data_1EKP
#
_model_server_result.job_id            CIZO0stuMxW5K3hWthq1RA 
_model_server_result.datetime_utc      '2024-10-11 19:20:25' 
_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          1ekp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":370}' 
#
_entry.id    1EKP 
#
_exptl.entry_id    1EKP 
_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          95.89 
_cell.angle_gamma         90 
_cell.entry_id            1EKP 
_cell.length_a            59.63 
_cell.length_b            111.64 
_cell.length_c            59.9 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1EKP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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 202 A LYS 202 1_555 C C4A PLP . A PLP 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? 
covale ? covale2 B NZ LYS 202 B LYS 202 1_555 D C4A PLP . B PLP 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? 
#
_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                     1EKP 
_atom_sites.fract_transf_matrix[1][1]    0.01677 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00173 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008957 
_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]    0.016783 
_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 1 370 370 PLP PLP . 
D 2 PLP B 1 370 370 PLP PLP . 
E 3 HOH A 1 371 2 HOH HOH . 
E 3 HOH A 2 372 6 HOH HOH . 
E 3 HOH A 3 373 8 HOH HOH . 
E 3 HOH A 4 374 9 HOH HOH . 
E 3 HOH A 5 375 13 HOH HOH . 
E 3 HOH A 6 376 15 HOH HOH . 
E 3 HOH A 7 377 16 HOH HOH . 
E 3 HOH A 8 378 18 HOH HOH . 
E 3 HOH A 9 379 19 HOH HOH . 
E 3 HOH A 10 380 20 HOH HOH . 
E 3 HOH A 11 381 21 HOH HOH . 
E 3 HOH A 12 382 23 HOH HOH . 
E 3 HOH A 13 383 24 HOH HOH . 
E 3 HOH A 14 384 25 HOH HOH . 
E 3 HOH A 15 385 26 HOH HOH . 
E 3 HOH A 16 386 27 HOH HOH . 
E 3 HOH A 17 387 29 HOH HOH . 
E 3 HOH A 18 388 30 HOH HOH . 
E 3 HOH A 19 389 33 HOH HOH . 
E 3 HOH A 20 390 41 HOH HOH . 
E 3 HOH A 21 391 42 HOH HOH . 
E 3 HOH A 22 392 43 HOH HOH . 
E 3 HOH A 23 393 45 HOH HOH . 
E 3 HOH A 24 394 46 HOH HOH . 
E 3 HOH A 25 395 47 HOH HOH . 
E 3 HOH A 26 396 49 HOH HOH . 
E 3 HOH A 27 397 51 HOH HOH . 
E 3 HOH A 28 398 53 HOH HOH . 
E 3 HOH A 29 399 54 HOH HOH . 
E 3 HOH A 30 400 55 HOH HOH . 
E 3 HOH A 31 401 57 HOH HOH . 
E 3 HOH A 32 402 58 HOH HOH . 
E 3 HOH A 33 403 60 HOH HOH . 
E 3 HOH A 34 404 63 HOH HOH . 
E 3 HOH A 35 405 73 HOH HOH . 
E 3 HOH A 36 406 74 HOH HOH . 
E 3 HOH A 37 407 75 HOH HOH . 
E 3 HOH A 38 408 76 HOH HOH . 
E 3 HOH A 39 409 78 HOH HOH . 
E 3 HOH A 40 410 85 HOH HOH . 
E 3 HOH A 41 411 87 HOH HOH . 
E 3 HOH A 42 412 88 HOH HOH . 
E 3 HOH A 43 413 89 HOH HOH . 
E 3 HOH A 44 414 90 HOH HOH . 
E 3 HOH A 45 415 91 HOH HOH . 
E 3 HOH A 46 416 92 HOH HOH . 
E 3 HOH A 47 417 93 HOH HOH . 
E 3 HOH A 48 418 97 HOH HOH . 
E 3 HOH A 49 419 98 HOH HOH . 
E 3 HOH A 50 420 99 HOH HOH . 
E 3 HOH A 51 421 101 HOH HOH . 
E 3 HOH A 52 422 104 HOH HOH . 
E 3 HOH A 53 423 105 HOH HOH . 
E 3 HOH A 54 424 110 HOH HOH . 
E 3 HOH A 55 425 111 HOH HOH . 
E 3 HOH A 56 426 112 HOH HOH . 
E 3 HOH A 57 427 113 HOH HOH . 
E 3 HOH A 58 428 114 HOH HOH . 
E 3 HOH A 59 429 115 HOH HOH . 
E 3 HOH A 60 430 118 HOH HOH . 
E 3 HOH A 61 431 121 HOH HOH . 
E 3 HOH A 62 432 123 HOH HOH . 
E 3 HOH A 63 433 124 HOH HOH . 
E 3 HOH A 64 434 128 HOH HOH . 
E 3 HOH A 65 435 129 HOH HOH . 
E 3 HOH A 66 436 130 HOH HOH . 
E 3 HOH A 67 437 131 HOH HOH . 
E 3 HOH A 68 438 134 HOH HOH . 
E 3 HOH A 69 439 137 HOH HOH . 
E 3 HOH A 70 440 138 HOH HOH . 
E 3 HOH A 71 441 140 HOH HOH . 
E 3 HOH A 72 442 141 HOH HOH . 
E 3 HOH A 73 443 142 HOH HOH . 
E 3 HOH A 74 444 147 HOH HOH . 
E 3 HOH A 75 445 149 HOH HOH . 
E 3 HOH A 76 446 150 HOH HOH . 
E 3 HOH A 77 447 152 HOH HOH . 
E 3 HOH A 78 448 153 HOH HOH . 
E 3 HOH A 79 449 160 HOH HOH . 
E 3 HOH A 80 450 162 HOH HOH . 
E 3 HOH A 81 451 164 HOH HOH . 
E 3 HOH A 82 452 165 HOH HOH . 
E 3 HOH A 83 453 166 HOH HOH . 
E 3 HOH A 84 454 170 HOH HOH . 
E 3 HOH A 85 455 171 HOH HOH . 
E 3 HOH A 86 456 172 HOH HOH . 
E 3 HOH A 87 457 173 HOH HOH . 
E 3 HOH A 88 458 176 HOH HOH . 
E 3 HOH A 89 459 180 HOH HOH . 
E 3 HOH A 90 460 181 HOH HOH . 
E 3 HOH A 91 461 184 HOH HOH . 
E 3 HOH A 92 462 185 HOH HOH . 
E 3 HOH A 93 463 187 HOH HOH . 
E 3 HOH A 94 464 188 HOH HOH . 
E 3 HOH A 95 465 192 HOH HOH . 
E 3 HOH A 96 466 194 HOH HOH . 
E 3 HOH A 97 467 195 HOH HOH . 
F 3 HOH B 1 371 1 HOH HOH . 
F 3 HOH B 2 372 3 HOH HOH . 
F 3 HOH B 3 373 4 HOH HOH . 
F 3 HOH B 4 374 5 HOH HOH . 
F 3 HOH B 5 375 7 HOH HOH . 
F 3 HOH B 6 376 10 HOH HOH . 
F 3 HOH B 7 377 11 HOH HOH . 
F 3 HOH B 8 378 12 HOH HOH . 
F 3 HOH B 9 379 14 HOH HOH . 
F 3 HOH B 10 380 17 HOH HOH . 
F 3 HOH B 11 381 22 HOH HOH . 
F 3 HOH B 12 382 28 HOH HOH . 
F 3 HOH B 13 383 31 HOH HOH . 
F 3 HOH B 14 384 32 HOH HOH . 
F 3 HOH B 15 385 34 HOH HOH . 
F 3 HOH B 16 386 35 HOH HOH . 
F 3 HOH B 17 387 36 HOH HOH . 
F 3 HOH B 18 388 37 HOH HOH . 
F 3 HOH B 19 389 38 HOH HOH . 
F 3 HOH B 20 390 39 HOH HOH . 
F 3 HOH B 21 391 40 HOH HOH . 
F 3 HOH B 22 392 44 HOH HOH . 
F 3 HOH B 23 393 48 HOH HOH . 
F 3 HOH B 24 394 50 HOH HOH . 
F 3 HOH B 25 395 52 HOH HOH . 
F 3 HOH B 26 396 56 HOH HOH . 
F 3 HOH B 27 397 59 HOH HOH . 
F 3 HOH B 28 398 61 HOH HOH . 
F 3 HOH B 29 399 62 HOH HOH . 
F 3 HOH B 30 400 64 HOH HOH . 
F 3 HOH B 31 401 65 HOH HOH . 
F 3 HOH B 32 402 66 HOH HOH . 
F 3 HOH B 33 403 67 HOH HOH . 
F 3 HOH B 34 404 68 HOH HOH . 
F 3 HOH B 35 405 69 HOH HOH . 
F 3 HOH B 36 406 70 HOH HOH . 
F 3 HOH B 37 407 71 HOH HOH . 
F 3 HOH B 38 408 72 HOH HOH . 
F 3 HOH B 39 409 77 HOH HOH . 
F 3 HOH B 40 410 79 HOH HOH . 
F 3 HOH B 41 411 80 HOH HOH . 
F 3 HOH B 42 412 81 HOH HOH . 
F 3 HOH B 43 413 82 HOH HOH . 
F 3 HOH B 44 414 83 HOH HOH . 
F 3 HOH B 45 415 84 HOH HOH . 
F 3 HOH B 46 416 86 HOH HOH . 
F 3 HOH B 47 417 94 HOH HOH . 
F 3 HOH B 48 418 95 HOH HOH . 
F 3 HOH B 49 419 96 HOH HOH . 
F 3 HOH B 50 420 100 HOH HOH . 
F 3 HOH B 51 421 102 HOH HOH . 
F 3 HOH B 52 422 103 HOH HOH . 
F 3 HOH B 53 423 106 HOH HOH . 
F 3 HOH B 54 424 107 HOH HOH . 
F 3 HOH B 55 425 108 HOH HOH . 
F 3 HOH B 56 426 109 HOH HOH . 
F 3 HOH B 57 427 116 HOH HOH . 
F 3 HOH B 58 428 117 HOH HOH . 
F 3 HOH B 59 429 119 HOH HOH . 
F 3 HOH B 60 430 120 HOH HOH . 
F 3 HOH B 61 431 122 HOH HOH . 
F 3 HOH B 62 432 125 HOH HOH . 
F 3 HOH B 63 433 126 HOH HOH . 
F 3 HOH B 64 434 127 HOH HOH . 
F 3 HOH B 65 435 132 HOH HOH . 
F 3 HOH B 66 436 133 HOH HOH . 
F 3 HOH B 67 437 135 HOH HOH . 
F 3 HOH B 68 438 136 HOH HOH . 
F 3 HOH B 69 439 139 HOH HOH . 
F 3 HOH B 70 440 143 HOH HOH . 
F 3 HOH B 71 441 144 HOH HOH . 
F 3 HOH B 72 442 145 HOH HOH . 
F 3 HOH B 73 443 146 HOH HOH . 
F 3 HOH B 74 444 148 HOH HOH . 
F 3 HOH B 75 445 151 HOH HOH . 
F 3 HOH B 76 446 154 HOH HOH . 
F 3 HOH B 77 447 155 HOH HOH . 
F 3 HOH B 78 448 156 HOH HOH . 
F 3 HOH B 79 449 157 HOH HOH . 
F 3 HOH B 80 450 158 HOH HOH . 
F 3 HOH B 81 451 159 HOH HOH . 
F 3 HOH B 82 452 161 HOH HOH . 
F 3 HOH B 83 453 163 HOH HOH . 
F 3 HOH B 84 454 167 HOH HOH . 
F 3 HOH B 85 455 168 HOH HOH . 
F 3 HOH B 86 456 169 HOH HOH . 
F 3 HOH B 87 457 174 HOH HOH . 
F 3 HOH B 88 458 175 HOH HOH . 
F 3 HOH B 89 459 177 HOH HOH . 
F 3 HOH B 90 460 178 HOH HOH . 
F 3 HOH B 91 461 179 HOH HOH . 
F 3 HOH B 92 462 182 HOH HOH . 
F 3 HOH B 93 463 183 HOH HOH . 
F 3 HOH B 94 464 186 HOH HOH . 
F 3 HOH B 95 465 189 HOH HOH . 
F 3 HOH B 96 466 190 HOH HOH . 
F 3 HOH B 97 467 191 HOH HOH . 
F 3 HOH B 98 468 193 HOH HOH . 
F 3 HOH B 99 469 196 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 . . . D 2 -4.599 -5.359 1.965 1 18.9 ? N1 PLP 370 B 1 
HETATM 2 C C2 PLP . . . D 2 -4.248 -5.187 3.263 1 22.14 ? C2 PLP 370 B 1 
HETATM 3 C C2A PLP . . . D 2 -3.555 -3.882 3.658 1 19.3 ? C2A PLP 370 B 1 
HETATM 4 C C3 PLP . . . D 2 -4.535 -6.202 4.185 1 20.02 ? C3 PLP 370 B 1 
HETATM 5 O O3 PLP . . . D 2 -4.182 -6.022 5.474 1 20 ? O3 PLP 370 B 1 
HETATM 6 C C4 PLP . . . D 2 -5.176 -7.389 3.768 1 20.04 ? C4 PLP 370 B 1 
HETATM 7 C C4A PLP . . . D 2 -5.462 -8.491 4.825 1 24.14 ? C4A PLP 370 B 1 
HETATM 8 C C5 PLP . . . D 2 -5.534 -7.511 2.388 1 19.44 ? C5 PLP 370 B 1 
HETATM 9 C C6 PLP . . . D 2 -5.233 -6.493 1.524 1 20.6 ? C6 PLP 370 B 1 
HETATM 10 C C5A PLP . . . D 2 -6.28 -8.663 1.786 1 21.59 ? C5A PLP 370 B 1 
HETATM 11 O O4P PLP . . . D 2 -5.767 -9.926 2.034 1 20.41 ? O4P PLP 370 B 1 
HETATM 12 P P PLP . . . D 2 -6.724 -11.166 2.173 1 15.21 ? P PLP 370 B 1 
HETATM 13 O O1P PLP . . . D 2 -7.546 -11.13 3.365 1 18.93 ? O1P PLP 370 B 1 
HETATM 14 O O2P PLP . . . D 2 -5.64 -12.262 2.405 1 14.09 ? O2P PLP 370 B 1 
HETATM 15 O O3P PLP . . . D 2 -7.324 -11.446 0.857 1 15.28 ? O3P PLP 370 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           15 
#