data_5E4Z
#
_model_server_result.job_id            jkW_HErXlsJKpWN7o5bnHw 
_model_server_result.datetime_utc      '2024-11-16 22:55:47' 
_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          5e4z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":404}' 
#
_entry.id    5E4Z 
#
_exptl.entry_id    5E4Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            5E4Z 
_cell.length_a            56.29 
_cell.length_b            122.631 
_cell.length_c            127.296 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5E4Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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    1,2,3,4 
#
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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -127.296 
4 'crystal symmetry operation' 4_554 x,-y,-z-1 1 0 0 0 -1 0 0 0 -1 0 0 -127.296 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 210 A LYS 210 1_555 E C4A PLP . A PLP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
metalc ? metalc1 D NA NA . A NA 403 1_555 F O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? 
metalc ? metalc2 D NA NA . A NA 403 1_555 F O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc3 D NA NA . A NA 403 1_555 F O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
#
_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 313 n y 
N1 C6 PLP sing 314 n y 
C2 C2A PLP sing 315 n n 
C2 C3 PLP sing 316 n y 
C2A H2A1 PLP sing 317 n n 
C2A H2A2 PLP sing 318 n n 
C2A H2A3 PLP sing 319 n n 
C3 O3 PLP sing 320 n n 
C3 C4 PLP doub 321 n y 
O3 HO3 PLP sing 322 n n 
C4 C4A PLP sing 323 n n 
C4 C5 PLP sing 324 n y 
C4A O4A PLP doub 325 n n 
C4A H4A PLP sing 326 n n 
C5 C6 PLP doub 327 n y 
C5 C5A PLP sing 328 n n 
C6 H6 PLP sing 329 n n 
C5A O4P PLP sing 330 n n 
C5A H5A1 PLP sing 331 n n 
C5A H5A2 PLP sing 332 n n 
O4P P PLP sing 333 n n 
P O1P PLP doub 334 n n 
P O2P PLP sing 335 n n 
P O3P PLP sing 336 n n 
O2P HOP2 PLP sing 337 n n 
O3P HOP3 PLP sing 338 n n 
#
_atom_sites.entry_id                     5E4Z 
_atom_sites.fract_transf_matrix[1][1]    0.017765 
_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]    0.008155 
_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]    0.007856 
_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
B 2 1PE A 1 401 400 1PE 1PE . 
C 3 PEG A 1 402 1 PEG PEG . 
D 4 NA A 1 403 1 NA NA . 
E 5 PLP A 1 404 210 PLP PLP . 
F 6 HOH A 1 501 107 HOH HOH . 
F 6 HOH A 2 502 90 HOH HOH . 
F 6 HOH A 3 503 39 HOH HOH . 
F 6 HOH A 4 504 85 HOH HOH . 
F 6 HOH A 5 505 8 HOH HOH . 
F 6 HOH A 6 506 57 HOH HOH . 
F 6 HOH A 7 507 17 HOH HOH . 
F 6 HOH A 8 508 86 HOH HOH . 
F 6 HOH A 9 509 6 HOH HOH . 
F 6 HOH A 10 510 78 HOH HOH . 
F 6 HOH A 11 511 24 HOH HOH . 
F 6 HOH A 12 512 52 HOH HOH . 
F 6 HOH A 13 513 83 HOH HOH . 
F 6 HOH A 14 514 81 HOH HOH . 
F 6 HOH A 15 515 75 HOH HOH . 
F 6 HOH A 16 516 55 HOH HOH . 
F 6 HOH A 17 517 60 HOH HOH . 
F 6 HOH A 18 518 67 HOH HOH . 
F 6 HOH A 19 519 76 HOH HOH . 
F 6 HOH A 20 520 54 HOH HOH . 
F 6 HOH A 21 521 45 HOH HOH . 
F 6 HOH A 22 522 21 HOH HOH . 
F 6 HOH A 23 523 12 HOH HOH . 
F 6 HOH A 24 524 37 HOH HOH . 
F 6 HOH A 25 525 10 HOH HOH . 
F 6 HOH A 26 526 65 HOH HOH . 
F 6 HOH A 27 527 68 HOH HOH . 
F 6 HOH A 28 528 28 HOH HOH . 
F 6 HOH A 29 529 31 HOH HOH . 
F 6 HOH A 30 530 77 HOH HOH . 
F 6 HOH A 31 531 104 HOH HOH . 
F 6 HOH A 32 532 9 HOH HOH . 
F 6 HOH A 33 533 33 HOH HOH . 
F 6 HOH A 34 534 48 HOH HOH . 
F 6 HOH A 35 535 22 HOH HOH . 
F 6 HOH A 36 536 11 HOH HOH . 
F 6 HOH A 37 537 49 HOH HOH . 
F 6 HOH A 38 538 56 HOH HOH . 
F 6 HOH A 39 539 5 HOH HOH . 
F 6 HOH A 40 540 63 HOH HOH . 
F 6 HOH A 41 541 91 HOH HOH . 
F 6 HOH A 42 542 64 HOH HOH . 
F 6 HOH A 43 543 59 HOH HOH . 
F 6 HOH A 44 544 46 HOH HOH . 
F 6 HOH A 45 545 27 HOH HOH . 
F 6 HOH A 46 546 29 HOH HOH . 
F 6 HOH A 47 547 38 HOH HOH . 
F 6 HOH A 48 548 20 HOH HOH . 
F 6 HOH A 49 549 98 HOH HOH . 
F 6 HOH A 50 550 16 HOH HOH . 
F 6 HOH A 51 551 19 HOH HOH . 
F 6 HOH A 52 552 14 HOH HOH . 
F 6 HOH A 53 553 13 HOH HOH . 
F 6 HOH A 54 554 35 HOH HOH . 
F 6 HOH A 55 555 71 HOH HOH . 
F 6 HOH A 56 556 18 HOH HOH . 
F 6 HOH A 57 557 23 HOH HOH . 
F 6 HOH A 58 558 51 HOH HOH . 
F 6 HOH A 59 559 43 HOH HOH . 
F 6 HOH A 60 560 70 HOH HOH . 
F 6 HOH A 61 561 30 HOH HOH . 
F 6 HOH A 62 562 66 HOH HOH . 
F 6 HOH A 63 563 41 HOH HOH . 
F 6 HOH A 64 564 69 HOH HOH . 
F 6 HOH A 65 565 36 HOH HOH . 
F 6 HOH A 66 566 89 HOH HOH . 
F 6 HOH A 67 567 94 HOH HOH . 
F 6 HOH A 68 568 34 HOH HOH . 
F 6 HOH A 69 569 79 HOH HOH . 
F 6 HOH A 70 570 1 HOH HOH . 
F 6 HOH A 71 571 58 HOH HOH . 
F 6 HOH A 72 572 102 HOH HOH . 
F 6 HOH A 73 573 15 HOH HOH . 
F 6 HOH A 74 574 2 HOH HOH . 
F 6 HOH A 75 575 50 HOH HOH . 
F 6 HOH A 76 576 72 HOH HOH . 
F 6 HOH A 77 577 32 HOH HOH . 
F 6 HOH A 78 578 42 HOH HOH . 
F 6 HOH A 79 579 95 HOH HOH . 
F 6 HOH A 80 580 44 HOH HOH . 
F 6 HOH A 81 581 7 HOH HOH . 
F 6 HOH A 82 582 40 HOH HOH . 
F 6 HOH A 83 583 26 HOH HOH . 
F 6 HOH A 84 584 84 HOH HOH . 
F 6 HOH A 85 585 62 HOH HOH . 
F 6 HOH A 86 586 3 HOH HOH . 
F 6 HOH A 87 587 87 HOH HOH . 
F 6 HOH A 88 588 82 HOH HOH . 
F 6 HOH A 89 589 108 HOH HOH . 
F 6 HOH A 90 590 80 HOH HOH . 
F 6 HOH A 91 591 93 HOH HOH . 
F 6 HOH A 92 592 74 HOH HOH . 
F 6 HOH A 93 593 73 HOH HOH . 
F 6 HOH A 94 594 25 HOH HOH . 
F 6 HOH A 95 595 4 HOH HOH . 
F 6 HOH A 96 596 101 HOH HOH . 
F 6 HOH A 97 597 97 HOH HOH . 
F 6 HOH A 98 598 103 HOH HOH . 
F 6 HOH A 99 599 106 HOH HOH . 
F 6 HOH A 100 600 96 HOH HOH . 
F 6 HOH A 101 601 47 HOH HOH . 
F 6 HOH A 102 602 99 HOH HOH . 
F 6 HOH A 103 603 88 HOH HOH . 
F 6 HOH A 104 604 105 HOH HOH . 
F 6 HOH A 105 605 61 HOH HOH . 
F 6 HOH A 106 606 100 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 5 -4.671 -21.366 -49.369 1 38.4 ? N1 PLP 404 A 1 
HETATM 2 C C2 PLP . . . E 5 -5.359 -20.663 -48.475 1 40.09 ? C2 PLP 404 A 1 
HETATM 3 C C2A PLP . . . E 5 -5.241 -21.026 -46.961 1 38.53 ? C2A PLP 404 A 1 
HETATM 4 C C3 PLP . . . E 5 -6.186 -19.583 -48.904 1 42.47 ? C3 PLP 404 A 1 
HETATM 5 O O3 PLP . . . E 5 -6.894 -18.869 -47.921 1 44 ? O3 PLP 404 A 1 
HETATM 6 C C4 PLP . . . E 5 -6.287 -19.252 -50.247 1 41.77 ? C4 PLP 404 A 1 
HETATM 7 C C4A PLP . . . E 5 -7.237 -18.012 -50.695 1 43.02 ? C4A PLP 404 A 1 
HETATM 8 C C5 PLP . . . E 5 -5.571 -19.987 -51.164 1 44.17 ? C5 PLP 404 A 1 
HETATM 9 C C6 PLP . . . E 5 -4.762 -21.049 -50.729 1 43.95 ? C6 PLP 404 A 1 
HETATM 10 C C5A PLP . . . E 5 -5.612 -19.746 -52.707 1 41.55 ? C5A PLP 404 A 1 
HETATM 11 O O4P PLP . . . E 5 -4.939 -18.57 -53.095 1 49.27 ? O4P PLP 404 A 1 
HETATM 12 P P PLP . . . E 5 -5.286 -17.899 -54.456 1 39.56 ? P PLP 404 A 1 
HETATM 13 O O1P PLP . . . E 5 -5.121 -18.889 -55.561 1 37.2 ? O1P PLP 404 A 1 
HETATM 14 O O2P PLP . . . E 5 -6.696 -17.468 -54.4 1 39.17 ? O2P PLP 404 A 1 
HETATM 15 O O3P PLP . . . E 5 -4.31 -16.737 -54.659 1 34.55 ? O3P PLP 404 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           27 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           15 
#