data_1EKV
#
_model_server_result.job_id            MPL8w8KktyS8x63QL17EaA 
_model_server_result.datetime_utc      '2024-10-11 19:16:04' 
_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          1ekv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":370}' 
#
_entry.id    1EKV 
#
_exptl.entry_id    1EKV 
_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         120 
_cell.entry_id            1EKV 
_cell.length_a            83.74 
_cell.length_b            83.74 
_cell.length_c            104.81 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1EKV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32' 
#
_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,G,H 
_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 E 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 D C1 TRS . A TRS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? 
covale ? covale2 C C4A PLP . A PLP 370 1_555 D N TRS . A TRS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? 
covale ? covale3 B NZ LYS 202 B LYS 202 1_555 F C1 TRS . B TRS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? 
covale ? covale4 E C4A PLP . B PLP 370 1_555 F N TRS . B TRS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
#
_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                     1EKV 
_atom_sites.fract_transf_matrix[1][1]    0.011942 
_atom_sites.fract_transf_matrix[1][2]    0.006895 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013789 
_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]    0.009541 
_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 3 TRS A 1 371 371 TRS TRS . 
E 2 PLP B 1 370 370 PLP PLP . 
F 3 TRS B 1 371 371 TRS TRS . 
G 4 HOH A 1 372 1 HOH HOH . 
G 4 HOH A 2 373 2 HOH HOH . 
G 4 HOH A 3 374 6 HOH HOH . 
G 4 HOH A 4 375 8 HOH HOH . 
G 4 HOH A 5 376 9 HOH HOH . 
G 4 HOH A 6 377 12 HOH HOH . 
G 4 HOH A 7 378 15 HOH HOH . 
G 4 HOH A 8 379 17 HOH HOH . 
G 4 HOH A 9 380 20 HOH HOH . 
G 4 HOH A 10 381 22 HOH HOH . 
G 4 HOH A 11 382 25 HOH HOH . 
G 4 HOH A 12 383 27 HOH HOH . 
G 4 HOH A 13 384 30 HOH HOH . 
G 4 HOH A 14 385 33 HOH HOH . 
G 4 HOH A 15 386 35 HOH HOH . 
G 4 HOH A 16 387 36 HOH HOH . 
G 4 HOH A 17 388 41 HOH HOH . 
G 4 HOH A 18 389 42 HOH HOH . 
G 4 HOH A 19 390 43 HOH HOH . 
G 4 HOH A 20 391 44 HOH HOH . 
G 4 HOH A 21 392 45 HOH HOH . 
G 4 HOH A 22 393 46 HOH HOH . 
G 4 HOH A 23 394 48 HOH HOH . 
G 4 HOH A 24 395 49 HOH HOH . 
G 4 HOH A 25 396 51 HOH HOH . 
G 4 HOH A 26 397 53 HOH HOH . 
G 4 HOH A 27 398 54 HOH HOH . 
G 4 HOH A 28 399 56 HOH HOH . 
G 4 HOH A 29 400 57 HOH HOH . 
G 4 HOH A 30 401 58 HOH HOH . 
G 4 HOH A 31 402 64 HOH HOH . 
G 4 HOH A 32 403 65 HOH HOH . 
G 4 HOH A 33 404 66 HOH HOH . 
G 4 HOH A 34 405 67 HOH HOH . 
G 4 HOH A 35 406 71 HOH HOH . 
G 4 HOH A 36 407 72 HOH HOH . 
G 4 HOH A 37 408 73 HOH HOH . 
G 4 HOH A 38 409 76 HOH HOH . 
G 4 HOH A 39 410 78 HOH HOH . 
G 4 HOH A 40 411 79 HOH HOH . 
G 4 HOH A 41 412 81 HOH HOH . 
G 4 HOH A 42 413 82 HOH HOH . 
G 4 HOH A 43 414 84 HOH HOH . 
G 4 HOH A 44 415 85 HOH HOH . 
G 4 HOH A 45 416 87 HOH HOH . 
G 4 HOH A 46 417 91 HOH HOH . 
G 4 HOH A 47 418 95 HOH HOH . 
G 4 HOH A 48 419 97 HOH HOH . 
G 4 HOH A 49 420 98 HOH HOH . 
G 4 HOH A 50 421 100 HOH HOH . 
G 4 HOH A 51 422 103 HOH HOH . 
G 4 HOH A 52 423 104 HOH HOH . 
G 4 HOH A 53 424 105 HOH HOH . 
G 4 HOH A 54 425 107 HOH HOH . 
G 4 HOH A 55 426 110 HOH HOH . 
G 4 HOH A 56 427 112 HOH HOH . 
G 4 HOH A 57 428 113 HOH HOH . 
G 4 HOH A 58 429 117 HOH HOH . 
G 4 HOH A 59 430 119 HOH HOH . 
G 4 HOH A 60 431 120 HOH HOH . 
G 4 HOH A 61 432 121 HOH HOH . 
G 4 HOH A 62 433 122 HOH HOH . 
G 4 HOH A 63 434 123 HOH HOH . 
G 4 HOH A 64 435 124 HOH HOH . 
G 4 HOH A 65 436 125 HOH HOH . 
G 4 HOH A 66 437 126 HOH HOH . 
G 4 HOH A 67 438 127 HOH HOH . 
G 4 HOH A 68 439 129 HOH HOH . 
G 4 HOH A 69 440 130 HOH HOH . 
G 4 HOH A 70 441 133 HOH HOH . 
G 4 HOH A 71 442 134 HOH HOH . 
G 4 HOH A 72 443 138 HOH HOH . 
G 4 HOH A 73 444 140 HOH HOH . 
G 4 HOH A 74 445 144 HOH HOH . 
G 4 HOH A 75 446 146 HOH HOH . 
G 4 HOH A 76 447 147 HOH HOH . 
G 4 HOH A 77 448 149 HOH HOH . 
G 4 HOH A 78 449 151 HOH HOH . 
G 4 HOH A 79 450 154 HOH HOH . 
G 4 HOH A 80 451 159 HOH HOH . 
G 4 HOH A 81 452 161 HOH HOH . 
G 4 HOH A 82 453 162 HOH HOH . 
G 4 HOH A 83 454 164 HOH HOH . 
G 4 HOH A 84 455 165 HOH HOH . 
G 4 HOH A 85 456 169 HOH HOH . 
G 4 HOH A 86 457 172 HOH HOH . 
G 4 HOH A 87 458 173 HOH HOH . 
G 4 HOH A 88 459 176 HOH HOH . 
G 4 HOH A 89 460 177 HOH HOH . 
G 4 HOH A 90 461 179 HOH HOH . 
G 4 HOH A 91 462 180 HOH HOH . 
G 4 HOH A 92 463 182 HOH HOH . 
G 4 HOH A 93 464 185 HOH HOH . 
G 4 HOH A 94 465 188 HOH HOH . 
G 4 HOH A 95 466 190 HOH HOH . 
G 4 HOH A 96 467 195 HOH HOH . 
G 4 HOH A 97 468 197 HOH HOH . 
G 4 HOH A 98 469 199 HOH HOH . 
G 4 HOH A 99 470 200 HOH HOH . 
G 4 HOH A 100 471 203 HOH HOH . 
G 4 HOH A 101 472 205 HOH HOH . 
G 4 HOH A 102 473 206 HOH HOH . 
G 4 HOH A 103 474 207 HOH HOH . 
G 4 HOH A 104 475 208 HOH HOH . 
G 4 HOH A 105 476 209 HOH HOH . 
G 4 HOH A 106 477 210 HOH HOH . 
G 4 HOH A 107 478 212 HOH HOH . 
H 4 HOH B 1 372 3 HOH HOH . 
H 4 HOH B 2 373 4 HOH HOH . 
H 4 HOH B 3 374 5 HOH HOH . 
H 4 HOH B 4 375 7 HOH HOH . 
H 4 HOH B 5 376 10 HOH HOH . 
H 4 HOH B 6 377 11 HOH HOH . 
H 4 HOH B 7 378 13 HOH HOH . 
H 4 HOH B 8 379 14 HOH HOH . 
H 4 HOH B 9 380 16 HOH HOH . 
H 4 HOH B 10 381 18 HOH HOH . 
H 4 HOH B 11 382 19 HOH HOH . 
H 4 HOH B 12 383 21 HOH HOH . 
H 4 HOH B 13 384 23 HOH HOH . 
H 4 HOH B 14 385 24 HOH HOH . 
H 4 HOH B 15 386 26 HOH HOH . 
H 4 HOH B 16 387 28 HOH HOH . 
H 4 HOH B 17 388 29 HOH HOH . 
H 4 HOH B 18 389 31 HOH HOH . 
H 4 HOH B 19 390 32 HOH HOH . 
H 4 HOH B 20 391 34 HOH HOH . 
H 4 HOH B 21 392 37 HOH HOH . 
H 4 HOH B 22 393 38 HOH HOH . 
H 4 HOH B 23 394 39 HOH HOH . 
H 4 HOH B 24 395 40 HOH HOH . 
H 4 HOH B 25 396 47 HOH HOH . 
H 4 HOH B 26 397 50 HOH HOH . 
H 4 HOH B 27 398 52 HOH HOH . 
H 4 HOH B 28 399 55 HOH HOH . 
H 4 HOH B 29 400 59 HOH HOH . 
H 4 HOH B 30 401 60 HOH HOH . 
H 4 HOH B 31 402 61 HOH HOH . 
H 4 HOH B 32 403 62 HOH HOH . 
H 4 HOH B 33 404 63 HOH HOH . 
H 4 HOH B 34 405 68 HOH HOH . 
H 4 HOH B 35 406 69 HOH HOH . 
H 4 HOH B 36 407 70 HOH HOH . 
H 4 HOH B 37 408 74 HOH HOH . 
H 4 HOH B 38 409 75 HOH HOH . 
H 4 HOH B 39 410 77 HOH HOH . 
H 4 HOH B 40 411 80 HOH HOH . 
H 4 HOH B 41 412 83 HOH HOH . 
H 4 HOH B 42 413 86 HOH HOH . 
H 4 HOH B 43 414 88 HOH HOH . 
H 4 HOH B 44 415 89 HOH HOH . 
H 4 HOH B 45 416 90 HOH HOH . 
H 4 HOH B 46 417 92 HOH HOH . 
H 4 HOH B 47 418 93 HOH HOH . 
H 4 HOH B 48 419 94 HOH HOH . 
H 4 HOH B 49 420 96 HOH HOH . 
H 4 HOH B 50 421 99 HOH HOH . 
H 4 HOH B 51 422 101 HOH HOH . 
H 4 HOH B 52 423 102 HOH HOH . 
H 4 HOH B 53 424 106 HOH HOH . 
H 4 HOH B 54 425 108 HOH HOH . 
H 4 HOH B 55 426 109 HOH HOH . 
H 4 HOH B 56 427 111 HOH HOH . 
H 4 HOH B 57 428 114 HOH HOH . 
H 4 HOH B 58 429 115 HOH HOH . 
H 4 HOH B 59 430 116 HOH HOH . 
H 4 HOH B 60 431 118 HOH HOH . 
H 4 HOH B 61 432 128 HOH HOH . 
H 4 HOH B 62 433 131 HOH HOH . 
H 4 HOH B 63 434 132 HOH HOH . 
H 4 HOH B 64 435 135 HOH HOH . 
H 4 HOH B 65 436 136 HOH HOH . 
H 4 HOH B 66 437 137 HOH HOH . 
H 4 HOH B 67 438 139 HOH HOH . 
H 4 HOH B 68 439 141 HOH HOH . 
H 4 HOH B 69 440 142 HOH HOH . 
H 4 HOH B 70 441 143 HOH HOH . 
H 4 HOH B 71 442 145 HOH HOH . 
H 4 HOH B 72 443 148 HOH HOH . 
H 4 HOH B 73 444 150 HOH HOH . 
H 4 HOH B 74 445 152 HOH HOH . 
H 4 HOH B 75 446 153 HOH HOH . 
H 4 HOH B 76 447 155 HOH HOH . 
H 4 HOH B 77 448 156 HOH HOH . 
H 4 HOH B 78 449 157 HOH HOH . 
H 4 HOH B 79 450 158 HOH HOH . 
H 4 HOH B 80 451 160 HOH HOH . 
H 4 HOH B 81 452 163 HOH HOH . 
H 4 HOH B 82 453 166 HOH HOH . 
H 4 HOH B 83 454 167 HOH HOH . 
H 4 HOH B 84 455 168 HOH HOH . 
H 4 HOH B 85 456 170 HOH HOH . 
H 4 HOH B 86 457 171 HOH HOH . 
H 4 HOH B 87 458 174 HOH HOH . 
H 4 HOH B 88 459 175 HOH HOH . 
H 4 HOH B 89 460 178 HOH HOH . 
H 4 HOH B 90 461 181 HOH HOH . 
H 4 HOH B 91 462 183 HOH HOH . 
H 4 HOH B 92 463 184 HOH HOH . 
H 4 HOH B 93 464 186 HOH HOH . 
H 4 HOH B 94 465 187 HOH HOH . 
H 4 HOH B 95 466 189 HOH HOH . 
H 4 HOH B 96 467 191 HOH HOH . 
H 4 HOH B 97 468 192 HOH HOH . 
H 4 HOH B 98 469 193 HOH HOH . 
H 4 HOH B 99 470 194 HOH HOH . 
H 4 HOH B 100 471 196 HOH HOH . 
H 4 HOH B 101 472 198 HOH HOH . 
H 4 HOH B 102 473 201 HOH HOH . 
H 4 HOH B 103 474 202 HOH HOH . 
H 4 HOH B 104 475 204 HOH HOH . 
H 4 HOH B 105 476 211 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 . . . E 2 28.711 27.042 -0.47 1 20.54 ? N1 PLP 370 B 1 
HETATM 2 C C2 PLP . . . E 2 28.439 25.768 -0.948 1 21.16 ? C2 PLP 370 B 1 
HETATM 3 C C2A PLP . . . E 2 27.007 25.387 -1.345 1 17.9 ? C2A PLP 370 B 1 
HETATM 4 C C3 PLP . . . E 2 29.478 24.83 -1.05 1 21.24 ? C3 PLP 370 B 1 
HETATM 5 O O3 PLP . . . E 2 29.214 23.585 -1.528 1 21.15 ? O3 PLP 370 B 1 
HETATM 6 C C4 PLP . . . E 2 30.811 25.174 -0.68 1 22.83 ? C4 PLP 370 B 1 
HETATM 7 C C4A PLP . . . E 2 31.986 24.094 -0.798 1 24.3 ? C4A PLP 370 B 1 
HETATM 8 C C5 PLP . . . E 2 31.065 26.506 -0.192 1 21.33 ? C5 PLP 370 B 1 
HETATM 9 C C6 PLP . . . E 2 30.001 27.414 -0.104 1 22.3 ? C6 PLP 370 B 1 
HETATM 10 C C5A PLP . . . E 2 32.492 26.974 0.223 1 20.98 ? C5A PLP 370 B 1 
HETATM 11 O O4P PLP . . . E 2 32.978 26.5 1.463 1 15.51 ? O4P PLP 370 B 1 
HETATM 12 P P PLP . . . E 2 34.509 26.38 1.753 1 17.74 ? P PLP 370 B 1 
HETATM 13 O O1P PLP . . . E 2 35 25.366 0.83 1 11.7 ? O1P PLP 370 B 1 
HETATM 14 O O2P PLP . . . E 2 34.629 25.814 3.195 1 12.32 ? O2P PLP 370 B 1 
HETATM 15 O O3P PLP . . . E 2 35.143 27.727 1.79 1 17.05 ? 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    14 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           15 
#