data_3QBO
#
_model_server_result.job_id            KwTXr1PpR2500HWQdIUAZw 
_model_server_result.datetime_utc      '2025-07-03 23:12:24' 
_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          3qbo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    3QBO 
#
_exptl.entry_id    3QBO 
_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    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            3QBO 
_cell.length_a            78.338 
_cell.length_b            87.951 
_cell.length_c            106.177 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QBO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 C N N 
? 2 D N N 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            NZ 
_struct_conn.ptnr1_label_comp_id            LYS 
_struct_conn.ptnr1_label_seq_id             200 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             LYS 
_struct_conn.ptnr1_auth_seq_id              197 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            C 
_struct_conn.ptnr2_label_atom_id            C4A 
_struct_conn.ptnr2_label_comp_id            PLP 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             PLP 
_struct_conn.ptnr2_auth_seq_id              501 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.387 
_struct_conn.pdbx_value_order               ? 
#
_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                     3QBO 
_atom_sites.fract_transf_matrix[1][1]    0.012765 
_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]    0.01137 
_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]    0.009418 
_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 PLP A 1 501 501 PLP PLP . 
D 2 PLP B 1 501 501 PLP PLP . 
E 3 HOH A 1 362 3 HOH HOH . 
E 3 HOH A 2 363 5 HOH HOH . 
E 3 HOH A 3 364 6 HOH HOH . 
E 3 HOH A 4 365 8 HOH HOH . 
E 3 HOH A 5 366 10 HOH HOH . 
E 3 HOH A 6 367 13 HOH HOH . 
E 3 HOH A 7 368 17 HOH HOH . 
E 3 HOH A 8 369 18 HOH HOH . 
E 3 HOH A 9 370 19 HOH HOH . 
E 3 HOH A 10 371 20 HOH HOH . 
E 3 HOH A 11 372 24 HOH HOH . 
E 3 HOH A 12 373 30 HOH HOH . 
E 3 HOH A 13 374 32 HOH HOH . 
E 3 HOH A 14 375 34 HOH HOH . 
E 3 HOH A 15 376 36 HOH HOH . 
E 3 HOH A 16 377 38 HOH HOH . 
E 3 HOH A 17 378 40 HOH HOH . 
E 3 HOH A 18 379 44 HOH HOH . 
E 3 HOH A 19 380 45 HOH HOH . 
E 3 HOH A 20 381 47 HOH HOH . 
E 3 HOH A 21 382 49 HOH HOH . 
E 3 HOH A 22 383 51 HOH HOH . 
E 3 HOH A 23 384 54 HOH HOH . 
E 3 HOH A 24 385 57 HOH HOH . 
E 3 HOH A 25 386 58 HOH HOH . 
E 3 HOH A 26 387 61 HOH HOH . 
E 3 HOH A 27 388 64 HOH HOH . 
E 3 HOH A 28 389 66 HOH HOH . 
E 3 HOH A 29 390 70 HOH HOH . 
E 3 HOH A 30 391 74 HOH HOH . 
E 3 HOH A 31 392 75 HOH HOH . 
E 3 HOH A 32 393 76 HOH HOH . 
E 3 HOH A 33 394 77 HOH HOH . 
E 3 HOH A 34 395 82 HOH HOH . 
E 3 HOH A 35 396 87 HOH HOH . 
E 3 HOH A 36 397 89 HOH HOH . 
E 3 HOH A 37 398 93 HOH HOH . 
E 3 HOH A 38 399 99 HOH HOH . 
E 3 HOH A 39 400 109 HOH HOH . 
E 3 HOH A 40 401 110 HOH HOH . 
E 3 HOH A 41 402 112 HOH HOH . 
E 3 HOH A 42 403 113 HOH HOH . 
E 3 HOH A 43 404 119 HOH HOH . 
E 3 HOH A 44 405 120 HOH HOH . 
E 3 HOH A 45 406 122 HOH HOH . 
E 3 HOH A 46 407 124 HOH HOH . 
E 3 HOH A 47 408 126 HOH HOH . 
E 3 HOH A 48 409 127 HOH HOH . 
E 3 HOH A 49 410 135 HOH HOH . 
E 3 HOH A 50 411 140 HOH HOH . 
E 3 HOH A 51 412 144 HOH HOH . 
E 3 HOH A 52 413 145 HOH HOH . 
E 3 HOH A 53 414 148 HOH HOH . 
E 3 HOH A 54 415 150 HOH HOH . 
E 3 HOH A 55 416 151 HOH HOH . 
E 3 HOH A 56 417 152 HOH HOH . 
E 3 HOH A 57 418 155 HOH HOH . 
E 3 HOH A 58 419 156 HOH HOH . 
E 3 HOH A 59 420 159 HOH HOH . 
E 3 HOH A 60 421 160 HOH HOH . 
E 3 HOH A 61 422 161 HOH HOH . 
E 3 HOH A 62 423 164 HOH HOH . 
E 3 HOH A 63 424 168 HOH HOH . 
E 3 HOH A 64 425 170 HOH HOH . 
E 3 HOH A 65 426 171 HOH HOH . 
E 3 HOH A 66 427 173 HOH HOH . 
E 3 HOH A 67 428 178 HOH HOH . 
E 3 HOH A 68 429 182 HOH HOH . 
E 3 HOH A 69 430 183 HOH HOH . 
E 3 HOH A 70 431 184 HOH HOH . 
E 3 HOH A 71 432 186 HOH HOH . 
E 3 HOH A 72 433 188 HOH HOH . 
E 3 HOH A 73 434 189 HOH HOH . 
E 3 HOH A 74 435 190 HOH HOH . 
E 3 HOH A 75 436 191 HOH HOH . 
E 3 HOH A 76 437 192 HOH HOH . 
E 3 HOH A 77 438 193 HOH HOH . 
E 3 HOH A 78 439 194 HOH HOH . 
E 3 HOH A 79 440 195 HOH HOH . 
E 3 HOH A 80 441 196 HOH HOH . 
E 3 HOH A 81 442 207 HOH HOH . 
E 3 HOH A 82 443 208 HOH HOH . 
E 3 HOH A 83 444 209 HOH HOH . 
F 3 HOH B 1 362 1 HOH HOH . 
F 3 HOH B 2 363 2 HOH HOH . 
F 3 HOH B 3 364 11 HOH HOH . 
F 3 HOH B 4 365 12 HOH HOH . 
F 3 HOH B 5 366 14 HOH HOH . 
F 3 HOH B 6 367 15 HOH HOH . 
F 3 HOH B 7 368 16 HOH HOH . 
F 3 HOH B 8 369 21 HOH HOH . 
F 3 HOH B 9 370 23 HOH HOH . 
F 3 HOH B 10 371 27 HOH HOH . 
F 3 HOH B 11 372 28 HOH HOH . 
F 3 HOH B 12 373 29 HOH HOH . 
F 3 HOH B 13 374 31 HOH HOH . 
F 3 HOH B 14 375 33 HOH HOH . 
F 3 HOH B 15 376 35 HOH HOH . 
F 3 HOH B 16 377 37 HOH HOH . 
F 3 HOH B 17 378 39 HOH HOH . 
F 3 HOH B 18 379 41 HOH HOH . 
F 3 HOH B 19 380 42 HOH HOH . 
F 3 HOH B 20 381 43 HOH HOH . 
F 3 HOH B 21 382 46 HOH HOH . 
F 3 HOH B 22 383 48 HOH HOH . 
F 3 HOH B 23 384 50 HOH HOH . 
F 3 HOH B 24 385 52 HOH HOH . 
F 3 HOH B 25 386 53 HOH HOH . 
F 3 HOH B 26 387 55 HOH HOH . 
F 3 HOH B 27 388 59 HOH HOH . 
F 3 HOH B 28 389 62 HOH HOH . 
F 3 HOH B 29 390 63 HOH HOH . 
F 3 HOH B 30 391 65 HOH HOH . 
F 3 HOH B 31 392 67 HOH HOH . 
F 3 HOH B 32 393 68 HOH HOH . 
F 3 HOH B 33 394 69 HOH HOH . 
F 3 HOH B 34 395 71 HOH HOH . 
F 3 HOH B 35 396 72 HOH HOH . 
F 3 HOH B 36 397 78 HOH HOH . 
F 3 HOH B 37 398 79 HOH HOH . 
F 3 HOH B 38 399 80 HOH HOH . 
F 3 HOH B 39 400 81 HOH HOH . 
F 3 HOH B 40 401 83 HOH HOH . 
F 3 HOH B 41 402 84 HOH HOH . 
F 3 HOH B 42 403 85 HOH HOH . 
F 3 HOH B 43 404 86 HOH HOH . 
F 3 HOH B 44 405 88 HOH HOH . 
F 3 HOH B 45 406 90 HOH HOH . 
F 3 HOH B 46 407 92 HOH HOH . 
F 3 HOH B 47 408 94 HOH HOH . 
F 3 HOH B 48 409 95 HOH HOH . 
F 3 HOH B 49 410 96 HOH HOH . 
F 3 HOH B 50 411 97 HOH HOH . 
F 3 HOH B 51 412 100 HOH HOH . 
F 3 HOH B 52 413 101 HOH HOH . 
F 3 HOH B 53 414 102 HOH HOH . 
F 3 HOH B 54 415 103 HOH HOH . 
F 3 HOH B 55 416 104 HOH HOH . 
F 3 HOH B 56 417 105 HOH HOH . 
F 3 HOH B 57 418 106 HOH HOH . 
F 3 HOH B 58 419 107 HOH HOH . 
F 3 HOH B 59 420 108 HOH HOH . 
F 3 HOH B 60 421 111 HOH HOH . 
F 3 HOH B 61 422 114 HOH HOH . 
F 3 HOH B 62 423 115 HOH HOH . 
F 3 HOH B 63 424 116 HOH HOH . 
F 3 HOH B 64 425 117 HOH HOH . 
F 3 HOH B 65 426 118 HOH HOH . 
F 3 HOH B 66 427 121 HOH HOH . 
F 3 HOH B 67 428 123 HOH HOH . 
F 3 HOH B 68 429 130 HOH HOH . 
F 3 HOH B 69 430 131 HOH HOH . 
F 3 HOH B 70 431 132 HOH HOH . 
F 3 HOH B 71 432 133 HOH HOH . 
F 3 HOH B 72 433 134 HOH HOH . 
F 3 HOH B 73 434 136 HOH HOH . 
F 3 HOH B 74 435 137 HOH HOH . 
F 3 HOH B 75 436 139 HOH HOH . 
F 3 HOH B 76 437 141 HOH HOH . 
F 3 HOH B 77 438 143 HOH HOH . 
F 3 HOH B 78 439 147 HOH HOH . 
F 3 HOH B 79 440 153 HOH HOH . 
F 3 HOH B 80 441 154 HOH HOH . 
F 3 HOH B 81 442 158 HOH HOH . 
F 3 HOH B 82 443 167 HOH HOH . 
F 3 HOH B 83 444 172 HOH HOH . 
F 3 HOH B 84 445 174 HOH HOH . 
F 3 HOH B 85 446 175 HOH HOH . 
F 3 HOH B 86 447 176 HOH HOH . 
F 3 HOH B 87 448 177 HOH HOH . 
F 3 HOH B 88 449 180 HOH HOH . 
F 3 HOH B 89 450 181 HOH HOH . 
F 3 HOH B 90 451 185 HOH HOH . 
F 3 HOH B 91 452 187 HOH HOH . 
F 3 HOH B 92 453 197 HOH HOH . 
F 3 HOH B 93 454 198 HOH HOH . 
F 3 HOH B 94 455 199 HOH HOH . 
F 3 HOH B 95 456 200 HOH HOH . 
F 3 HOH B 96 457 201 HOH HOH . 
F 3 HOH B 97 458 202 HOH HOH . 
F 3 HOH B 98 459 203 HOH HOH . 
F 3 HOH B 99 460 204 HOH HOH . 
F 3 HOH B 100 461 206 HOH HOH . 
F 3 HOH B 101 462 210 HOH HOH . 
F 3 HOH B 102 463 211 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 . . . C 2 56.646 72.682 19.018 1 17.67 ? N1 PLP 501 A 1 
HETATM 2 C C2 PLP . . . C 2 56.515 71.854 17.96 1 17.28 ? C2 PLP 501 A 1 
HETATM 3 C C2A PLP . . . C 2 55.523 70.694 17.904 1 16.99 ? C2A PLP 501 A 1 
HETATM 4 C C3 PLP . . . C 2 57.367 72.08 16.781 1 18.74 ? C3 PLP 501 A 1 
HETATM 5 O O3 PLP . . . C 2 57.248 71.279 15.721 1 21.9 ? O3 PLP 501 A 1 
HETATM 6 C C4 PLP . . . C 2 58.362 73.165 16.744 1 21.66 ? C4 PLP 501 A 1 
HETATM 7 C C4A PLP . . . C 2 59.266 73.514 15.63 1 24.23 ? C4A PLP 501 A 1 
HETATM 8 C C5 PLP . . . C 2 58.422 73.98 17.979 1 19.19 ? C5 PLP 501 A 1 
HETATM 9 C C6 PLP . . . C 2 57.557 73.706 19.045 1 18.85 ? C6 PLP 501 A 1 
HETATM 10 C C5A PLP . . . C 2 59.4 75.153 18.041 1 22.65 ? C5A PLP 501 A 1 
HETATM 11 O O4P PLP . . . C 2 59.004 76.133 17.078 1 20.11 ? O4P PLP 501 A 1 
HETATM 12 P P PLP . . . C 2 59.803 77.559 16.99 1 12.86 ? P PLP 501 A 1 
HETATM 13 O O1P PLP . . . C 2 61.234 77.246 16.314 1 13.12 ? O1P PLP 501 A 1 
HETATM 14 O O2P PLP . . . C 2 59.962 78.109 18.504 1 14.33 ? O2P PLP 501 A 1 
HETATM 15 O O3P PLP . . . C 2 58.785 78.364 16.208 1 7.92 ? O3P PLP 501 A 1 
#
_model_server_stats.io_time_ms              108 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           327 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#