data_5YB0
#
_model_server_result.job_id            QcLvwKHh1WminPesqaeS7w 
_model_server_result.datetime_utc      '2025-04-11 17:01:00' 
_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          5yb0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":401}' 
#
_entry.id    5YB0 
#
_exptl.entry_id    5YB0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    10 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         62.85 
_cell.angle_beta          88.58 
_cell.angle_gamma         74.92 
_cell.entry_id            5YB0 
_cell.length_a            66.446 
_cell.length_b            134.073 
_cell.length_c            139.064 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YB0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
? dimeric 2 author_defined_assembly 4 
? dimeric 2 author_defined_assembly 5 
? dimeric 2 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,M,N,O,P,BA,CA 1 1 
C,D,Q,R,S,T,DA,EA 2 1 
E,H,U,V,Y,FA,IA 3 1 
F,G,W,X,GA,HA 4 1 
I,J,Z,JA,KA 5 1 
K,L,AA,LA,MA 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
? 2 M N N 
? 2 O N N 
? 2 Q N N 
? 2 S N N 
? 2 U N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA 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 B NZ LYS 191 B LYS 191 1_555 O O4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? 
covale ? covale2 C NZ LYS 191 C LYS 191 1_555 Q O4A PLP . C PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? 
covale ? covale3 D NZ LYS 191 D LYS 191 1_555 S O4A PLP . D PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? 
covale ? covale4 E NZ LYS 191 E LYS 191 1_555 U O4A PLP . E PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? 
covale ? covale5 F NZ LYS 191 F LYS 191 1_555 W O4A PLP . F PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? 
covale ? covale6 G NZ LYS 191 G LYS 191 1_555 X O4A PLP . G PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? 
covale ? covale7 I NZ LYS 191 I LYS 191 1_555 Z O4A PLP . I PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? 
#
_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                     5YB0 
_atom_sites.fract_transf_matrix[1][1]    0.01505 
_atom_sites.fract_transf_matrix[1][2]    -0.004054 
_atom_sites.fract_transf_matrix[1][3]    0.001712 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007724 
_atom_sites.fract_transf_matrix[2][3]    -0.004069 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.00813 
_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
M 2 PLP A 1 401 401 PLP PLP . 
N 3 CL A 1 402 402 CL CL . 
O 2 PLP B 1 401 401 PLP PLP . 
P 3 CL B 1 402 402 CL CL . 
Q 2 PLP C 1 401 401 PLP PLP . 
R 3 CL C 1 402 402 CL CL . 
S 2 PLP D 1 401 401 PLP PLP . 
T 3 CL D 1 402 402 CL CL . 
U 2 PLP E 1 401 401 PLP PLP . 
V 3 CL E 1 402 402 CL CL . 
W 2 PLP F 1 401 401 PLP PLP . 
X 2 PLP G 1 401 401 PLP PLP . 
Y 2 PLP H 1 401 401 PLP PLP . 
Z 2 PLP I 1 401 401 PLP PLP . 
AA 2 PLP K 1 401 401 PLP PLP . 
BA 4 HOH A 1 501 514 HOH HOH . 
BA 4 HOH A 2 502 503 HOH HOH . 
BA 4 HOH A 3 503 509 HOH HOH . 
BA 4 HOH A 4 504 510 HOH HOH . 
BA 4 HOH A 5 505 502 HOH HOH . 
BA 4 HOH A 6 506 501 HOH HOH . 
BA 4 HOH A 7 507 507 HOH HOH . 
BA 4 HOH A 8 508 508 HOH HOH . 
BA 4 HOH A 9 509 516 HOH HOH . 
BA 4 HOH A 10 510 505 HOH HOH . 
BA 4 HOH A 11 511 504 HOH HOH . 
BA 4 HOH A 12 512 513 HOH HOH . 
BA 4 HOH A 13 513 516 HOH HOH . 
BA 4 HOH A 14 514 515 HOH HOH . 
CA 4 HOH B 1 501 511 HOH HOH . 
CA 4 HOH B 2 502 512 HOH HOH . 
CA 4 HOH B 3 503 503 HOH HOH . 
CA 4 HOH B 4 504 501 HOH HOH . 
CA 4 HOH B 5 505 510 HOH HOH . 
CA 4 HOH B 6 506 507 HOH HOH . 
CA 4 HOH B 7 507 508 HOH HOH . 
CA 4 HOH B 8 508 516 HOH HOH . 
CA 4 HOH B 9 509 505 HOH HOH . 
CA 4 HOH B 10 510 506 HOH HOH . 
CA 4 HOH B 11 511 509 HOH HOH . 
CA 4 HOH B 12 512 504 HOH HOH . 
DA 4 HOH C 1 501 507 HOH HOH . 
DA 4 HOH C 2 502 510 HOH HOH . 
DA 4 HOH C 3 503 502 HOH HOH . 
DA 4 HOH C 4 504 505 HOH HOH . 
DA 4 HOH C 5 505 506 HOH HOH . 
DA 4 HOH C 6 506 501 HOH HOH . 
DA 4 HOH C 7 507 512 HOH HOH . 
DA 4 HOH C 8 508 511 HOH HOH . 
DA 4 HOH C 9 509 514 HOH HOH . 
DA 4 HOH C 10 510 508 HOH HOH . 
DA 4 HOH C 11 511 520 HOH HOH . 
DA 4 HOH C 12 512 406 HOH HOH . 
DA 4 HOH C 13 513 504 HOH HOH . 
DA 4 HOH C 14 514 515 HOH HOH . 
DA 4 HOH C 15 515 517 HOH HOH . 
DA 4 HOH C 16 516 509 HOH HOH . 
EA 4 HOH D 1 501 405 HOH HOH . 
EA 4 HOH D 2 502 401 HOH HOH . 
EA 4 HOH D 3 503 501 HOH HOH . 
EA 4 HOH D 4 504 508 HOH HOH . 
EA 4 HOH D 5 505 507 HOH HOH . 
EA 4 HOH D 6 506 510 HOH HOH . 
EA 4 HOH D 7 507 504 HOH HOH . 
EA 4 HOH D 8 508 505 HOH HOH . 
EA 4 HOH D 9 509 503 HOH HOH . 
EA 4 HOH D 10 510 506 HOH HOH . 
EA 4 HOH D 11 511 502 HOH HOH . 
FA 4 HOH E 1 501 506 HOH HOH . 
FA 4 HOH E 2 502 514 HOH HOH . 
FA 4 HOH E 3 503 512 HOH HOH . 
FA 4 HOH E 4 504 511 HOH HOH . 
FA 4 HOH E 5 505 517 HOH HOH . 
FA 4 HOH E 6 506 509 HOH HOH . 
FA 4 HOH E 7 507 507 HOH HOH . 
FA 4 HOH E 8 508 518 HOH HOH . 
FA 4 HOH E 9 509 505 HOH HOH . 
FA 4 HOH E 10 510 501 HOH HOH . 
FA 4 HOH E 11 511 503 HOH HOH . 
FA 4 HOH E 12 512 504 HOH HOH . 
FA 4 HOH E 13 513 506 HOH HOH . 
FA 4 HOH E 14 514 519 HOH HOH . 
FA 4 HOH E 15 515 516 HOH HOH . 
FA 4 HOH E 16 516 513 HOH HOH . 
FA 4 HOH E 17 517 515 HOH HOH . 
FA 4 HOH E 18 518 508 HOH HOH . 
GA 4 HOH F 1 501 512 HOH HOH . 
GA 4 HOH F 2 502 505 HOH HOH . 
GA 4 HOH F 3 503 513 HOH HOH . 
GA 4 HOH F 4 504 509 HOH HOH . 
GA 4 HOH F 5 505 511 HOH HOH . 
GA 4 HOH F 6 506 510 HOH HOH . 
GA 4 HOH F 7 507 514 HOH HOH . 
GA 4 HOH F 8 508 508 HOH HOH . 
GA 4 HOH F 9 509 501 HOH HOH . 
HA 4 HOH G 1 501 512 HOH HOH . 
HA 4 HOH G 2 502 506 HOH HOH . 
HA 4 HOH G 3 503 516 HOH HOH . 
HA 4 HOH G 4 504 504 HOH HOH . 
HA 4 HOH G 5 505 511 HOH HOH . 
HA 4 HOH G 6 506 510 HOH HOH . 
HA 4 HOH G 7 507 503 HOH HOH . 
HA 4 HOH G 8 508 513 HOH HOH . 
HA 4 HOH G 9 509 515 HOH HOH . 
HA 4 HOH G 10 510 507 HOH HOH . 
HA 4 HOH G 11 511 502 HOH HOH . 
HA 4 HOH G 12 512 514 HOH HOH . 
HA 4 HOH G 13 513 509 HOH HOH . 
IA 4 HOH H 1 501 515 HOH HOH . 
IA 4 HOH H 2 502 513 HOH HOH . 
IA 4 HOH H 3 503 506 HOH HOH . 
IA 4 HOH H 4 504 509 HOH HOH . 
IA 4 HOH H 5 505 510 HOH HOH . 
IA 4 HOH H 6 506 508 HOH HOH . 
IA 4 HOH H 7 507 512 HOH HOH . 
IA 4 HOH H 8 508 511 HOH HOH . 
IA 4 HOH H 9 509 514 HOH HOH . 
IA 4 HOH H 10 510 510 HOH HOH . 
IA 4 HOH H 11 511 519 HOH HOH . 
IA 4 HOH H 12 512 516 HOH HOH . 
IA 4 HOH H 13 513 502 HOH HOH . 
IA 4 HOH H 14 514 504 HOH HOH . 
IA 4 HOH H 15 515 507 HOH HOH . 
IA 4 HOH H 16 516 503 HOH HOH . 
IA 4 HOH H 17 517 518 HOH HOH . 
IA 4 HOH H 18 518 517 HOH HOH . 
IA 4 HOH H 19 519 505 HOH HOH . 
JA 4 HOH I 1 501 513 HOH HOH . 
JA 4 HOH I 2 502 501 HOH HOH . 
JA 4 HOH I 3 503 521 HOH HOH . 
JA 4 HOH I 4 504 506 HOH HOH . 
JA 4 HOH I 5 505 508 HOH HOH . 
JA 4 HOH I 6 506 517 HOH HOH . 
JA 4 HOH I 7 507 515 HOH HOH . 
JA 4 HOH I 8 508 503 HOH HOH . 
JA 4 HOH I 9 509 522 HOH HOH . 
JA 4 HOH I 10 510 509 HOH HOH . 
JA 4 HOH I 11 511 505 HOH HOH . 
JA 4 HOH I 12 512 502 HOH HOH . 
JA 4 HOH I 13 513 520 HOH HOH . 
JA 4 HOH I 14 514 510 HOH HOH . 
JA 4 HOH I 15 515 503 HOH HOH . 
JA 4 HOH I 16 516 504 HOH HOH . 
JA 4 HOH I 17 517 514 HOH HOH . 
JA 4 HOH I 18 518 518 HOH HOH . 
JA 4 HOH I 19 519 516 HOH HOH . 
JA 4 HOH I 20 520 507 HOH HOH . 
JA 4 HOH I 21 521 519 HOH HOH . 
JA 4 HOH I 22 522 512 HOH HOH . 
JA 4 HOH I 23 523 511 HOH HOH . 
KA 4 HOH J 1 401 411 HOH HOH . 
KA 4 HOH J 2 402 403 HOH HOH . 
KA 4 HOH J 3 403 402 HOH HOH . 
KA 4 HOH J 4 404 410 HOH HOH . 
KA 4 HOH J 5 405 407 HOH HOH . 
KA 4 HOH J 6 406 408 HOH HOH . 
KA 4 HOH J 7 407 401 HOH HOH . 
KA 4 HOH J 8 408 404 HOH HOH . 
KA 4 HOH J 9 409 414 HOH HOH . 
KA 4 HOH J 10 410 412 HOH HOH . 
LA 4 HOH K 1 501 502 HOH HOH . 
LA 4 HOH K 2 502 506 HOH HOH . 
LA 4 HOH K 3 503 508 HOH HOH . 
LA 4 HOH K 4 504 505 HOH HOH . 
LA 4 HOH K 5 505 501 HOH HOH . 
LA 4 HOH K 6 506 503 HOH HOH . 
LA 4 HOH K 7 507 507 HOH HOH . 
LA 4 HOH K 8 508 504 HOH HOH . 
MA 4 HOH L 1 401 402 HOH HOH . 
MA 4 HOH L 2 402 404 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 . . . X 2 17.74 14.198 -39.534 1 86.39 ? N1 PLP 401 G 1 
HETATM 2 C C2 PLP . . . X 2 18.72 14.555 -38.664 1 86.92 ? C2 PLP 401 G 1 
HETATM 3 C C2A PLP . . . X 2 20.172 14.373 -39.008 1 89.92 ? C2A PLP 401 G 1 
HETATM 4 C C3 PLP . . . X 2 18.371 15.109 -37.348 1 86.34 ? C3 PLP 401 G 1 
HETATM 5 O O3 PLP . . . X 2 19.358 15.461 -36.487 1 91.33 ? O3 PLP 401 G 1 
HETATM 6 C C4 PLP . . . X 2 16.934 15.27 -37.032 1 86.2 ? C4 PLP 401 G 1 
HETATM 7 C C4A PLP . . . X 2 16.468 15.824 -35.742 1 88.81 ? C4A PLP 401 G 1 
HETATM 8 O O4A PLP . . . X 2 17.29 16.15 -34.902 1 89.24 ? O4A PLP 401 G 1 
HETATM 9 C C5 PLP . . . X 2 15.961 14.844 -38.058 1 87.79 ? C5 PLP 401 G 1 
HETATM 10 C C6 PLP . . . X 2 16.426 14.328 -39.271 1 87.99 ? C6 PLP 401 G 1 
HETATM 11 C C5A PLP . . . X 2 14.479 14.994 -37.803 1 84.64 ? C5A PLP 401 G 1 
HETATM 12 O O4P PLP . . . X 2 14.179 16.382 -37.908 1 79.92 ? O4P PLP 401 G 1 
HETATM 13 P P PLP . . . X 2 12.722 16.879 -38.34 1 76.87 ? P PLP 401 G 1 
HETATM 14 O O1P PLP . . . X 2 12.292 16.094 -39.554 1 73.78 ? O1P PLP 401 G 1 
HETATM 15 O O2P PLP . . . X 2 12.927 18.344 -38.66 1 72.26 ? O2P PLP 401 G 1 
HETATM 16 O O3P PLP . . . X 2 12.003 16.52 -37.074 1 69.69 ? O3P PLP 401 G 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           16 
#