data_8XHD
#
_model_server_result.job_id            IMR4LMKou4cng3pjGp6O8g 
_model_server_result.datetime_utc      '2024-11-29 06:09:10' 
_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          8xhd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    8XHD 
#
_exptl.entry_id    8XHD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          3 
_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         120 
_cell.entry_id            8XHD 
_cell.length_a            117.734 
_cell.length_b            117.734 
_cell.length_c            145.018 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XHD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 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,E,F 
_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 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 304 n y 
N1 C6 PLP sing 305 n y 
C2 C2A PLP sing 306 n n 
C2 C3 PLP sing 307 n y 
C2A H2A1 PLP sing 308 n n 
C2A H2A2 PLP sing 309 n n 
C2A H2A3 PLP sing 310 n n 
C3 O3 PLP sing 311 n n 
C3 C4 PLP doub 312 n y 
O3 HO3 PLP sing 313 n n 
C4 C4A PLP sing 314 n n 
C4 C5 PLP sing 315 n y 
C4A O4A PLP doub 316 n n 
C4A H4A PLP sing 317 n n 
C5 C6 PLP doub 318 n y 
C5 C5A PLP sing 319 n n 
C6 H6 PLP sing 320 n n 
C5A O4P PLP sing 321 n n 
C5A H5A1 PLP sing 322 n n 
C5A H5A2 PLP sing 323 n n 
O4P P PLP sing 324 n n 
P O1P PLP doub 325 n n 
P O2P PLP sing 326 n n 
P O3P PLP sing 327 n n 
O2P HOP2 PLP sing 328 n n 
O3P HOP3 PLP sing 329 n n 
#
_atom_sites.entry_id                     8XHD 
_atom_sites.fract_transf_matrix[1][1]    0.008494 
_atom_sites.fract_transf_matrix[1][2]    0.004904 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009808 
_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]    0.006896 
_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 PGU A 1 501 501 PGU PGU . 
D 3 PLP B 1 501 501 PLP PLP . 
E 4 HOH A 1 601 21 HOH HOH . 
E 4 HOH A 2 602 23 HOH HOH . 
E 4 HOH A 3 603 6 HOH HOH . 
E 4 HOH A 4 604 2 HOH HOH . 
E 4 HOH A 5 605 20 HOH HOH . 
E 4 HOH A 6 606 28 HOH HOH . 
E 4 HOH A 7 607 16 HOH HOH . 
E 4 HOH A 8 608 18 HOH HOH . 
E 4 HOH A 9 609 7 HOH HOH . 
E 4 HOH A 10 610 29 HOH HOH . 
E 4 HOH A 11 611 10 HOH HOH . 
E 4 HOH A 12 612 30 HOH HOH . 
E 4 HOH A 13 613 31 HOH HOH . 
F 4 HOH B 1 601 19 HOH HOH . 
F 4 HOH B 2 602 22 HOH HOH . 
F 4 HOH B 3 603 5 HOH HOH . 
F 4 HOH B 4 604 14 HOH HOH . 
F 4 HOH B 5 605 1 HOH HOH . 
F 4 HOH B 6 606 26 HOH HOH . 
F 4 HOH B 7 607 9 HOH HOH . 
F 4 HOH B 8 608 13 HOH HOH . 
F 4 HOH B 9 609 3 HOH HOH . 
F 4 HOH B 10 610 8 HOH HOH . 
F 4 HOH B 11 611 15 HOH HOH . 
F 4 HOH B 12 612 4 HOH HOH . 
F 4 HOH B 13 613 27 HOH HOH . 
F 4 HOH B 14 614 25 HOH HOH . 
F 4 HOH B 15 615 17 HOH HOH . 
F 4 HOH B 16 616 11 HOH HOH . 
F 4 HOH B 17 617 32 HOH HOH . 
F 4 HOH B 18 618 24 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 . . . D 3 56.415 -15.908 -18.277 1 60.58 ? N1 PLP 501 B 1 
HETATM 2 C C2 PLP . . . D 3 56.584 -14.8 -19.082 1 56.6 ? C2 PLP 501 B 1 
HETATM 3 C C2A PLP . . . D 3 57.965 -14.397 -19.507 1 51.76 ? C2A PLP 501 B 1 
HETATM 4 C C3 PLP . . . D 3 55.478 -14.068 -19.496 1 55.4 ? C3 PLP 501 B 1 
HETATM 5 O O3 PLP . . . D 3 55.654 -12.969 -20.294 1 64.55 ? O3 PLP 501 B 1 
HETATM 6 C C4 PLP . . . D 3 54.193 -14.436 -19.104 1 59.44 ? C4 PLP 501 B 1 
HETATM 7 C C4A PLP . . . D 3 53.127 -13.376 -19.145 1 60.82 ? C4A PLP 501 B 1 
HETATM 8 O O4A PLP . . . D 3 53.421 -12.18 -19.112 1 68.42 ? O4A PLP 501 B 1 
HETATM 9 C C5 PLP . . . D 3 54.032 -15.557 -18.286 1 55.83 ? C5 PLP 501 B 1 
HETATM 10 C C6 PLP . . . D 3 55.148 -16.285 -17.883 1 50.73 ? C6 PLP 501 B 1 
HETATM 11 C C5A PLP . . . D 3 52.666 -16.028 -17.823 1 56.88 ? C5A PLP 501 B 1 
HETATM 12 O O4P PLP . . . D 3 51.696 -15.933 -18.846 1 61.35 ? O4P PLP 501 B 1 
HETATM 13 P P PLP . . . D 3 50.275 -16.678 -18.707 1 54.41 ? P PLP 501 B 1 
HETATM 14 O O1P PLP . . . D 3 50.293 -17.97 -19.489 1 50.69 -1 O1P PLP 501 B 1 
HETATM 15 O O2P PLP . . . D 3 49.183 -15.77 -19.229 1 54.93 -1 O2P PLP 501 B 1 
HETATM 16 O O3P PLP . . . D 3 50.025 -16.95 -17.245 1 54.87 ? O3P PLP 501 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#