data_6DNA
#
_model_server_result.job_id            -a8Cs-4m08ppNJWY2M1LvA 
_model_server_result.datetime_utc      '2024-11-16 12:28:22' 
_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          6dna 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":501}' 
#
_entry.id    6DNA 
#
_exptl.entry_id    6DNA 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          89.98 
_cell.angle_gamma         90 
_cell.entry_id            6DNA 
_cell.length_a            257.7 
_cell.length_b            148.626 
_cell.length_c            83.183 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DNA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
PISA monomeric 1 author_and_software_defined_assembly 5 
PISA monomeric 1 author_and_software_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,H 1 1 
B,I,J,P 2 1 
C,K,Q 3 1 
D,L,M 4 1 
E,N,R 5 1 
F,O,S 6 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 H N N 
? 3 J N N 
? 3 K N N 
? 3 M N N 
? 3 N N N 
? 3 O 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 290 n y 
N1 C6 PLP sing 291 n y 
C2 C2A PLP sing 292 n n 
C2 C3 PLP sing 293 n y 
C2A H2A1 PLP sing 294 n n 
C2A H2A2 PLP sing 295 n n 
C2A H2A3 PLP sing 296 n n 
C3 O3 PLP sing 297 n n 
C3 C4 PLP doub 298 n y 
O3 HO3 PLP sing 299 n n 
C4 C4A PLP sing 300 n n 
C4 C5 PLP sing 301 n y 
C4A O4A PLP doub 302 n n 
C4A H4A PLP sing 303 n n 
C5 C6 PLP doub 304 n y 
C5 C5A PLP sing 305 n n 
C6 H6 PLP sing 306 n n 
C5A O4P PLP sing 307 n n 
C5A H5A1 PLP sing 308 n n 
C5A H5A2 PLP sing 309 n n 
O4P P PLP sing 310 n n 
P O1P PLP doub 311 n n 
P O2P PLP sing 312 n n 
P O3P PLP sing 313 n n 
O2P HOP2 PLP sing 314 n n 
O3P HOP3 PLP sing 315 n n 
#
_atom_sites.entry_id                     6DNA 
_atom_sites.fract_transf_matrix[1][1]    0.00388 
_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]    0.006728 
_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]    0.012022 
_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 PG4 A 1 501 3 PG4 PG4 . 
H 3 PLP A 1 502 2 PLP PLP . 
I 2 PG4 B 1 501 1 PG4 PG4 . 
J 3 PLP B 1 502 1 PLP PLP . 
K 3 PLP C 1 501 3 PLP PLP . 
L 2 PG4 D 1 501 2 PG4 PG4 . 
M 3 PLP D 1 502 4 PLP PLP . 
N 3 PLP E 1 501 5 PLP PLP . 
O 3 PLP F 1 501 6 PLP PLP . 
P 4 HOH B 1 601 4 HOH HOH . 
Q 4 HOH C 1 601 5 HOH HOH . 
Q 4 HOH C 2 602 1 HOH HOH . 
Q 4 HOH C 3 603 9 HOH HOH . 
R 4 HOH E 1 601 6 HOH HOH . 
R 4 HOH E 2 602 2 HOH HOH . 
R 4 HOH E 3 603 7 HOH HOH . 
S 4 HOH F 1 601 3 HOH HOH . 
S 4 HOH F 2 602 8 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 . . . O 3 -99.781 -28.591 -8.876 0.8 82.37 ? N1 PLP 501 F 1 
HETATM 2 C C2 PLP . . . O 3 -99.432 -27.879 -9.974 0.8 84.52 ? C2 PLP 501 F 1 
HETATM 3 C C2A PLP . . . O 3 -99.024 -28.555 -11.274 0.8 75.7 ? C2A PLP 501 F 1 
HETATM 4 C C3 PLP . . . O 3 -99.451 -26.402 -9.873 0.8 89.56 ? C3 PLP 501 F 1 
HETATM 5 O O3 PLP . . . O 3 -99.097 -25.637 -10.944 0.8 96.87 ? O3 PLP 501 F 1 
HETATM 6 C C4 PLP . . . O 3 -99.853 -25.784 -8.585 0.8 89.53 ? C4 PLP 501 F 1 
HETATM 7 C C4A PLP . . . O 3 -99.903 -24.319 -8.446 0.8 96.59 ? C4A PLP 501 F 1 
HETATM 8 O O4A PLP . . . O 3 -99.68 -23.62 -9.419 0.8 100.45 ? O4A PLP 501 F 1 
HETATM 9 C C5 PLP . . . O 3 -100.216 -26.675 -7.463 0.8 93.62 ? C5 PLP 501 F 1 
HETATM 10 C C6 PLP . . . O 3 -100.152 -28.053 -7.692 0.8 87.9 ? C6 PLP 501 F 1 
HETATM 11 C C5A PLP . . . O 3 -100.645 -26.171 -6.081 1 101.12 ? C5A PLP 501 F 1 
HETATM 12 O O4P PLP . . . O 3 -100.737 -24.74 -5.878 1 106.3 ? O4P PLP 501 F 1 
HETATM 13 P P PLP . . . O 3 -101.38 -24.086 -4.523 1 103.05 ? P PLP 501 F 1 
HETATM 14 O O1P PLP . . . O 3 -102.781 -23.723 -4.952 1 110.47 ? O1P PLP 501 F 1 
HETATM 15 O O2P PLP . . . O 3 -101.293 -25.197 -3.481 1 90.93 ? O2P PLP 501 F 1 
HETATM 16 O O3P PLP . . . O 3 -100.637 -22.808 -4.19 1 88.26 ? O3P PLP 501 F 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    66 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           16 
#