data_6DNA
#
_model_server_result.job_id            aK0ypbUCzW1RguOYGnQhHA 
_model_server_result.datetime_utc      '2024-11-16 12:33:58' 
_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":"M","auth_seq_id":502}' 
#
_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 . . . M 3 -97.259 -75.001 20.877 0.8 88.99 ? N1 PLP 502 D 1 
HETATM 2 C C2 PLP . . . M 3 -96.869 -75.514 22.071 0.8 79.75 ? C2 PLP 502 D 1 
HETATM 3 C C2A PLP . . . M 3 -96.741 -74.695 23.327 0.8 78.19 ? C2A PLP 502 D 1 
HETATM 4 C C3 PLP . . . M 3 -96.555 -76.94 22.176 0.8 81.03 ? C3 PLP 502 D 1 
HETATM 5 O O3 PLP . . . M 3 -96.176 -77.434 23.377 0.8 80.66 ? O3 PLP 502 D 1 
HETATM 6 C C4 PLP . . . M 3 -96.658 -77.77 20.969 0.8 92.57 ? C4 PLP 502 D 1 
HETATM 7 C C4A PLP . . . M 3 -96.325 -79.203 20.999 0.8 101.96 ? C4A PLP 502 D 1 
HETATM 8 O O4A PLP . . . M 3 -95.887 -79.707 22.01 0.8 108.95 ? O4A PLP 502 D 1 
HETATM 9 C C5 PLP . . . M 3 -97.112 -77.1 19.72 0.8 107.2 ? C5 PLP 502 D 1 
HETATM 10 C C6 PLP . . . M 3 -97.378 -75.732 19.746 0.8 97.52 ? C6 PLP 502 D 1 
HETATM 11 C C5A PLP . . . M 3 -97.219 -77.842 18.399 1 123.67 ? C5A PLP 502 D 1 
HETATM 12 O O4P PLP . . . M 3 -98.524 -78.125 17.881 1 129.57 ? O4P PLP 502 D 1 
HETATM 13 P P PLP . . . M 3 -98.653 -79.344 16.815 1 143.6 ? P PLP 502 D 1 
HETATM 14 O O1P PLP . . . M 3 -98.101 -78.786 15.514 1 132.89 ? O1P PLP 502 D 1 
HETATM 15 O O2P PLP . . . M 3 -100.136 -79.579 16.777 1 148.94 ? O2P PLP 502 D 1 
HETATM 16 O O3P PLP . . . M 3 -97.911 -80.543 17.374 1 131.09 ? O3P PLP 502 D 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    53 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           16 
#