data_5NM8
#
_model_server_result.job_id            WWDko9IZIixu9kTilVLv0Q 
_model_server_result.datetime_utc      '2025-02-27 15:04:19' 
_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          5nm8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    5NM8 
#
_exptl.entry_id    5NM8 
_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            5NM8 
_cell.length_a            46.627 
_cell.length_b            98.937 
_cell.length_c            103.737 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NM8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F 1 1 
B,D,E,G 2 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 26 A LYS 26 1_555 C C4A PLP . A PLP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? 
covale ? covale2 B NZ LYS 26 B LYS 26 1_555 D C4A PLP . B PLP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.253 ? 
metalc ? metalc1 F O HOH . A HOH 469 2_455 E CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc2 F O HOH . A HOH 491 2_455 E CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc3 B O PRO 63 B PRO 63 1_555 E CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc4 E CA CA . B CA 302 1_555 G O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc5 E CA CA . B CA 302 1_555 G O HOH . B HOH 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc6 E CA CA . B CA 302 1_555 G O HOH . B HOH 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
metalc ? metalc7 E CA CA . B CA 302 1_555 G O HOH . B HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
#
_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                     5NM8 
_atom_sites.fract_transf_matrix[1][1]    0.021447 
_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]    0.010107 
_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]    0.00964 
_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 1 301 1 PLP PLP . 
D 2 PLP B 1 301 2 PLP PLP . 
E 3 CA B 1 302 1 CA CA . 
F 4 HOH A 1 401 126 HOH HOH . 
F 4 HOH A 2 402 96 HOH HOH . 
F 4 HOH A 3 403 164 HOH HOH . 
F 4 HOH A 4 404 89 HOH HOH . 
F 4 HOH A 5 405 31 HOH HOH . 
F 4 HOH A 6 406 36 HOH HOH . 
F 4 HOH A 7 407 109 HOH HOH . 
F 4 HOH A 8 408 60 HOH HOH . 
F 4 HOH A 9 409 6 HOH HOH . 
F 4 HOH A 10 410 141 HOH HOH . 
F 4 HOH A 11 411 145 HOH HOH . 
F 4 HOH A 12 412 9 HOH HOH . 
F 4 HOH A 13 413 69 HOH HOH . 
F 4 HOH A 14 414 29 HOH HOH . 
F 4 HOH A 15 415 107 HOH HOH . 
F 4 HOH A 16 416 80 HOH HOH . 
F 4 HOH A 17 417 115 HOH HOH . 
F 4 HOH A 18 418 77 HOH HOH . 
F 4 HOH A 19 419 71 HOH HOH . 
F 4 HOH A 20 420 70 HOH HOH . 
F 4 HOH A 21 421 2 HOH HOH . 
F 4 HOH A 22 422 134 HOH HOH . 
F 4 HOH A 23 423 59 HOH HOH . 
F 4 HOH A 24 424 76 HOH HOH . 
F 4 HOH A 25 425 135 HOH HOH . 
F 4 HOH A 26 426 105 HOH HOH . 
F 4 HOH A 27 427 42 HOH HOH . 
F 4 HOH A 28 428 152 HOH HOH . 
F 4 HOH A 29 429 108 HOH HOH . 
F 4 HOH A 30 430 68 HOH HOH . 
F 4 HOH A 31 431 4 HOH HOH . 
F 4 HOH A 32 432 74 HOH HOH . 
F 4 HOH A 33 433 81 HOH HOH . 
F 4 HOH A 34 434 78 HOH HOH . 
F 4 HOH A 35 435 73 HOH HOH . 
F 4 HOH A 36 436 83 HOH HOH . 
F 4 HOH A 37 437 95 HOH HOH . 
F 4 HOH A 38 438 8 HOH HOH . 
F 4 HOH A 39 439 34 HOH HOH . 
F 4 HOH A 40 440 123 HOH HOH . 
F 4 HOH A 41 441 56 HOH HOH . 
F 4 HOH A 42 442 22 HOH HOH . 
F 4 HOH A 43 443 67 HOH HOH . 
F 4 HOH A 44 444 90 HOH HOH . 
F 4 HOH A 45 445 143 HOH HOH . 
F 4 HOH A 46 446 65 HOH HOH . 
F 4 HOH A 47 447 61 HOH HOH . 
F 4 HOH A 48 448 92 HOH HOH . 
F 4 HOH A 49 449 159 HOH HOH . 
F 4 HOH A 50 450 144 HOH HOH . 
F 4 HOH A 51 451 38 HOH HOH . 
F 4 HOH A 52 452 53 HOH HOH . 
F 4 HOH A 53 453 125 HOH HOH . 
F 4 HOH A 54 454 151 HOH HOH . 
F 4 HOH A 55 455 79 HOH HOH . 
F 4 HOH A 56 456 35 HOH HOH . 
F 4 HOH A 57 457 72 HOH HOH . 
F 4 HOH A 58 458 133 HOH HOH . 
F 4 HOH A 59 459 111 HOH HOH . 
F 4 HOH A 60 460 116 HOH HOH . 
F 4 HOH A 61 461 15 HOH HOH . 
F 4 HOH A 62 462 5 HOH HOH . 
F 4 HOH A 63 463 14 HOH HOH . 
F 4 HOH A 64 464 33 HOH HOH . 
F 4 HOH A 65 465 11 HOH HOH . 
F 4 HOH A 66 466 3 HOH HOH . 
F 4 HOH A 67 467 62 HOH HOH . 
F 4 HOH A 68 468 13 HOH HOH . 
F 4 HOH A 69 469 102 HOH HOH . 
F 4 HOH A 70 470 93 HOH HOH . 
F 4 HOH A 71 471 136 HOH HOH . 
F 4 HOH A 72 472 41 HOH HOH . 
F 4 HOH A 73 473 37 HOH HOH . 
F 4 HOH A 74 474 122 HOH HOH . 
F 4 HOH A 75 475 23 HOH HOH . 
F 4 HOH A 76 476 118 HOH HOH . 
F 4 HOH A 77 477 94 HOH HOH . 
F 4 HOH A 78 478 97 HOH HOH . 
F 4 HOH A 79 479 82 HOH HOH . 
F 4 HOH A 80 480 88 HOH HOH . 
F 4 HOH A 81 481 91 HOH HOH . 
F 4 HOH A 82 482 163 HOH HOH . 
F 4 HOH A 83 483 40 HOH HOH . 
F 4 HOH A 84 484 155 HOH HOH . 
F 4 HOH A 85 485 148 HOH HOH . 
F 4 HOH A 86 486 75 HOH HOH . 
F 4 HOH A 87 487 27 HOH HOH . 
F 4 HOH A 88 488 106 HOH HOH . 
F 4 HOH A 89 489 87 HOH HOH . 
F 4 HOH A 90 490 149 HOH HOH . 
F 4 HOH A 91 491 99 HOH HOH . 
F 4 HOH A 92 492 32 HOH HOH . 
F 4 HOH A 93 493 66 HOH HOH . 
F 4 HOH A 94 494 58 HOH HOH . 
F 4 HOH A 95 495 57 HOH HOH . 
F 4 HOH A 96 496 114 HOH HOH . 
F 4 HOH A 97 497 39 HOH HOH . 
F 4 HOH A 98 498 146 HOH HOH . 
F 4 HOH A 99 499 153 HOH HOH . 
F 4 HOH A 100 500 64 HOH HOH . 
F 4 HOH A 101 501 63 HOH HOH . 
G 4 HOH B 1 401 16 HOH HOH . 
G 4 HOH B 2 402 121 HOH HOH . 
G 4 HOH B 3 403 139 HOH HOH . 
G 4 HOH B 4 404 158 HOH HOH . 
G 4 HOH B 5 405 46 HOH HOH . 
G 4 HOH B 6 406 132 HOH HOH . 
G 4 HOH B 7 407 47 HOH HOH . 
G 4 HOH B 8 408 101 HOH HOH . 
G 4 HOH B 9 409 130 HOH HOH . 
G 4 HOH B 10 410 140 HOH HOH . 
G 4 HOH B 11 411 104 HOH HOH . 
G 4 HOH B 12 412 18 HOH HOH . 
G 4 HOH B 13 413 20 HOH HOH . 
G 4 HOH B 14 414 86 HOH HOH . 
G 4 HOH B 15 415 19 HOH HOH . 
G 4 HOH B 16 416 24 HOH HOH . 
G 4 HOH B 17 417 1 HOH HOH . 
G 4 HOH B 18 418 12 HOH HOH . 
G 4 HOH B 19 419 119 HOH HOH . 
G 4 HOH B 20 420 28 HOH HOH . 
G 4 HOH B 21 421 157 HOH HOH . 
G 4 HOH B 22 422 54 HOH HOH . 
G 4 HOH B 23 423 30 HOH HOH . 
G 4 HOH B 24 424 117 HOH HOH . 
G 4 HOH B 25 425 150 HOH HOH . 
G 4 HOH B 26 426 127 HOH HOH . 
G 4 HOH B 27 427 124 HOH HOH . 
G 4 HOH B 28 428 10 HOH HOH . 
G 4 HOH B 29 429 100 HOH HOH . 
G 4 HOH B 30 430 7 HOH HOH . 
G 4 HOH B 31 431 51 HOH HOH . 
G 4 HOH B 32 432 103 HOH HOH . 
G 4 HOH B 33 433 98 HOH HOH . 
G 4 HOH B 34 434 45 HOH HOH . 
G 4 HOH B 35 435 43 HOH HOH . 
G 4 HOH B 36 436 25 HOH HOH . 
G 4 HOH B 37 437 154 HOH HOH . 
G 4 HOH B 38 438 84 HOH HOH . 
G 4 HOH B 39 439 128 HOH HOH . 
G 4 HOH B 40 440 21 HOH HOH . 
G 4 HOH B 41 441 142 HOH HOH . 
G 4 HOH B 42 442 52 HOH HOH . 
G 4 HOH B 43 443 112 HOH HOH . 
G 4 HOH B 44 444 129 HOH HOH . 
G 4 HOH B 45 445 55 HOH HOH . 
G 4 HOH B 46 446 113 HOH HOH . 
G 4 HOH B 47 447 26 HOH HOH . 
G 4 HOH B 48 448 49 HOH HOH . 
G 4 HOH B 49 449 48 HOH HOH . 
G 4 HOH B 50 450 44 HOH HOH . 
G 4 HOH B 51 451 160 HOH HOH . 
G 4 HOH B 52 452 162 HOH HOH . 
G 4 HOH B 53 453 138 HOH HOH . 
G 4 HOH B 54 454 110 HOH HOH . 
G 4 HOH B 55 455 161 HOH HOH . 
G 4 HOH B 56 456 85 HOH HOH . 
G 4 HOH B 57 457 120 HOH HOH . 
G 4 HOH B 58 458 131 HOH HOH . 
G 4 HOH B 59 459 50 HOH HOH . 
G 4 HOH B 60 460 137 HOH HOH . 
G 4 HOH B 61 461 147 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 -16.031 -20.284 21.362 1 36.65 ? N1 PLP 301 A 1 
HETATM 2 C C2 PLP . . . C 2 -15.954 -21.478 20.73 1 38.52 ? C2 PLP 301 A 1 
HETATM 3 C C2A PLP . . . C 2 -15.581 -21.583 19.275 1 36.39 ? C2A PLP 301 A 1 
HETATM 4 C C3 PLP . . . C 2 -16.22 -22.713 21.484 1 40.95 ? C3 PLP 301 A 1 
HETATM 5 O O3 PLP . . . C 2 -16.131 -23.922 20.884 1 40.21 ? O3 PLP 301 A 1 
HETATM 6 C C4 PLP . . . C 2 -16.591 -22.602 22.911 1 39.65 ? C4 PLP 301 A 1 
HETATM 7 C C4A PLP . . . C 2 -16.858 -23.834 23.699 1 39.73 ? C4A PLP 301 A 1 
HETATM 8 C C5 PLP . . . C 2 -16.646 -21.231 23.488 1 38.13 ? C5 PLP 301 A 1 
HETATM 9 C C6 PLP . . . C 2 -16.368 -20.152 22.662 1 37.32 ? C6 PLP 301 A 1 
HETATM 10 C C5A PLP . . . C 2 -16.985 -21.033 24.945 1 36.82 ? C5A PLP 301 A 1 
HETATM 11 O O4P PLP . . . C 2 -15.904 -21.58 25.729 1 37.5 ? O4P PLP 301 A 1 
HETATM 12 P P PLP . . . C 2 -15.839 -21.302 27.324 1 38.01 ? P PLP 301 A 1 
HETATM 13 O O1P PLP . . . C 2 -16.033 -19.799 27.434 1 31.69 ? O1P PLP 301 A 1 
HETATM 14 O O2P PLP . . . C 2 -14.485 -21.795 27.702 1 36.97 ? O2P PLP 301 A 1 
HETATM 15 O O3P PLP . . . C 2 -16.966 -22.123 27.952 1 36.14 ? O3P PLP 301 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           15 
#