data_3E5P
#
_model_server_result.job_id            TYg6ak5cHuGL-JpGH-QQtA 
_model_server_result.datetime_utc      '2024-10-31 09:33:14' 
_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          3e5p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":390}' 
#
_entry.id    3E5P 
#
_exptl.entry_id    3E5P 
_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    3 
_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            3E5P 
_cell.length_a            94.634 
_cell.length_b            156.516 
_cell.length_c            147.878 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E5P 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_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,D,E,F,I,J,K,L,N 1 1 
B,G,H,M 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 G N N 
? 2 J 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 40 A LYS 40 1_555 D O4A PLP . A PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? 
covale ? covale2 A CE LYS 40 A LYS 40 1_555 D O4A PLP . A PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.942 ? 
covale ? covale3 B NZ LYS 40 B LYS 40 1_555 G O4A PLP . B PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.677 ? 
covale ? covale4 B CE LYS 40 B LYS 40 1_555 G O4A PLP . B PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.997 ? 
covale ? covale5 C NZ LYS 40 C LYS 40 1_555 J O4A PLP . C PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.168 ? 
covale ? covale6 C CE LYS 40 C LYS 40 1_555 J O4A PLP . C PLP 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.058 ? 
#
_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 358 n y 
N1 C6 PLP sing 359 n y 
C2 C2A PLP sing 360 n n 
C2 C3 PLP sing 361 n y 
C2A H2A1 PLP sing 362 n n 
C2A H2A2 PLP sing 363 n n 
C2A H2A3 PLP sing 364 n n 
C3 O3 PLP sing 365 n n 
C3 C4 PLP doub 366 n y 
O3 HO3 PLP sing 367 n n 
C4 C4A PLP sing 368 n n 
C4 C5 PLP sing 369 n y 
C4A O4A PLP doub 370 n n 
C4A H4A PLP sing 371 n n 
C5 C6 PLP doub 372 n y 
C5 C5A PLP sing 373 n n 
C6 H6 PLP sing 374 n n 
C5A O4P PLP sing 375 n n 
C5A H5A1 PLP sing 376 n n 
C5A H5A2 PLP sing 377 n n 
O4P P PLP sing 378 n n 
P O1P PLP doub 379 n n 
P O2P PLP sing 380 n n 
P O3P PLP sing 381 n n 
O2P HOP2 PLP sing 382 n n 
O3P HOP3 PLP sing 383 n n 
#
_atom_sites.entry_id                     3E5P 
_atom_sites.fract_transf_matrix[1][1]    0.010567 
_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]    0.006389 
_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]    0.006762 
_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
D 2 PLP A 1 390 390 PLP PLP . 
E 3 PPI A 1 400 400 PPI PPI . 
F 4 EPE A 1 430 430 EPE EPE . 
G 2 PLP B 1 390 390 PLP PLP . 
H 3 PPI B 1 400 400 PPI PPI . 
I 5 2PE C 1 401 401 2PE 2PE . 
J 2 PLP C 1 390 390 PLP PLP . 
K 3 PPI C 1 400 400 PPI PPI . 
L 6 HOH A 1 431 431 HOH HOH . 
L 6 HOH A 2 432 432 HOH HOH . 
L 6 HOH A 3 433 433 HOH HOH . 
L 6 HOH A 4 434 434 HOH HOH . 
L 6 HOH A 5 435 435 HOH HOH . 
L 6 HOH A 6 436 436 HOH HOH . 
L 6 HOH A 7 437 437 HOH HOH . 
L 6 HOH A 8 438 438 HOH HOH . 
L 6 HOH A 9 439 439 HOH HOH . 
L 6 HOH A 10 440 440 HOH HOH . 
L 6 HOH A 11 441 441 HOH HOH . 
L 6 HOH A 12 442 442 HOH HOH . 
L 6 HOH A 13 443 443 HOH HOH . 
L 6 HOH A 14 444 444 HOH HOH . 
L 6 HOH A 15 445 445 HOH HOH . 
L 6 HOH A 16 446 446 HOH HOH . 
L 6 HOH A 17 447 447 HOH HOH . 
L 6 HOH A 18 448 448 HOH HOH . 
L 6 HOH A 19 449 449 HOH HOH . 
L 6 HOH A 20 450 450 HOH HOH . 
L 6 HOH A 21 451 451 HOH HOH . 
L 6 HOH A 22 452 452 HOH HOH . 
L 6 HOH A 23 453 453 HOH HOH . 
L 6 HOH A 24 454 454 HOH HOH . 
L 6 HOH A 25 455 455 HOH HOH . 
L 6 HOH A 26 456 456 HOH HOH . 
L 6 HOH A 27 457 457 HOH HOH . 
L 6 HOH A 28 458 458 HOH HOH . 
L 6 HOH A 29 459 459 HOH HOH . 
L 6 HOH A 30 460 460 HOH HOH . 
L 6 HOH A 31 461 461 HOH HOH . 
L 6 HOH A 32 462 462 HOH HOH . 
L 6 HOH A 33 463 463 HOH HOH . 
L 6 HOH A 34 464 464 HOH HOH . 
L 6 HOH A 35 465 465 HOH HOH . 
L 6 HOH A 36 466 466 HOH HOH . 
L 6 HOH A 37 467 467 HOH HOH . 
L 6 HOH A 38 468 468 HOH HOH . 
L 6 HOH A 39 469 469 HOH HOH . 
L 6 HOH A 40 470 470 HOH HOH . 
L 6 HOH A 41 471 471 HOH HOH . 
L 6 HOH A 42 472 472 HOH HOH . 
L 6 HOH A 43 473 473 HOH HOH . 
L 6 HOH A 44 474 474 HOH HOH . 
L 6 HOH A 45 475 475 HOH HOH . 
L 6 HOH A 46 476 476 HOH HOH . 
L 6 HOH A 47 477 477 HOH HOH . 
L 6 HOH A 48 478 478 HOH HOH . 
L 6 HOH A 49 479 479 HOH HOH . 
L 6 HOH A 50 480 480 HOH HOH . 
L 6 HOH A 51 481 481 HOH HOH . 
L 6 HOH A 52 482 482 HOH HOH . 
L 6 HOH A 53 483 483 HOH HOH . 
L 6 HOH A 54 484 484 HOH HOH . 
L 6 HOH A 55 485 485 HOH HOH . 
L 6 HOH A 56 486 486 HOH HOH . 
L 6 HOH A 57 487 487 HOH HOH . 
M 6 HOH B 1 401 401 HOH HOH . 
M 6 HOH B 2 402 402 HOH HOH . 
M 6 HOH B 3 403 403 HOH HOH . 
M 6 HOH B 4 404 404 HOH HOH . 
M 6 HOH B 5 405 405 HOH HOH . 
M 6 HOH B 6 406 406 HOH HOH . 
M 6 HOH B 7 407 407 HOH HOH . 
M 6 HOH B 8 408 408 HOH HOH . 
M 6 HOH B 9 409 409 HOH HOH . 
M 6 HOH B 10 410 410 HOH HOH . 
M 6 HOH B 11 411 411 HOH HOH . 
M 6 HOH B 12 412 412 HOH HOH . 
M 6 HOH B 13 413 413 HOH HOH . 
M 6 HOH B 14 414 414 HOH HOH . 
M 6 HOH B 15 415 415 HOH HOH . 
M 6 HOH B 16 416 416 HOH HOH . 
M 6 HOH B 17 417 417 HOH HOH . 
M 6 HOH B 18 418 418 HOH HOH . 
M 6 HOH B 19 419 419 HOH HOH . 
M 6 HOH B 20 420 420 HOH HOH . 
M 6 HOH B 21 421 421 HOH HOH . 
M 6 HOH B 22 422 422 HOH HOH . 
M 6 HOH B 23 423 423 HOH HOH . 
M 6 HOH B 24 424 424 HOH HOH . 
M 6 HOH B 25 425 425 HOH HOH . 
M 6 HOH B 26 426 426 HOH HOH . 
M 6 HOH B 27 427 427 HOH HOH . 
M 6 HOH B 28 428 428 HOH HOH . 
M 6 HOH B 29 429 429 HOH HOH . 
M 6 HOH B 30 430 430 HOH HOH . 
M 6 HOH B 31 431 431 HOH HOH . 
M 6 HOH B 32 432 432 HOH HOH . 
M 6 HOH B 33 433 433 HOH HOH . 
M 6 HOH B 34 434 434 HOH HOH . 
M 6 HOH B 35 435 435 HOH HOH . 
M 6 HOH B 36 436 436 HOH HOH . 
M 6 HOH B 37 437 437 HOH HOH . 
M 6 HOH B 38 438 438 HOH HOH . 
M 6 HOH B 39 439 439 HOH HOH . 
M 6 HOH B 40 440 440 HOH HOH . 
M 6 HOH B 41 441 441 HOH HOH . 
M 6 HOH B 42 442 442 HOH HOH . 
M 6 HOH B 43 444 444 HOH HOH . 
M 6 HOH B 44 445 445 HOH HOH . 
M 6 HOH B 45 446 446 HOH HOH . 
M 6 HOH B 46 447 447 HOH HOH . 
M 6 HOH B 47 448 448 HOH HOH . 
M 6 HOH B 48 449 449 HOH HOH . 
N 6 HOH C 1 411 411 HOH HOH . 
N 6 HOH C 2 412 412 HOH HOH . 
N 6 HOH C 3 413 413 HOH HOH . 
N 6 HOH C 4 414 414 HOH HOH . 
N 6 HOH C 5 415 415 HOH HOH . 
N 6 HOH C 6 416 416 HOH HOH . 
N 6 HOH C 7 417 417 HOH HOH . 
N 6 HOH C 8 418 418 HOH HOH . 
N 6 HOH C 9 419 419 HOH HOH . 
N 6 HOH C 10 420 420 HOH HOH . 
N 6 HOH C 11 421 421 HOH HOH . 
N 6 HOH C 12 422 422 HOH HOH . 
N 6 HOH C 13 423 423 HOH HOH . 
N 6 HOH C 14 424 424 HOH HOH . 
N 6 HOH C 15 425 425 HOH HOH . 
N 6 HOH C 16 426 426 HOH HOH . 
N 6 HOH C 17 427 427 HOH HOH . 
N 6 HOH C 18 428 428 HOH HOH . 
N 6 HOH C 19 429 429 HOH HOH . 
N 6 HOH C 20 430 430 HOH HOH . 
N 6 HOH C 21 431 431 HOH HOH . 
N 6 HOH C 22 432 432 HOH HOH . 
N 6 HOH C 23 433 433 HOH HOH . 
N 6 HOH C 24 434 434 HOH HOH . 
N 6 HOH C 25 435 435 HOH HOH . 
N 6 HOH C 26 436 436 HOH HOH . 
N 6 HOH C 27 437 437 HOH HOH . 
N 6 HOH C 28 438 438 HOH HOH . 
N 6 HOH C 29 439 439 HOH HOH . 
N 6 HOH C 30 440 440 HOH HOH . 
N 6 HOH C 31 441 441 HOH HOH . 
N 6 HOH C 32 442 442 HOH HOH . 
N 6 HOH C 33 443 443 HOH HOH . 
N 6 HOH C 34 444 444 HOH HOH . 
N 6 HOH C 35 445 445 HOH HOH . 
N 6 HOH C 36 446 446 HOH HOH . 
N 6 HOH C 37 447 447 HOH HOH . 
N 6 HOH C 38 448 448 HOH HOH . 
N 6 HOH C 39 450 450 HOH HOH . 
N 6 HOH C 40 451 451 HOH HOH . 
N 6 HOH C 41 452 452 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 . . . G 2 -11.911 -15.062 15.418 1 20 ? N1 PLP 390 B 1 
HETATM 2 C C2 PLP . . . G 2 -11.862 -13.761 15.664 1 20 ? C2 PLP 390 B 1 
HETATM 3 C C2A PLP . . . G 2 -11.948 -13.383 17.061 1 20 ? C2A PLP 390 B 1 
HETATM 4 C C3 PLP . . . G 2 -11.752 -12.825 14.701 1 20 ? C3 PLP 390 B 1 
HETATM 5 O O3 PLP . . . G 2 -11.499 -11.549 15.065 1 20 ? O3 PLP 390 B 1 
HETATM 6 C C4 PLP . . . G 2 -11.687 -13.194 13.381 1 20 ? C4 PLP 390 B 1 
HETATM 7 C C4A PLP . . . G 2 -11.807 -12.1 12.34 1 20 ? C4A PLP 390 B 1 
HETATM 8 O O4A PLP . . . G 2 -12.816 -11.494 11.996 1 20 ? O4A PLP 390 B 1 
HETATM 9 C C5 PLP . . . G 2 -11.707 -14.576 13.145 1 20 ? C5 PLP 390 B 1 
HETATM 10 C C6 PLP . . . G 2 -11.844 -15.488 14.147 1 20 ? C6 PLP 390 B 1 
HETATM 11 C C5A PLP . . . G 2 -11.529 -15.195 11.82 1 20 ? C5A PLP 390 B 1 
HETATM 12 O O4P PLP . . . G 2 -10.509 -16.146 11.681 1 20 ? O4P PLP 390 B 1 
HETATM 13 P P PLP . . . G 2 -9.672 -16.157 10.344 1 20 ? P PLP 390 B 1 
HETATM 14 O O1P PLP . . . G 2 -9.634 -17.39 9.685 1 20 ? O1P PLP 390 B 1 
HETATM 15 O O2P PLP . . . G 2 -8.277 -15.963 10.593 1 20 ? O2P PLP 390 B 1 
HETATM 16 O O3P PLP . . . G 2 -10.281 -15.258 9.396 1 20 ? O3P PLP 390 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           16 
#