data_6WNN
#
_model_server_result.job_id            2DGmAa6-OaM2WRux7n84xw 
_model_server_result.datetime_utc      '2025-07-13 23:28:26' 
_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          6wnn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    6WNN 
#
_exptl.entry_id    6WNN 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              248.173 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "4'-DEOXY-4'-AMINOPYRIDOXAL-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         96.15 
_cell.angle_beta          106.04 
_cell.angle_gamma         99.23 
_cell.entry_id            6WNN 
_cell.length_a            58.3 
_cell.length_b            60.54 
_cell.length_c            62.72 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6WNN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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 
_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                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C8 H13 N2 O5 P' 
_chem_comp.formula_weight    248.173 
_chem_comp.id                PMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "PYRIDOXAMINE-5'-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 PMP doub 305 n y 
N1 C6 PMP sing 306 n y 
C2 C2A PMP sing 307 n n 
C2 C3 PMP sing 308 n y 
C2A H2A1 PMP sing 309 n n 
C2A H2A2 PMP sing 310 n n 
C2A H2A3 PMP sing 311 n n 
C3 O3 PMP sing 312 n n 
C3 C4 PMP doub 313 n y 
O3 HO3 PMP sing 314 n n 
C4 C4A PMP sing 315 n n 
C4 C5 PMP sing 316 n y 
C4A N4A PMP sing 317 n n 
C4A H4A1 PMP sing 318 n n 
C4A H4A2 PMP sing 319 n n 
N4A HNA1 PMP sing 320 n n 
N4A HNA2 PMP sing 321 n n 
C5 C6 PMP doub 322 n y 
C5 C5A PMP sing 323 n n 
C6 H6 PMP sing 324 n n 
C5A O4P PMP sing 325 n n 
C5A H5A1 PMP sing 326 n n 
C5A H5A2 PMP sing 327 n n 
O4P P PMP sing 328 n n 
P O1P PMP doub 329 n n 
P O2P PMP sing 330 n n 
P O3P PMP sing 331 n n 
O2P HOP2 PMP sing 332 n n 
O3P HOP3 PMP sing 333 n n 
#
_atom_sites.entry_id                     6WNN 
_atom_sites.fract_transf_matrix[1][1]    0.017153 
_atom_sites.fract_transf_matrix[1][2]    0.002788 
_atom_sites.fract_transf_matrix[1][3]    0.005445 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016735 
_atom_sites.fract_transf_matrix[2][3]    0.002705 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.016805 
_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 LLP A 1 501 1 LLP LLP . 
D 3 PMP B 1 501 1 PMP PMP . 
#
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 PMP . . . D 3 33.466 40.101 35.772 1 71.1 ? N1 PMP 501 B 1 
HETATM 2 C C2 PMP . . . D 3 33.76 41.116 36.648 1 74.63 ? C2 PMP 501 B 1 
HETATM 3 C C2A PMP . . . D 3 35.086 41.243 37.35 1 77.33 ? C2A PMP 501 B 1 
HETATM 4 C C3 PMP . . . D 3 32.748 42.159 36.957 1 71.42 ? C3 PMP 501 B 1 
HETATM 5 O O3 PMP . . . D 3 33.025 43.17 37.828 1 71.38 ? O3 PMP 501 B 1 
HETATM 6 C C4 PMP . . . D 3 31.425 42.061 36.291 1 68.1 ? C4 PMP 501 B 1 
HETATM 7 C C4A PMP . . . D 3 30.351 43.089 36.557 1 67.72 ? C4A PMP 501 B 1 
HETATM 8 N N4A PMP . . . D 3 30.951 44.276 37.106 1 67.78 ? N4A PMP 501 B 1 
HETATM 9 C C5 PMP . . . D 3 31.223 40.918 35.347 1 65.41 ? C5 PMP 501 B 1 
HETATM 10 C C6 PMP . . . D 3 32.264 39.986 35.146 1 68.62 ? C6 PMP 501 B 1 
HETATM 11 C C5A PMP . . . D 3 29.893 40.746 34.652 1 59.32 ? C5A PMP 501 B 1 
HETATM 12 O O4P PMP . . . D 3 29.918 41.067 33.266 1 51.66 ? O4P PMP 501 B 1 
HETATM 13 P P PMP . . . D 3 28.631 40.578 32.442 1 47.81 ? P PMP 501 B 1 
HETATM 14 O O1P PMP . . . D 3 28.717 41.11 31.018 1 51.59 ? O1P PMP 501 B 1 
HETATM 15 O O2P PMP . . . D 3 27.495 41.21 33.163 1 51.36 ? O2P PMP 501 B 1 
HETATM 16 O O3P PMP . . . D 3 28.763 39.085 32.641 1 46.78 ? O3P PMP 501 B 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           347 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           16 
#