data_8XND
#
_model_server_result.job_id            Cp3zqt-fvz8uuLC8sB95Hg 
_model_server_result.datetime_utc      '2025-07-14 15:28:45' 
_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          8xnd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":500}' 
#
_entry.id    8XND 
#
_exptl.entry_id    8XND 
_exptl.method      'X-RAY DIFFRACTION' 
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_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            8XND 
_cell.length_a            151.54 
_cell.length_b            151.54 
_cell.length_c            234.97 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XND 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 
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loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,H 1 1 
B,C,F,G 2 1 
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_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 F N N 
? 2 G N N 
? 2 H N N 
#
_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 258 n y 
N1 C6 PLP sing 259 n y 
C2 C2A PLP sing 260 n n 
C2 C3 PLP sing 261 n y 
C2A H2A1 PLP sing 262 n n 
C2A H2A2 PLP sing 263 n n 
C2A H2A3 PLP sing 264 n n 
C3 O3 PLP sing 265 n n 
C3 C4 PLP doub 266 n y 
O3 HO3 PLP sing 267 n n 
C4 C4A PLP sing 268 n n 
C4 C5 PLP sing 269 n y 
C4A O4A PLP doub 270 n n 
C4A H4A PLP sing 271 n n 
C5 C6 PLP doub 272 n y 
C5 C5A PLP sing 273 n n 
C6 H6 PLP sing 274 n n 
C5A O4P PLP sing 275 n n 
C5A H5A1 PLP sing 276 n n 
C5A H5A2 PLP sing 277 n n 
O4P P PLP sing 278 n n 
P O1P PLP doub 279 n n 
P O2P PLP sing 280 n n 
P O3P PLP sing 281 n n 
O2P HOP2 PLP sing 282 n n 
O3P HOP3 PLP sing 283 n n 
#
_atom_sites.entry_id                     8XND 
_atom_sites.fract_transf_matrix[1][1]    0.006599 
_atom_sites.fract_transf_matrix[1][2]    0.00381 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00762 
_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]    0.004256 
_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 1 500 500 PLP PLP . 
F 2 PLP B 1 500 500 PLP PLP . 
G 2 PLP C 1 500 500 PLP PLP . 
H 2 PLP D 1 500 500 PLP PLP . 
#
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 . . . G 2 -57.036 55.755 52.428 1 60.99 ? N1 PLP 500 C 1 
HETATM 2 C C2 PLP . . . G 2 -57.625 55.146 53.432 1 54.6 ? C2 PLP 500 C 1 
HETATM 3 C C2A PLP . . . G 2 -57.301 55.678 54.784 1 63.23 ? C2A PLP 500 C 1 
HETATM 4 C C3 PLP . . . G 2 -58.561 54.11 53.192 1 56.74 ? C3 PLP 500 C 1 
HETATM 5 O O3 PLP . . . G 2 -59.292 53.455 54.125 1 64.92 ? O3 PLP 500 C 1 
HETATM 6 C C4 PLP . . . G 2 -58.782 53.647 51.873 1 80.26 ? C4 PLP 500 C 1 
HETATM 7 C C4A PLP . . . G 2 -59.76 52.587 51.593 1 65.28 ? C4A PLP 500 C 1 
HETATM 8 C C5 PLP . . . G 2 -58.073 54.266 50.827 1 97.17 ? C5 PLP 500 C 1 
HETATM 9 C C6 PLP . . . G 2 -57.244 55.311 51.162 1 95.99 ? C6 PLP 500 C 1 
HETATM 10 C C5A PLP . . . G 2 -58.279 53.89 49.386 1 76.13 ? C5A PLP 500 C 1 
HETATM 11 O O4P PLP . . . G 2 -57.916 52.531 49.004 1 70.34 ? O4P PLP 500 C 1 
HETATM 12 P P PLP . . . G 2 -58.706 51.919 47.703 1 84.1 ? P PLP 500 C 1 
HETATM 13 O O1P PLP . . . G 2 -58.078 52.639 46.44 1 49.51 ? O1P PLP 500 C 1 
HETATM 14 O O2P PLP . . . G 2 -60.174 52.249 47.972 1 87.95 ? O2P PLP 500 C 1 
HETATM 15 O O3P PLP . . . G 2 -58.579 50.378 47.694 1 85.33 ? O3P PLP 500 C 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           352 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#