data_1D2F
#
_model_server_result.job_id            IivdzHWfIwwVHHIK9wBSxA 
_model_server_result.datetime_utc      '2025-03-26 19:23:52' 
_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          1d2f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":400}' 
#
_entry.id    1D2F 
#
_exptl.entry_id    1D2F 
_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            1D2F 
_cell.length_a            57.51 
_cell.length_b            107.19 
_cell.length_c            256.4 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1D2F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 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 
#
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 233 A LYS 233 1_555 C C4A PLP . A PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? 
covale ? covale2 B NZ LYS 233 B LYS 233 1_555 D C4A PLP . B PLP 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
#
_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                     1D2F 
_atom_sites.fract_transf_matrix[1][1]    0.01739 
_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]    0.00933 
_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]    0.0039 
_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 1 400 400 PLP PLP . 
D 2 PLP B 1 400 400 PLP PLP . 
E 3 HOH A 1 401 16 HOH TIP . 
E 3 HOH A 2 402 47 HOH TIP . 
E 3 HOH A 3 403 54 HOH TIP . 
E 3 HOH A 4 404 62 HOH TIP . 
E 3 HOH A 5 405 63 HOH TIP . 
E 3 HOH A 6 406 64 HOH TIP . 
E 3 HOH A 7 407 65 HOH TIP . 
E 3 HOH A 8 408 76 HOH TIP . 
E 3 HOH A 9 409 77 HOH TIP . 
E 3 HOH A 10 410 83 HOH TIP . 
E 3 HOH A 11 411 87 HOH TIP . 
E 3 HOH A 12 412 88 HOH TIP . 
E 3 HOH A 13 413 91 HOH TIP . 
E 3 HOH A 14 414 102 HOH TIP . 
E 3 HOH A 15 415 109 HOH TIP . 
E 3 HOH A 16 416 110 HOH TIP . 
E 3 HOH A 17 417 111 HOH TIP . 
E 3 HOH A 18 418 114 HOH TIP . 
E 3 HOH A 19 419 116 HOH TIP . 
E 3 HOH A 20 420 119 HOH TIP . 
E 3 HOH A 21 421 120 HOH TIP . 
E 3 HOH A 22 422 126 HOH TIP . 
E 3 HOH A 23 423 127 HOH TIP . 
E 3 HOH A 24 424 133 HOH TIP . 
E 3 HOH A 25 425 134 HOH TIP . 
E 3 HOH A 26 426 136 HOH TIP . 
E 3 HOH A 27 427 138 HOH TIP . 
E 3 HOH A 28 428 149 HOH TIP . 
E 3 HOH A 29 429 150 HOH TIP . 
E 3 HOH A 30 430 151 HOH TIP . 
E 3 HOH A 31 431 158 HOH TIP . 
E 3 HOH A 32 432 159 HOH TIP . 
E 3 HOH A 33 433 161 HOH TIP . 
E 3 HOH A 34 434 163 HOH TIP . 
E 3 HOH A 35 435 165 HOH TIP . 
F 3 HOH B 1 401 1 HOH TIP . 
F 3 HOH B 2 402 2 HOH TIP . 
F 3 HOH B 3 403 3 HOH TIP . 
F 3 HOH B 4 404 4 HOH TIP . 
F 3 HOH B 5 405 5 HOH TIP . 
F 3 HOH B 6 406 6 HOH TIP . 
F 3 HOH B 7 407 7 HOH TIP . 
F 3 HOH B 8 408 8 HOH TIP . 
F 3 HOH B 9 409 9 HOH TIP . 
F 3 HOH B 10 410 10 HOH TIP . 
F 3 HOH B 11 411 11 HOH TIP . 
F 3 HOH B 12 412 12 HOH TIP . 
F 3 HOH B 13 413 13 HOH TIP . 
F 3 HOH B 14 414 14 HOH TIP . 
F 3 HOH B 15 415 15 HOH TIP . 
F 3 HOH B 16 416 17 HOH TIP . 
F 3 HOH B 17 417 18 HOH TIP . 
F 3 HOH B 18 418 19 HOH TIP . 
F 3 HOH B 19 419 20 HOH TIP . 
F 3 HOH B 20 420 21 HOH TIP . 
F 3 HOH B 21 421 22 HOH TIP . 
F 3 HOH B 22 422 23 HOH TIP . 
F 3 HOH B 23 423 24 HOH TIP . 
F 3 HOH B 24 424 25 HOH TIP . 
F 3 HOH B 25 425 26 HOH TIP . 
F 3 HOH B 26 426 27 HOH TIP . 
F 3 HOH B 27 427 28 HOH TIP . 
F 3 HOH B 28 428 29 HOH TIP . 
F 3 HOH B 29 429 30 HOH TIP . 
F 3 HOH B 30 430 31 HOH TIP . 
F 3 HOH B 31 431 32 HOH TIP . 
F 3 HOH B 32 432 33 HOH TIP . 
F 3 HOH B 33 433 34 HOH TIP . 
F 3 HOH B 34 434 35 HOH TIP . 
F 3 HOH B 35 435 36 HOH TIP . 
F 3 HOH B 36 436 37 HOH TIP . 
F 3 HOH B 37 437 38 HOH TIP . 
F 3 HOH B 38 438 39 HOH TIP . 
F 3 HOH B 39 439 40 HOH TIP . 
F 3 HOH B 40 440 41 HOH TIP . 
F 3 HOH B 41 441 42 HOH TIP . 
F 3 HOH B 42 442 43 HOH TIP . 
F 3 HOH B 43 443 44 HOH TIP . 
F 3 HOH B 44 444 45 HOH TIP . 
F 3 HOH B 45 445 46 HOH TIP . 
F 3 HOH B 46 446 48 HOH TIP . 
F 3 HOH B 47 447 49 HOH TIP . 
F 3 HOH B 48 448 50 HOH TIP . 
F 3 HOH B 49 449 51 HOH TIP . 
F 3 HOH B 50 450 52 HOH TIP . 
F 3 HOH B 51 451 53 HOH TIP . 
F 3 HOH B 52 452 55 HOH TIP . 
F 3 HOH B 53 453 56 HOH TIP . 
F 3 HOH B 54 454 57 HOH TIP . 
F 3 HOH B 55 455 58 HOH TIP . 
F 3 HOH B 56 456 59 HOH TIP . 
F 3 HOH B 57 457 60 HOH TIP . 
F 3 HOH B 58 458 61 HOH TIP . 
F 3 HOH B 59 459 66 HOH TIP . 
F 3 HOH B 60 460 67 HOH TIP . 
F 3 HOH B 61 461 68 HOH TIP . 
F 3 HOH B 62 462 69 HOH TIP . 
F 3 HOH B 63 463 70 HOH TIP . 
F 3 HOH B 64 464 71 HOH TIP . 
F 3 HOH B 65 465 72 HOH TIP . 
F 3 HOH B 66 466 73 HOH TIP . 
F 3 HOH B 67 467 74 HOH TIP . 
F 3 HOH B 68 468 75 HOH TIP . 
F 3 HOH B 69 469 78 HOH TIP . 
F 3 HOH B 70 470 79 HOH TIP . 
F 3 HOH B 71 471 80 HOH TIP . 
F 3 HOH B 72 472 81 HOH TIP . 
F 3 HOH B 73 473 82 HOH TIP . 
F 3 HOH B 74 474 84 HOH TIP . 
F 3 HOH B 75 475 85 HOH TIP . 
F 3 HOH B 76 476 86 HOH TIP . 
F 3 HOH B 77 477 89 HOH TIP . 
F 3 HOH B 78 478 90 HOH TIP . 
F 3 HOH B 79 479 92 HOH TIP . 
F 3 HOH B 80 480 93 HOH TIP . 
F 3 HOH B 81 481 94 HOH TIP . 
F 3 HOH B 82 482 95 HOH TIP . 
F 3 HOH B 83 483 96 HOH TIP . 
F 3 HOH B 84 484 97 HOH TIP . 
F 3 HOH B 85 485 98 HOH TIP . 
F 3 HOH B 86 486 99 HOH TIP . 
F 3 HOH B 87 487 100 HOH TIP . 
F 3 HOH B 88 488 101 HOH TIP . 
F 3 HOH B 89 489 103 HOH TIP . 
F 3 HOH B 90 490 104 HOH TIP . 
F 3 HOH B 91 491 105 HOH TIP . 
F 3 HOH B 92 492 106 HOH TIP . 
F 3 HOH B 93 493 107 HOH TIP . 
F 3 HOH B 94 494 108 HOH TIP . 
F 3 HOH B 95 495 112 HOH TIP . 
F 3 HOH B 96 496 113 HOH TIP . 
F 3 HOH B 97 497 115 HOH TIP . 
F 3 HOH B 98 498 117 HOH TIP . 
F 3 HOH B 99 499 118 HOH TIP . 
F 3 HOH B 100 500 121 HOH TIP . 
F 3 HOH B 101 501 122 HOH TIP . 
F 3 HOH B 102 502 123 HOH TIP . 
F 3 HOH B 103 503 124 HOH TIP . 
F 3 HOH B 104 504 125 HOH TIP . 
F 3 HOH B 105 505 128 HOH TIP . 
F 3 HOH B 106 506 129 HOH TIP . 
F 3 HOH B 107 507 130 HOH TIP . 
F 3 HOH B 108 508 131 HOH TIP . 
F 3 HOH B 109 509 132 HOH TIP . 
F 3 HOH B 110 510 135 HOH TIP . 
F 3 HOH B 111 511 137 HOH TIP . 
F 3 HOH B 112 512 139 HOH TIP . 
F 3 HOH B 113 513 140 HOH TIP . 
F 3 HOH B 114 514 141 HOH TIP . 
F 3 HOH B 115 515 142 HOH TIP . 
F 3 HOH B 116 516 143 HOH TIP . 
F 3 HOH B 117 517 144 HOH TIP . 
F 3 HOH B 118 518 145 HOH TIP . 
F 3 HOH B 119 519 146 HOH TIP . 
F 3 HOH B 120 520 147 HOH TIP . 
F 3 HOH B 121 521 148 HOH TIP . 
F 3 HOH B 122 522 152 HOH TIP . 
F 3 HOH B 123 523 153 HOH TIP . 
F 3 HOH B 124 524 154 HOH TIP . 
F 3 HOH B 125 525 155 HOH TIP . 
F 3 HOH B 126 526 156 HOH TIP . 
F 3 HOH B 127 527 157 HOH TIP . 
F 3 HOH B 128 528 160 HOH TIP . 
F 3 HOH B 129 529 162 HOH TIP . 
F 3 HOH B 130 530 164 HOH TIP . 
F 3 HOH B 131 531 166 HOH TIP . 
F 3 HOH B 132 532 167 HOH TIP . 
#
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 . . . D 2 -41.083 -1.406 -45.18 1 21.11 ? N1 PLP 400 B 1 
HETATM 2 C C2 PLP . . . D 2 -41.637 -2.583 -45.702 1 18.55 ? C2 PLP 400 B 1 
HETATM 3 C C2A PLP . . . D 2 -42.351 -2.388 -47.002 1 17.31 ? C2A PLP 400 B 1 
HETATM 4 C C3 PLP . . . D 2 -41.454 -3.827 -44.91 1 19.68 ? C3 PLP 400 B 1 
HETATM 5 O O3 PLP . . . D 2 -42.065 -4.909 -45.44 1 25.72 ? O3 PLP 400 B 1 
HETATM 6 C C4 PLP . . . D 2 -40.739 -3.786 -43.712 1 21.6 ? C4 PLP 400 B 1 
HETATM 7 C C4A PLP . . . D 2 -40.544 -5.01 -42.94 1 17.6 ? C4A PLP 400 B 1 
HETATM 8 C C5 PLP . . . D 2 -40.189 -2.443 -43.275 1 27.17 ? C5 PLP 400 B 1 
HETATM 9 C C6 PLP . . . D 2 -40.393 -1.29 -44.031 1 20.73 ? C6 PLP 400 B 1 
HETATM 10 C C5A PLP . . . D 2 -39.311 -2.409 -42.062 1 28.16 ? C5A PLP 400 B 1 
HETATM 11 O O4P PLP . . . D 2 -39.698 -1.454 -41.167 1 39.44 ? O4P PLP 400 B 1 
HETATM 12 P P PLP . . . D 2 -38.893 -1.328 -39.738 1 50.83 ? P PLP 400 B 1 
HETATM 13 O O1P PLP . . . D 2 -39.533 -0.041 -39.19 1 36.43 ? O1P PLP 400 B 1 
HETATM 14 O O2P PLP . . . D 2 -37.413 -0.986 -40.194 1 35.93 ? O2P PLP 400 B 1 
HETATM 15 O O3P PLP . . . D 2 -39.239 -2.736 -39.172 1 27.13 ? O3P PLP 400 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#