data_8I7U
#
_model_server_result.job_id            12nKVlcHxsXUacNR9riQxA 
_model_server_result.datetime_utc      '2024-11-25 15:33:08' 
_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          8i7u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    8I7U 
#
_exptl.entry_id    8I7U 
_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    6 
_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         90 
_cell.entry_id            8I7U 
_cell.length_a            65.465 
_cell.length_b            110.462 
_cell.length_c            353.654 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8I7U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab (z,x,y)' 
_symmetry.space_group_name_H-M     'P 2 21 21' 
#
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 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,F,G,L,M,R 1 1 
B,E,H,K,N,Q 2 1 
C,I,O 3 1 
D,J,P 3 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' 3_655 -x+1,y+1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 65.465 55.231 176.827 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L 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 244 C LYS 254 1_555 G C4A PLP . C PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale2 B NZ LYS 244 A LYS 254 1_555 H C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale3 C NZ LYS 244 B LYS 254 1_555 I C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale4 D NZ LYS 244 D LYS 254 1_555 J C4A PLP . D PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale5 E NZ LYS 244 E LYS 254 1_555 K C4A PLP . E PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale6 F NZ LYS 244 F LYS 254 1_555 L C4A PLP . F PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
#
_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                     8I7U 
_atom_sites.fract_transf_matrix[1][1]    0.015275 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009053 
_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]    0.002828 
_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
G 2 PLP C 1 501 501 PLP PLP . 
H 2 PLP A 1 501 501 PLP PLP . 
I 2 PLP B 1 501 501 PLP PLP . 
J 2 PLP D 1 501 501 PLP PLP . 
K 2 PLP E 1 501 501 PLP PLP . 
L 2 PLP F 1 501 501 PLP PLP . 
M 3 HOH C 1 601 26 HOH HOH . 
M 3 HOH C 2 602 10 HOH HOH . 
M 3 HOH C 3 603 146 HOH HOH . 
M 3 HOH C 4 604 35 HOH HOH . 
M 3 HOH C 5 605 14 HOH HOH . 
M 3 HOH C 6 606 123 HOH HOH . 
M 3 HOH C 7 607 153 HOH HOH . 
M 3 HOH C 8 608 2 HOH HOH . 
M 3 HOH C 9 609 61 HOH HOH . 
M 3 HOH C 10 610 74 HOH HOH . 
M 3 HOH C 11 611 113 HOH HOH . 
M 3 HOH C 12 612 8 HOH HOH . 
M 3 HOH C 13 613 42 HOH HOH . 
M 3 HOH C 14 614 152 HOH HOH . 
M 3 HOH C 15 615 168 HOH HOH . 
M 3 HOH C 16 616 116 HOH HOH . 
M 3 HOH C 17 617 34 HOH HOH . 
M 3 HOH C 18 618 82 HOH HOH . 
M 3 HOH C 19 619 32 HOH HOH . 
M 3 HOH C 20 620 165 HOH HOH . 
M 3 HOH C 21 621 67 HOH HOH . 
M 3 HOH C 22 622 171 HOH HOH . 
M 3 HOH C 23 623 166 HOH HOH . 
M 3 HOH C 24 624 27 HOH HOH . 
M 3 HOH C 25 625 77 HOH HOH . 
M 3 HOH C 26 626 124 HOH HOH . 
M 3 HOH C 27 627 83 HOH HOH . 
M 3 HOH C 28 628 134 HOH HOH . 
M 3 HOH C 29 629 163 HOH HOH . 
M 3 HOH C 30 630 169 HOH HOH . 
M 3 HOH C 31 631 154 HOH HOH . 
M 3 HOH C 32 632 110 HOH HOH . 
M 3 HOH C 33 633 167 HOH HOH . 
M 3 HOH C 34 634 115 HOH HOH . 
M 3 HOH C 35 635 122 HOH HOH . 
N 3 HOH A 1 601 33 HOH HOH . 
N 3 HOH A 2 602 17 HOH HOH . 
N 3 HOH A 3 603 4 HOH HOH . 
N 3 HOH A 4 604 5 HOH HOH . 
N 3 HOH A 5 605 106 HOH HOH . 
N 3 HOH A 6 606 16 HOH HOH . 
N 3 HOH A 7 607 99 HOH HOH . 
N 3 HOH A 8 608 49 HOH HOH . 
N 3 HOH A 9 609 145 HOH HOH . 
N 3 HOH A 10 610 63 HOH HOH . 
N 3 HOH A 11 611 102 HOH HOH . 
N 3 HOH A 12 612 41 HOH HOH . 
N 3 HOH A 13 613 114 HOH HOH . 
N 3 HOH A 14 614 78 HOH HOH . 
N 3 HOH A 15 615 98 HOH HOH . 
N 3 HOH A 16 616 6 HOH HOH . 
N 3 HOH A 17 617 60 HOH HOH . 
N 3 HOH A 18 618 150 HOH HOH . 
N 3 HOH A 19 619 37 HOH HOH . 
N 3 HOH A 20 620 105 HOH HOH . 
N 3 HOH A 21 621 144 HOH HOH . 
N 3 HOH A 22 622 109 HOH HOH . 
N 3 HOH A 23 623 125 HOH HOH . 
N 3 HOH A 24 624 176 HOH HOH . 
O 3 HOH B 1 601 147 HOH HOH . 
O 3 HOH B 2 602 132 HOH HOH . 
O 3 HOH B 3 603 156 HOH HOH . 
O 3 HOH B 4 604 73 HOH HOH . 
O 3 HOH B 5 605 48 HOH HOH . 
O 3 HOH B 6 606 86 HOH HOH . 
O 3 HOH B 7 607 85 HOH HOH . 
O 3 HOH B 8 608 40 HOH HOH . 
O 3 HOH B 9 609 173 HOH HOH . 
O 3 HOH B 10 610 84 HOH HOH . 
O 3 HOH B 11 611 69 HOH HOH . 
O 3 HOH B 12 612 1 HOH HOH . 
O 3 HOH B 13 613 79 HOH HOH . 
O 3 HOH B 14 614 29 HOH HOH . 
O 3 HOH B 15 615 139 HOH HOH . 
O 3 HOH B 16 616 15 HOH HOH . 
O 3 HOH B 17 617 175 HOH HOH . 
O 3 HOH B 18 618 65 HOH HOH . 
O 3 HOH B 19 619 130 HOH HOH . 
O 3 HOH B 20 620 140 HOH HOH . 
O 3 HOH B 21 621 93 HOH HOH . 
O 3 HOH B 22 622 174 HOH HOH . 
O 3 HOH B 23 623 87 HOH HOH . 
O 3 HOH B 24 624 72 HOH HOH . 
O 3 HOH B 25 625 80 HOH HOH . 
O 3 HOH B 26 626 120 HOH HOH . 
O 3 HOH B 27 627 172 HOH HOH . 
O 3 HOH B 28 628 107 HOH HOH . 
O 3 HOH B 29 629 133 HOH HOH . 
P 3 HOH D 1 601 46 HOH HOH . 
P 3 HOH D 2 602 43 HOH HOH . 
P 3 HOH D 3 603 160 HOH HOH . 
P 3 HOH D 4 604 62 HOH HOH . 
P 3 HOH D 5 605 7 HOH HOH . 
P 3 HOH D 6 606 126 HOH HOH . 
P 3 HOH D 7 607 20 HOH HOH . 
P 3 HOH D 8 608 119 HOH HOH . 
P 3 HOH D 9 609 31 HOH HOH . 
P 3 HOH D 10 610 111 HOH HOH . 
P 3 HOH D 11 611 9 HOH HOH . 
P 3 HOH D 12 612 44 HOH HOH . 
P 3 HOH D 13 613 128 HOH HOH . 
P 3 HOH D 14 614 135 HOH HOH . 
P 3 HOH D 15 615 148 HOH HOH . 
P 3 HOH D 16 616 103 HOH HOH . 
P 3 HOH D 17 617 23 HOH HOH . 
P 3 HOH D 18 618 36 HOH HOH . 
P 3 HOH D 19 619 159 HOH HOH . 
P 3 HOH D 20 620 108 HOH HOH . 
P 3 HOH D 21 621 100 HOH HOH . 
P 3 HOH D 22 622 75 HOH HOH . 
P 3 HOH D 23 623 92 HOH HOH . 
P 3 HOH D 24 624 161 HOH HOH . 
P 3 HOH D 25 625 104 HOH HOH . 
Q 3 HOH E 1 601 51 HOH HOH . 
Q 3 HOH E 2 602 155 HOH HOH . 
Q 3 HOH E 3 603 3 HOH HOH . 
Q 3 HOH E 4 604 11 HOH HOH . 
Q 3 HOH E 5 605 71 HOH HOH . 
Q 3 HOH E 6 606 24 HOH HOH . 
Q 3 HOH E 7 607 22 HOH HOH . 
Q 3 HOH E 8 608 57 HOH HOH . 
Q 3 HOH E 9 609 64 HOH HOH . 
Q 3 HOH E 10 610 131 HOH HOH . 
Q 3 HOH E 11 611 127 HOH HOH . 
Q 3 HOH E 12 612 28 HOH HOH . 
Q 3 HOH E 13 613 54 HOH HOH . 
Q 3 HOH E 14 614 45 HOH HOH . 
Q 3 HOH E 15 615 70 HOH HOH . 
Q 3 HOH E 16 616 52 HOH HOH . 
Q 3 HOH E 17 617 38 HOH HOH . 
Q 3 HOH E 18 618 138 HOH HOH . 
Q 3 HOH E 19 619 143 HOH HOH . 
R 3 HOH F 1 601 164 HOH HOH . 
R 3 HOH F 2 602 59 HOH HOH . 
R 3 HOH F 3 603 30 HOH HOH . 
R 3 HOH F 4 604 13 HOH HOH . 
R 3 HOH F 5 605 94 HOH HOH . 
R 3 HOH F 6 606 18 HOH HOH . 
R 3 HOH F 7 607 50 HOH HOH . 
R 3 HOH F 8 608 157 HOH HOH . 
R 3 HOH F 9 609 12 HOH HOH . 
R 3 HOH F 10 610 19 HOH HOH . 
R 3 HOH F 11 611 66 HOH HOH . 
R 3 HOH F 12 612 95 HOH HOH . 
R 3 HOH F 13 613 55 HOH HOH . 
R 3 HOH F 14 614 88 HOH HOH . 
R 3 HOH F 15 615 76 HOH HOH . 
R 3 HOH F 16 616 56 HOH HOH . 
R 3 HOH F 17 617 21 HOH HOH . 
R 3 HOH F 18 618 81 HOH HOH . 
R 3 HOH F 19 619 39 HOH HOH . 
R 3 HOH F 20 620 68 HOH HOH . 
R 3 HOH F 21 621 101 HOH HOH . 
R 3 HOH F 22 622 90 HOH HOH . 
R 3 HOH F 23 623 112 HOH HOH . 
R 3 HOH F 24 624 142 HOH HOH . 
R 3 HOH F 25 625 118 HOH HOH . 
R 3 HOH F 26 626 136 HOH HOH . 
R 3 HOH F 27 627 91 HOH HOH . 
R 3 HOH F 28 628 89 HOH HOH . 
R 3 HOH F 29 629 151 HOH HOH . 
R 3 HOH F 30 630 137 HOH HOH . 
R 3 HOH F 31 631 162 HOH HOH . 
R 3 HOH F 32 632 170 HOH HOH . 
R 3 HOH F 33 633 117 HOH HOH . 
R 3 HOH F 34 634 149 HOH HOH . 
R 3 HOH F 35 635 121 HOH HOH . 
R 3 HOH F 36 636 96 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 . . . J 2 56.87 45.969 78.948 1 42.24 ? N1 PLP 501 D 1 
HETATM 2 C C2 PLP . . . J 2 57.173 45.485 77.71 1 47.48 ? C2 PLP 501 D 1 
HETATM 3 C C2A PLP . . . J 2 58.205 46.197 76.907 1 47.16 ? C2A PLP 501 D 1 
HETATM 4 C C3 PLP . . . J 2 56.51 44.379 77.212 1 44.85 ? C3 PLP 501 D 1 
HETATM 5 O O3 PLP . . . J 2 56.843 43.902 75.967 1 43.32 ? O3 PLP 501 D 1 
HETATM 6 C C4 PLP . . . J 2 55.558 43.724 77.967 1 46.49 ? C4 PLP 501 D 1 
HETATM 7 C C4A PLP . . . J 2 55.313 42.253 77.739 1 40.92 ? C4A PLP 501 D 1 
HETATM 8 C C5 PLP . . . J 2 55.254 44.21 79.209 1 44.2 ? C5 PLP 501 D 1 
HETATM 9 C C6 PLP . . . J 2 55.902 45.348 79.683 1 44.98 ? C6 PLP 501 D 1 
HETATM 10 C C5A PLP . . . J 2 54.186 43.537 80.06 1 41.03 ? C5A PLP 501 D 1 
HETATM 11 O O4P PLP . . . J 2 54.744 42.525 80.859 1 44 ? O4P PLP 501 D 1 
HETATM 12 P P PLP . . . J 2 53.804 41.658 81.83 1 39.66 ? P PLP 501 D 1 
HETATM 13 O O1P PLP . . . J 2 52.727 40.973 81.032 1 36.12 ? O1P PLP 501 D 1 
HETATM 14 O O2P PLP . . . J 2 53.137 42.596 82.792 1 40.09 ? O2P PLP 501 D 1 
HETATM 15 O O3P PLP . . . J 2 54.729 40.692 82.542 1 40.35 ? O3P PLP 501 D 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           15 
#