data_3RBF
#
_model_server_result.job_id            '_kdFWsKrkVNtKtOCEA_z3Q' 
_model_server_result.datetime_utc      '2024-10-19 00:58:11' 
_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          3rbf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":481}' 
#
_entry.id    3RBF 
#
_exptl.entry_id    3RBF 
_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         90 
_cell.entry_id            3RBF 
_cell.length_a            175.84 
_cell.length_b            175.84 
_cell.length_c            74.96 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RBF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     3RBF 
_atom_sites.fract_transf_matrix[1][1]    0.005687 
_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]    0.005687 
_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]    0.01334 
_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 1 481 1 PLP PLP . 
D 3 CL B 1 481 1 CL CL . 
E 3 CL B 1 482 2 CL CL . 
#
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 -50.535 -26.845 -18.674 0.5 38.37 ? N1 PLP 481 A 1 
HETATM 2 C C2 PLP . . . C 2 -51.336 -27.87 -18.198 0.5 38.74 ? C2 PLP 481 A 1 
HETATM 3 C C2A PLP . . . C 2 -51.34 -28.223 -16.738 0.5 37.12 ? C2A PLP 481 A 1 
HETATM 4 C C3 PLP . . . C 2 -52.145 -28.579 -19.082 0.5 39.7 ? C3 PLP 481 A 1 
HETATM 5 O O3 PLP . . . C 2 -52.948 -29.583 -18.605 0.5 40.36 ? O3 PLP 481 A 1 
HETATM 6 C C4 PLP . . . C 2 -52.133 -28.264 -20.442 0.5 40.13 ? C4 PLP 481 A 1 
HETATM 7 C C4A PLP . . . C 2 -53.028 -28.988 -21.407 0.5 41.79 ? C4A PLP 481 A 1 
HETATM 8 O O4A PLP . . . C 2 -53.472 -28.346 -22.393 0.5 44 ? O4A PLP 481 A 1 
HETATM 9 C C5 PLP . . . C 2 -51.329 -27.233 -20.918 0.5 39.62 ? C5 PLP 481 A 1 
HETATM 10 C C6 PLP . . . C 2 -50.528 -26.525 -20.02 0.5 38.56 ? C6 PLP 481 A 1 
HETATM 11 C C5A PLP . . . C 2 -51.328 -26.878 -22.401 0.5 39.54 ? C5A PLP 481 A 1 
HETATM 12 O O4P PLP . . . C 2 -52.629 -26.539 -22.861 0.5 40.09 ? O4P PLP 481 A 1 
HETATM 13 P P PLP . . . C 2 -52.869 -26.169 -24.419 0.5 40.39 ? P PLP 481 A 1 
HETATM 14 O O1P PLP . . . C 2 -53.2 -27.451 -25.161 0.5 40.14 ? O1P PLP 481 A 1 
HETATM 15 O O2P PLP . . . C 2 -51.589 -25.555 -24.93 0.5 39.57 ? O2P PLP 481 A 1 
HETATM 16 O O3P PLP . . . C 2 -54.005 -25.188 -24.635 0.5 40.32 ? O3P PLP 481 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           354 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#