data_1XI9
#
_model_server_result.job_id            wOpxaXHNBpAC3Zc2cWEQqg 
_model_server_result.datetime_utc      '2024-12-12 21:45:28' 
_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          1xi9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":501}' 
#
_entry.id    1XI9 
#
_exptl.entry_id    1XI9 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          89.79 
_cell.angle_gamma         90 
_cell.entry_id            1XI9 
_cell.length_a            61.804 
_cell.length_b            188.089 
_cell.length_c            72.583 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1XI9 
_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
? tetrameric 4 author_defined_assembly 1 
PISA,PQS dimeric 2 software_defined_assembly 2 
PISA,PQS dimeric 2 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,B,C,D,E,F,G,H,I,J,K,L 1 1 
A,B,E,F,I,J 2 1 
C,D,G,H,K,L 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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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 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                     1XI9 
_atom_sites.fract_transf_matrix[1][1]    0.01618 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    -0.000059 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005317 
_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]    0.013777 
_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
E 2 PLP A 1 501 501 PLP PLP . 
F 2 PLP B 1 501 501 PLP PLP . 
G 2 PLP C 1 501 501 PLP PLP . 
H 2 PLP D 1 501 501 PLP PLP . 
I 3 HOH A 1 502 101 HOH HOH . 
I 3 HOH A 2 503 102 HOH HOH . 
I 3 HOH A 3 504 103 HOH HOH . 
I 3 HOH A 4 505 104 HOH HOH . 
I 3 HOH A 5 506 105 HOH HOH . 
I 3 HOH A 6 507 106 HOH HOH . 
I 3 HOH A 7 508 107 HOH HOH . 
I 3 HOH A 8 509 108 HOH HOH . 
I 3 HOH A 9 510 109 HOH HOH . 
I 3 HOH A 10 511 110 HOH HOH . 
I 3 HOH A 11 512 111 HOH HOH . 
I 3 HOH A 12 513 112 HOH HOH . 
I 3 HOH A 13 514 113 HOH HOH . 
I 3 HOH A 14 515 114 HOH HOH . 
I 3 HOH A 15 516 115 HOH HOH . 
I 3 HOH A 16 517 116 HOH HOH . 
I 3 HOH A 17 518 117 HOH HOH . 
I 3 HOH A 18 519 118 HOH HOH . 
I 3 HOH A 19 520 119 HOH HOH . 
I 3 HOH A 20 521 121 HOH HOH . 
I 3 HOH A 21 522 122 HOH HOH . 
I 3 HOH A 22 523 123 HOH HOH . 
I 3 HOH A 23 524 124 HOH HOH . 
I 3 HOH A 24 525 424 HOH HOH . 
I 3 HOH A 25 526 425 HOH HOH . 
I 3 HOH A 26 527 426 HOH HOH . 
I 3 HOH A 27 528 430 HOH HOH . 
I 3 HOH A 28 529 435 HOH HOH . 
J 3 HOH B 1 502 201 HOH HOH . 
J 3 HOH B 2 503 202 HOH HOH . 
J 3 HOH B 3 504 203 HOH HOH . 
J 3 HOH B 4 505 204 HOH HOH . 
J 3 HOH B 5 506 205 HOH HOH . 
J 3 HOH B 6 507 206 HOH HOH . 
J 3 HOH B 7 508 207 HOH HOH . 
J 3 HOH B 8 509 208 HOH HOH . 
J 3 HOH B 9 510 209 HOH HOH . 
J 3 HOH B 10 511 210 HOH HOH . 
J 3 HOH B 11 512 211 HOH HOH . 
J 3 HOH B 12 513 212 HOH HOH . 
J 3 HOH B 13 514 213 HOH HOH . 
J 3 HOH B 14 515 214 HOH HOH . 
J 3 HOH B 15 516 215 HOH HOH . 
J 3 HOH B 16 517 216 HOH HOH . 
J 3 HOH B 17 518 217 HOH HOH . 
J 3 HOH B 18 519 218 HOH HOH . 
J 3 HOH B 19 520 219 HOH HOH . 
J 3 HOH B 20 521 220 HOH HOH . 
J 3 HOH B 21 522 428 HOH HOH . 
J 3 HOH B 22 523 429 HOH HOH . 
K 3 HOH C 1 502 301 HOH HOH . 
K 3 HOH C 2 503 302 HOH HOH . 
K 3 HOH C 3 504 303 HOH HOH . 
K 3 HOH C 4 505 304 HOH HOH . 
K 3 HOH C 5 506 305 HOH HOH . 
K 3 HOH C 6 507 306 HOH HOH . 
K 3 HOH C 7 508 307 HOH HOH . 
K 3 HOH C 8 509 308 HOH HOH . 
K 3 HOH C 9 510 309 HOH HOH . 
K 3 HOH C 10 511 310 HOH HOH . 
K 3 HOH C 11 512 311 HOH HOH . 
K 3 HOH C 12 513 312 HOH HOH . 
K 3 HOH C 13 514 313 HOH HOH . 
K 3 HOH C 14 515 314 HOH HOH . 
K 3 HOH C 15 516 315 HOH HOH . 
K 3 HOH C 16 517 316 HOH HOH . 
K 3 HOH C 17 518 317 HOH HOH . 
K 3 HOH C 18 519 318 HOH HOH . 
K 3 HOH C 19 520 319 HOH HOH . 
K 3 HOH C 20 521 321 HOH HOH . 
K 3 HOH C 21 522 322 HOH HOH . 
K 3 HOH C 22 523 323 HOH HOH . 
K 3 HOH C 23 524 324 HOH HOH . 
K 3 HOH C 24 525 325 HOH HOH . 
K 3 HOH C 25 526 326 HOH HOH . 
K 3 HOH C 26 527 327 HOH HOH . 
K 3 HOH C 27 528 328 HOH HOH . 
K 3 HOH C 28 529 329 HOH HOH . 
K 3 HOH C 29 530 427 HOH HOH . 
K 3 HOH C 30 531 431 HOH HOH . 
K 3 HOH C 31 532 432 HOH HOH . 
L 3 HOH D 1 401 401 HOH HOH . 
L 3 HOH D 2 402 402 HOH HOH . 
L 3 HOH D 3 403 403 HOH HOH . 
L 3 HOH D 4 404 404 HOH HOH . 
L 3 HOH D 5 405 405 HOH HOH . 
L 3 HOH D 6 406 406 HOH HOH . 
L 3 HOH D 7 407 407 HOH HOH . 
L 3 HOH D 8 408 408 HOH HOH . 
L 3 HOH D 9 409 409 HOH HOH . 
L 3 HOH D 10 410 410 HOH HOH . 
L 3 HOH D 11 411 411 HOH HOH . 
L 3 HOH D 12 412 412 HOH HOH . 
L 3 HOH D 13 413 413 HOH HOH . 
L 3 HOH D 14 414 414 HOH HOH . 
L 3 HOH D 15 415 415 HOH HOH . 
L 3 HOH D 16 416 416 HOH HOH . 
L 3 HOH D 17 417 417 HOH HOH . 
L 3 HOH D 18 418 418 HOH HOH . 
L 3 HOH D 19 420 420 HOH HOH . 
L 3 HOH D 20 421 421 HOH HOH . 
L 3 HOH D 21 422 422 HOH HOH . 
L 3 HOH D 22 423 423 HOH HOH . 
L 3 HOH D 23 433 433 HOH HOH . 
L 3 HOH D 24 434 434 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 . . . H 2 81.58 165.174 5.564 1 44.69 ? N1 PLP 501 D 1 
HETATM 2 C C2 PLP . . . H 2 82.785 165.589 4.989 1 44.18 ? C2 PLP 501 D 1 
HETATM 3 C C2A PLP . . . H 2 83.018 165.208 3.542 1 45.5 ? C2A PLP 501 D 1 
HETATM 4 C C3 PLP . . . H 2 83.722 166.382 5.713 1 43.62 ? C3 PLP 501 D 1 
HETATM 5 O O3 PLP . . . H 2 84.653 167.1 5.001 1 42.25 ? O3 PLP 501 D 1 
HETATM 6 C C4 PLP . . . H 2 83.425 166.74 7.051 1 43.96 ? C4 PLP 501 D 1 
HETATM 7 C C4A PLP . . . H 2 84.233 167.837 7.707 1 44.43 ? C4A PLP 501 D 1 
HETATM 8 C C5 PLP . . . H 2 82.21 166.289 7.649 1 42.92 ? C5 PLP 501 D 1 
HETATM 9 C C6 PLP . . . H 2 81.295 165.5 6.889 1 43.18 ? C6 PLP 501 D 1 
HETATM 10 C C5A PLP . . . H 2 82.017 166.241 9.159 1 38.66 ? C5A PLP 501 D 1 
HETATM 11 O O4P PLP . . . H 2 81.48 167.51 9.46 1 33.16 ? O4P PLP 501 D 1 
HETATM 12 P P PLP . . . H 2 80.596 167.898 10.737 1 29.87 ? P PLP 501 D 1 
HETATM 13 O O1P PLP . . . H 2 79.167 168.03 10.282 1 29.09 ? O1P PLP 501 D 1 
HETATM 14 O O2P PLP . . . H 2 81.134 169.206 11.241 1 30.77 ? O2P PLP 501 D 1 
HETATM 15 O O3P PLP . . . H 2 80.696 166.943 11.898 1 30.5 ? O3P PLP 501 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           354 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#