data_6DND
#
_model_server_result.job_id            RN0_tH_L0a1pGfV8lIA0mw 
_model_server_result.datetime_utc      '2024-11-28 02:24:13' 
_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          6dnd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    6DND 
#
_exptl.entry_id    6DND 
_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    2 
_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            6DND 
_cell.length_a            91.036 
_cell.length_b            96.863 
_cell.length_c            97.871 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DND 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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 D N N 
? 3 F 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                     6DND 
_atom_sites.fract_transf_matrix[1][1]    0.010985 
_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]    0.010324 
_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]    0.010218 
_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 PG4 A 1 501 2 PG4 PG4 . 
D 3 PLP A 1 502 1 PLP PLP . 
E 2 PG4 B 1 501 1 PG4 PG4 . 
F 3 PLP B 1 502 2 PLP PLP . 
G 4 HOH A 1 601 28 HOH HOH . 
G 4 HOH A 2 602 41 HOH HOH . 
G 4 HOH A 3 603 65 HOH HOH . 
G 4 HOH A 4 604 97 HOH HOH . 
G 4 HOH A 5 605 53 HOH HOH . 
G 4 HOH A 6 606 17 HOH HOH . 
G 4 HOH A 7 607 45 HOH HOH . 
G 4 HOH A 8 608 27 HOH HOH . 
G 4 HOH A 9 609 32 HOH HOH . 
G 4 HOH A 10 610 98 HOH HOH . 
G 4 HOH A 11 611 71 HOH HOH . 
G 4 HOH A 12 612 12 HOH HOH . 
G 4 HOH A 13 613 14 HOH HOH . 
G 4 HOH A 14 614 11 HOH HOH . 
G 4 HOH A 15 615 94 HOH HOH . 
G 4 HOH A 16 616 88 HOH HOH . 
G 4 HOH A 17 617 36 HOH HOH . 
G 4 HOH A 18 618 95 HOH HOH . 
G 4 HOH A 19 619 38 HOH HOH . 
G 4 HOH A 20 620 1 HOH HOH . 
G 4 HOH A 21 621 16 HOH HOH . 
G 4 HOH A 22 622 31 HOH HOH . 
G 4 HOH A 23 623 76 HOH HOH . 
G 4 HOH A 24 624 99 HOH HOH . 
G 4 HOH A 25 625 89 HOH HOH . 
G 4 HOH A 26 626 64 HOH HOH . 
G 4 HOH A 27 627 75 HOH HOH . 
G 4 HOH A 28 628 50 HOH HOH . 
G 4 HOH A 29 629 101 HOH HOH . 
G 4 HOH A 30 630 6 HOH HOH . 
G 4 HOH A 31 631 18 HOH HOH . 
G 4 HOH A 32 632 29 HOH HOH . 
G 4 HOH A 33 633 96 HOH HOH . 
G 4 HOH A 34 634 100 HOH HOH . 
G 4 HOH A 35 635 77 HOH HOH . 
H 4 HOH B 1 601 44 HOH HOH . 
H 4 HOH B 2 602 61 HOH HOH . 
H 4 HOH B 3 603 86 HOH HOH . 
H 4 HOH B 4 604 91 HOH HOH . 
H 4 HOH B 5 605 19 HOH HOH . 
H 4 HOH B 6 606 84 HOH HOH . 
H 4 HOH B 7 607 9 HOH HOH . 
H 4 HOH B 8 608 85 HOH HOH . 
H 4 HOH B 9 609 63 HOH HOH . 
H 4 HOH B 10 610 57 HOH HOH . 
H 4 HOH B 11 611 37 HOH HOH . 
H 4 HOH B 12 612 82 HOH HOH . 
H 4 HOH B 13 613 20 HOH HOH . 
H 4 HOH B 14 614 49 HOH HOH . 
H 4 HOH B 15 615 42 HOH HOH . 
H 4 HOH B 16 616 25 HOH HOH . 
H 4 HOH B 17 617 23 HOH HOH . 
H 4 HOH B 18 618 74 HOH HOH . 
H 4 HOH B 19 619 7 HOH HOH . 
H 4 HOH B 20 620 59 HOH HOH . 
H 4 HOH B 21 621 22 HOH HOH . 
H 4 HOH B 22 622 68 HOH HOH . 
H 4 HOH B 23 623 5 HOH HOH . 
H 4 HOH B 24 624 35 HOH HOH . 
H 4 HOH B 25 625 62 HOH HOH . 
H 4 HOH B 26 626 43 HOH HOH . 
H 4 HOH B 27 627 72 HOH HOH . 
H 4 HOH B 28 628 93 HOH HOH . 
H 4 HOH B 29 629 4 HOH HOH . 
H 4 HOH B 30 630 34 HOH HOH . 
H 4 HOH B 31 631 79 HOH HOH . 
H 4 HOH B 32 632 73 HOH HOH . 
H 4 HOH B 33 633 69 HOH HOH . 
H 4 HOH B 34 634 15 HOH HOH . 
H 4 HOH B 35 635 54 HOH HOH . 
H 4 HOH B 36 636 8 HOH HOH . 
H 4 HOH B 37 637 48 HOH HOH . 
H 4 HOH B 38 638 90 HOH HOH . 
H 4 HOH B 39 639 2 HOH HOH . 
H 4 HOH B 40 640 58 HOH HOH . 
H 4 HOH B 41 641 60 HOH HOH . 
H 4 HOH B 42 642 47 HOH HOH . 
H 4 HOH B 43 643 26 HOH HOH . 
H 4 HOH B 44 644 55 HOH HOH . 
H 4 HOH B 45 645 51 HOH HOH . 
H 4 HOH B 46 646 46 HOH HOH . 
H 4 HOH B 47 647 70 HOH HOH . 
H 4 HOH B 48 648 67 HOH HOH . 
H 4 HOH B 49 649 3 HOH HOH . 
H 4 HOH B 50 650 33 HOH HOH . 
H 4 HOH B 51 651 56 HOH HOH . 
H 4 HOH B 52 652 78 HOH HOH . 
H 4 HOH B 53 653 21 HOH HOH . 
H 4 HOH B 54 654 13 HOH HOH . 
H 4 HOH B 55 655 83 HOH HOH . 
H 4 HOH B 56 656 30 HOH HOH . 
H 4 HOH B 57 657 52 HOH HOH . 
H 4 HOH B 58 658 40 HOH HOH . 
H 4 HOH B 59 659 39 HOH HOH . 
H 4 HOH B 60 660 66 HOH HOH . 
H 4 HOH B 61 661 24 HOH HOH . 
H 4 HOH B 62 662 10 HOH HOH . 
H 4 HOH B 63 663 81 HOH HOH . 
H 4 HOH B 64 664 87 HOH HOH . 
H 4 HOH B 65 665 92 HOH HOH . 
H 4 HOH B 66 666 80 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 . . . F 3 99.187 149.226 186.407 0.8 58.18 ? N1 PLP 502 B 1 
HETATM 2 C C2 PLP . . . F 3 98.38 150.218 185.983 0.8 62.12 ? C2 PLP 502 B 1 
HETATM 3 C C2A PLP . . . F 3 98.969 151.564 185.696 0.8 56.39 ? C2A PLP 502 B 1 
HETATM 4 C C3 PLP . . . F 3 96.933 149.977 185.812 0.8 63.96 ? C3 PLP 502 B 1 
HETATM 5 O O3 PLP . . . F 3 96.132 150.973 185.388 0.8 69.51 ? O3 PLP 502 B 1 
HETATM 6 C C4 PLP . . . F 3 96.408 148.623 186.099 0.8 67.56 ? C4 PLP 502 B 1 
HETATM 7 C C4A PLP . . . F 3 94.979 148.268 185.963 0.8 66.27 ? C4A PLP 502 B 1 
HETATM 8 O O4A PLP . . . F 3 94.264 148.715 185.094 0.8 71.18 ? O4A PLP 502 B 1 
HETATM 9 C C5 PLP . . . F 3 97.407 147.625 186.559 0.8 68.4 ? C5 PLP 502 B 1 
HETATM 10 C C6 PLP . . . F 3 98.739 148.005 186.678 0.8 66.43 ? C6 PLP 502 B 1 
HETATM 11 C C5A PLP . . . F 3 97.082 146.188 186.904 1 71.08 ? C5A PLP 502 B 1 
HETATM 12 O O4P PLP . . . F 3 95.735 145.792 187.028 1 49.54 ? O4P PLP 502 B 1 
HETATM 13 P P PLP . . . F 3 95.459 144.266 186.955 1 48 ? P PLP 502 B 1 
HETATM 14 O O1P PLP . . . F 3 95.867 143.941 185.624 1 54.36 ? O1P PLP 502 B 1 
HETATM 15 O O2P PLP . . . F 3 96.254 143.603 187.963 1 37.08 ? O2P PLP 502 B 1 
HETATM 16 O O3P PLP . . . F 3 94.028 144.252 187.112 1 43.37 ? O3P PLP 502 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#