D 24 724 21 HOH HOH . 
O 5 HOH D 25 725 94 HOH HOH . 
O 5 HOH D 26 726 95 HOH HOH . 
O 5 HOH D 27 727 57 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 . . . E 2 0.105 3.446 -1.106 1 30.27 ? N1 PLP 601 A 1 
HETATM 2 C C2 PLP . . . E 2 0.969 2.598 -1.73 1 25.84 ? C2 PLP 601 A 1 
HETATM 3 C C2A PLP . . . E 2 0.891 1.152 -1.456 1 25.78 ? C2A PLP 601 A 1 
HETATM 4 C C3 PLP . . . E 2 1.917 3.082 -2.625 1 29.86 ? C3 PLP 601 A 1 
HETATM 5 O O3 PLP . . . E 2 2.778 2.209 -3.245 1 30.25 ? O3 PLP 601 A 1 
HETATM 6 C C4 PLP . . . E 2 1.988 4.464 -2.892 1 30.12 ? C4 PLP 601 A 1 
HETATM 7 C C4A PLP . . . E 2 3.008 4.982 -3.86 1 31.9 ? C4A PLP 601 A 1 
HETATM 8 C C5 PLP . . . E 2 1.083 5.331 -2.237 1 29.42 ? C5 PLP 601 A 1 
HETATM 9 C C6 PLP . . . E 2 0.144 4.788 -1.338 1 31.9 ? C6 PLP 601 A 1 
HETATM 10 C C5A PLP . . . E 2 1.102 6.829 -2.46 1 27.51 ? C5A PLP 601 A 1 
HETATM 11 O O4P PLP . . . E 2 0.648 7.176 -3.754 1 31.06 ? O4P PLP 601 A 1 
HETATM 12 P P PLP . . . E 2 0.861 8.681 -4.258 1 33.38 ? P PLP 601 A 1 
HETATM 13 O O1P PLP . . . E 2 0.047 8.932 -5.543 1 32.94 ? O1P PLP 601 A 1 
HETATM 14 O O2P PLP . . . E 2 2.35 8.859 -4.546 1 33.91 ? O2P PLP 601 A 1 
HETATM 15 O O3P PLP . . . E 2 0.416 9.633 -3.137 1 26.3 ? O3P PLP 601 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           15 
#