data_5KQU
#
_model_server_result.job_id            sM_wuuq46o60S-YsRmBZng 
_model_server_result.datetime_utc      '2024-11-12 20:50:07' 
_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          5kqu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":501}' 
#
_entry.id    5KQU 
#
_exptl.entry_id    5KQU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          2 
_entity.src_method                  man 
_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          97.68 
_cell.angle_gamma         90 
_cell.entry_id            5KQU 
_cell.length_a            74.104 
_cell.length_b            146.886 
_cell.length_c            131.776 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KQU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,G,J,M,P 1 1 
B,C,H,I,N,O 2 1 
E,F,K,L,Q,R 3 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
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A NZ LYS 308 A LYS 288 1_555 G C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 B NZ LYS 308 B LYS 288 1_555 H C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.258 ? 
covale ? covale3 C NZ LYS 308 C LYS 288 1_555 I C4A PLP . C PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
covale ? covale4 D NZ LYS 308 D LYS 288 1_555 J C4A PLP . D PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? 
covale ? covale5 E NZ LYS 308 E LYS 288 1_555 K C4A PLP . E PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? 
covale ? covale6 F NZ LYS 308 F LYS 288 1_555 L C4A PLP . F PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? 
#
_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 260 n y 
N1 C6 PLP sing 261 n y 
C2 C2A PLP sing 262 n n 
C2 C3 PLP sing 263 n y 
C2A H2A1 PLP sing 264 n n 
C2A H2A2 PLP sing 265 n n 
C2A H2A3 PLP sing 266 n n 
C3 O3 PLP sing 267 n n 
C3 C4 PLP doub 268 n y 
O3 HO3 PLP sing 269 n n 
C4 C4A PLP sing 270 n n 
C4 C5 PLP sing 271 n y 
C4A O4A PLP doub 272 n n 
C4A H4A PLP sing 273 n n 
C5 C6 PLP doub 274 n y 
C5 C5A PLP sing 275 n n 
C6 H6 PLP sing 276 n n 
C5A O4P PLP sing 277 n n 
C5A H5A1 PLP sing 278 n n 
C5A H5A2 PLP sing 279 n n 
O4P P PLP sing 280 n n 
P O1P PLP doub 281 n n 
P O2P PLP sing 282 n n 
P O3P PLP sing 283 n n 
O2P HOP2 PLP sing 284 n n 
O3P HOP3 PLP sing 285 n n 
#
_atom_sites.entry_id                     5KQU 
_atom_sites.fract_transf_matrix[1][1]    0.013495 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001819 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006808 
_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]    0.007657 
_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 PLP A 1 501 501 PLP PLP . 
H 2 PLP B 1 501 501 PLP PLP . 
I 2 PLP C 1 501 501 PLP PLP . 
J 2 PLP D 1 501 501 PLP PLP . 
K 2 PLP E 1 501 501 PLP PLP . 
L 2 PLP F 1 501 501 PLP PLP . 
M 3 HOH A 1 601 601 HOH HOH . 
M 3 HOH A 2 602 602 HOH HOH . 
M 3 HOH A 3 603 603 HOH HOH . 
M 3 HOH A 4 604 604 HOH HOH . 
M 3 HOH A 5 605 605 HOH HOH . 
M 3 HOH A 6 606 606 HOH HOH . 
M 3 HOH A 7 607 607 HOH HOH . 
M 3 HOH A 8 608 608 HOH HOH . 
M 3 HOH A 9 609 609 HOH HOH . 
M 3 HOH A 10 610 610 HOH HOH . 
M 3 HOH A 11 611 611 HOH HOH . 
M 3 HOH A 12 612 612 HOH HOH . 
M 3 HOH A 13 613 613 HOH HOH . 
M 3 HOH A 14 614 614 HOH HOH . 
M 3 HOH A 15 615 615 HOH HOH . 
M 3 HOH A 16 616 616 HOH HOH . 
M 3 HOH A 17 617 617 HOH HOH . 
M 3 HOH A 18 618 618 HOH HOH . 
M 3 HOH A 19 619 619 HOH HOH . 
M 3 HOH A 20 620 620 HOH HOH . 
M 3 HOH A 21 621 621 HOH HOH . 
M 3 HOH A 22 622 622 HOH HOH . 
M 3 HOH A 23 623 623 HOH HOH . 
M 3 HOH A 24 624 624 HOH HOH . 
M 3 HOH A 25 625 625 HOH HOH . 
M 3 HOH A 26 626 626 HOH HOH . 
M 3 HOH A 27 627 627 HOH HOH . 
M 3 HOH A 28 628 628 HOH HOH . 
M 3 HOH A 29 629 629 HOH HOH . 
M 3 HOH A 30 630 630 HOH HOH . 
M 3 HOH A 31 631 631 HOH HOH . 
M 3 HOH A 32 632 632 HOH HOH . 
M 3 HOH A 33 633 633 HOH HOH . 
N 3 HOH B 1 601 601 HOH HOH . 
N 3 HOH B 2 602 602 HOH HOH . 
N 3 HOH B 3 603 603 HOH HOH . 
N 3 HOH B 4 604 604 HOH HOH . 
N 3 HOH B 5 605 605 HOH HOH . 
N 3 HOH B 6 606 606 HOH HOH . 
N 3 HOH B 7 607 607 HOH HOH . 
N 3 HOH B 8 608 608 HOH HOH . 
N 3 HOH B 9 609 609 HOH HOH . 
N 3 HOH B 10 610 610 HOH HOH . 
N 3 HOH B 11 611 611 HOH HOH . 
N 3 HOH B 12 612 612 HOH HOH . 
N 3 HOH B 13 613 613 HOH HOH . 
N 3 HOH B 14 614 614 HOH HOH . 
N 3 HOH B 15 615 615 HOH HOH . 
N 3 HOH B 16 616 616 HOH HOH . 
N 3 HOH B 17 617 617 HOH HOH . 
N 3 HOH B 18 618 618 HOH HOH . 
N 3 HOH B 19 619 619 HOH HOH . 
N 3 HOH B 20 620 620 HOH HOH . 
N 3 HOH B 21 621 621 HOH HOH . 
N 3 HOH B 22 622 622 HOH HOH . 
N 3 HOH B 23 623 623 HOH HOH . 
N 3 HOH B 24 624 624 HOH HOH . 
N 3 HOH B 25 625 625 HOH HOH . 
N 3 HOH B 26 626 626 HOH HOH . 
N 3 HOH B 27 627 627 HOH HOH . 
N 3 HOH B 28 628 628 HOH HOH . 
N 3 HOH B 29 629 629 HOH HOH . 
N 3 HOH B 30 630 630 HOH HOH . 
N 3 HOH B 31 631 631 HOH HOH . 
O 3 HOH C 1 601 601 HOH HOH . 
O 3 HOH C 2 602 602 HOH HOH . 
O 3 HOH C 3 603 603 HOH HOH . 
O 3 HOH C 4 604 604 HOH HOH . 
O 3 HOH C 5 605 605 HOH HOH . 
O 3 HOH C 6 606 606 HOH HOH . 
O 3 HOH C 7 607 607 HOH HOH . 
O 3 HOH C 8 608 608 HOH HOH . 
O 3 HOH C 9 609 609 HOH HOH . 
O 3 HOH C 10 610 610 HOH HOH . 
O 3 HOH C 11 611 611 HOH HOH . 
O 3 HOH C 12 612 612 HOH HOH . 
O 3 HOH C 13 613 613 HOH HOH . 
O 3 HOH C 14 614 614 HOH HOH . 
O 3 HOH C 15 615 615 HOH HOH . 
O 3 HOH C 16 616 616 HOH HOH . 
O 3 HOH C 17 617 617 HOH HOH . 
O 3 HOH C 18 618 618 HOH HOH . 
O 3 HOH C 19 619 619 HOH HOH . 
O 3 HOH C 20 620 620 HOH HOH . 
O 3 HOH C 21 621 621 HOH HOH . 
O 3 HOH C 22 622 622 HOH HOH . 
O 3 HOH C 23 623 623 HOH HOH . 
O 3 HOH C 24 624 624 HOH HOH . 
O 3 HOH C 25 625 625 HOH HOH . 
O 3 HOH C 26 626 626 HOH HOH . 
O 3 HOH C 27 627 627 HOH HOH . 
O 3 HOH C 28 628 628 HOH HOH . 
P 3 HOH D 1 601 601 HOH HOH . 
P 3 HOH D 2 602 602 HOH HOH . 
P 3 HOH D 3 603 603 HOH HOH . 
P 3 HOH D 4 604 604 HOH HOH . 
P 3 HOH D 5 605 605 HOH HOH . 
P 3 HOH D 6 606 606 HOH HOH . 
P 3 HOH D 7 607 607 HOH HOH . 
P 3 HOH D 8 608 608 HOH HOH . 
P 3 HOH D 9 609 609 HOH HOH . 
P 3 HOH D 10 610 610 HOH HOH . 
P 3 HOH D 11 611 611 HOH HOH . 
P 3 HOH D 12 612 612 HOH HOH . 
P 3 HOH D 13 613 613 HOH HOH . 
P 3 HOH D 14 614 614 HOH HOH . 
P 3 HOH D 15 615 615 HOH HOH . 
P 3 HOH D 16 616 616 HOH HOH . 
P 3 HOH D 17 617 617 HOH HOH . 
P 3 HOH D 18 618 618 HOH HOH . 
P 3 HOH D 19 619 619 HOH HOH . 
P 3 HOH D 20 620 620 HOH HOH . 
Q 3 HOH E 1 601 601 HOH HOH . 
Q 3 HOH E 2 602 602 HOH HOH . 
Q 3 HOH E 3 603 603 HOH HOH . 
Q 3 HOH E 4 604 604 HOH HOH . 
Q 3 HOH E 5 605 605 HOH HOH . 
Q 3 HOH E 6 606 606 HOH HOH . 
Q 3 HOH E 7 607 607 HOH HOH . 
Q 3 HOH E 8 608 608 HOH HOH . 
Q 3 HOH E 9 609 609 HOH HOH . 
Q 3 HOH E 10 610 610 HOH HOH . 
Q 3 HOH E 11 611 611 HOH HOH . 
R 3 HOH F 1 601 601 HOH HOH . 
R 3 HOH F 2 602 602 HOH HOH . 
R 3 HOH F 3 603 603 HOH HOH . 
R 3 HOH F 4 604 604 HOH HOH . 
R 3 HOH F 5 605 605 HOH HOH . 
R 3 HOH F 6 606 606 HOH HOH . 
R 3 HOH F 7 607 607 HOH HOH . 
R 3 HOH F 8 608 608 HOH HOH . 
R 3 HOH F 9 609 609 HOH HOH . 
R 3 HOH F 10 610 610 HOH HOH . 
R 3 HOH F 11 611 611 HOH HOH . 
R 3 HOH F 12 612 612 HOH HOH . 
R 3 HOH F 13 613 613 HOH HOH . 
R 3 HOH F 14 614 614 HOH HOH . 
R 3 HOH F 15 615 615 HOH HOH . 
R 3 HOH F 16 616 616 HOH HOH . 
R 3 HOH F 17 617 617 HOH HOH . 
R 3 HOH F 18 618 618 HOH HOH . 
R 3 HOH F 19 619 619 HOH HOH . 
R 3 HOH F 20 620 620 HOH HOH . 
R 3 HOH F 21 621 621 HOH HOH . 
R 3 HOH F 22 622 622 HOH HOH . 
R 3 HOH F 23 623 623 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 . . . L 2 -6.223 -30.475 -59.187 1 43.13 ? N1 PLP 501 F 1 
HETATM 2 C C2 PLP . . . L 2 -7.104 -29.659 -59.809 1 44.34 ? C2 PLP 501 F 1 
HETATM 3 C C2A PLP . . . L 2 -8.558 -29.892 -59.707 1 48.78 ? C2A PLP 501 F 1 
HETATM 4 C C3 PLP . . . L 2 -6.671 -28.489 -60.612 1 44.61 ? C3 PLP 501 F 1 
HETATM 5 O O3 PLP . . . L 2 -7.554 -27.679 -61.235 1 48.87 ? O3 PLP 501 F 1 
HETATM 6 C C4 PLP . . . L 2 -5.23 -28.224 -60.722 1 46.41 ? C4 PLP 501 F 1 
HETATM 7 C C4A PLP . . . L 2 -4.727 -27.035 -61.51 1 51.3 ? C4A PLP 501 F 1 
HETATM 8 C C5 PLP . . . L 2 -4.349 -29.207 -59.976 1 46.37 ? C5 PLP 501 F 1 
HETATM 9 C C6 PLP . . . L 2 -4.89 -30.285 -59.261 1 45.22 ? C6 PLP 501 F 1 
HETATM 10 C C5A PLP . . . L 2 -2.853 -29.026 -60.022 1 47.74 ? C5A PLP 501 F 1 
HETATM 11 O O4P PLP . . . L 2 -2.217 -30.092 -59.357 1 44.52 ? O4P PLP 501 F 1 
HETATM 12 P P PLP . . . L 2 -0.632 -30.045 -59.244 1 44.86 ? P PLP 501 F 1 
HETATM 13 O O1P PLP . . . L 2 -0.334 -29.652 -60.663 1 46.4 ? O1P PLP 501 F 1 
HETATM 14 O O2P PLP . . . L 2 -0.235 -31.465 -58.862 1 42.34 ? O2P PLP 501 F 1 
HETATM 15 O O3P PLP . . . L 2 -0.355 -28.973 -58.196 1 42.32 ? O3P PLP 501 F 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           264 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#