data_1ZOB
#
_model_server_result.job_id            g2osDoYlVxLwC-xmLHsekw 
_model_server_result.datetime_utc      '2024-10-11 08:25:09' 
_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          1zob 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":434}' 
#
_entry.id    1ZOB 
#
_exptl.entry_id    1ZOB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          4 
_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         120 
_cell.entry_id            1ZOB 
_cell.length_a            150.553 
_cell.length_b            150.553 
_cell.length_c            84.703 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZOB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        181 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 64 2 2' 
#
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 
PISA,PQS tetrameric 4 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,B,C,D,E,F 1 1 
A,B,C,D,E,F 2 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 75.2765 130.382723 0 
3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.234333 
4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 75.2765 130.382723 28.234333 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 272 A LYS 272 1_555 D C4A PLP . A PLP 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? 
metalc ? metalc1 A O LEU 78 A LEU 78 1_555 C CA CA . A CA 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? 
metalc ? metalc2 A O ALA 95 A ALA 95 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc3 A O THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc4 A OG1 THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.88 ? 
metalc ? metalc5 A O PRO 99 A PRO 99 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? 
metalc ? metalc6 A O LEU 102 A LEU 102 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc7 A O VAL 305 A VAL 305 1_555 C CA CA . A CA 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc8 A OD1 ASP 307 A ASP 307 1_555 C CA CA . A CA 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? 
metalc ? metalc9 B NA NA . A NA 435 1_555 F O HOH . A HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
metalc ? metalc10 C CA CA . A CA 436 1_555 F O HOH . A HOH 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc11 C CA CA . A CA 436 1_555 F O HOH . A HOH 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? 
#
_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 285 n y 
N1 C6 PLP sing 286 n y 
C2 C2A PLP sing 287 n n 
C2 C3 PLP sing 288 n y 
C2A H2A1 PLP sing 289 n n 
C2A H2A2 PLP sing 290 n n 
C2A H2A3 PLP sing 291 n n 
C3 O3 PLP sing 292 n n 
C3 C4 PLP doub 293 n y 
O3 HO3 PLP sing 294 n n 
C4 C4A PLP sing 295 n n 
C4 C5 PLP sing 296 n y 
C4A O4A PLP doub 297 n n 
C4A H4A PLP sing 298 n n 
C5 C6 PLP doub 299 n y 
C5 C5A PLP sing 300 n n 
C6 H6 PLP sing 301 n n 
C5A O4P PLP sing 302 n n 
C5A H5A1 PLP sing 303 n n 
C5A H5A2 PLP sing 304 n n 
O4P P PLP sing 305 n n 
P O1P PLP doub 306 n n 
P O2P PLP sing 307 n n 
P O3P PLP sing 308 n n 
O2P HOP2 PLP sing 309 n n 
O3P HOP3 PLP sing 310 n n 
#
_atom_sites.entry_id                     1ZOB 
_atom_sites.fract_transf_matrix[1][1]    0.006642 
_atom_sites.fract_transf_matrix[1][2]    0.003835 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00767 
_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]    0.011806 
_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 NA A 1 435 435 NA NA . 
C 3 CA A 1 436 436 CA CA . 
D 4 PLP A 1 434 434 PLP PLP . 
E 5 MES A 1 437 437 MES MES . 
F 6 HOH A 1 438 438 HOH WAT . 
F 6 HOH A 2 439 439 HOH WAT . 
F 6 HOH A 3 440 440 HOH WAT . 
F 6 HOH A 4 441 441 HOH WAT . 
F 6 HOH A 5 442 442 HOH WAT . 
F 6 HOH A 6 443 443 HOH WAT . 
F 6 HOH A 7 444 444 HOH WAT . 
F 6 HOH A 8 445 445 HOH WAT . 
F 6 HOH A 9 446 446 HOH WAT . 
F 6 HOH A 10 447 447 HOH WAT . 
F 6 HOH A 11 448 448 HOH WAT . 
F 6 HOH A 12 449 449 HOH WAT . 
F 6 HOH A 13 450 450 HOH WAT . 
F 6 HOH A 14 451 451 HOH WAT . 
F 6 HOH A 15 452 452 HOH WAT . 
F 6 HOH A 16 453 453 HOH WAT . 
F 6 HOH A 17 454 454 HOH WAT . 
F 6 HOH A 18 455 455 HOH WAT . 
F 6 HOH A 19 456 456 HOH WAT . 
F 6 HOH A 20 457 457 HOH WAT . 
F 6 HOH A 21 458 458 HOH WAT . 
F 6 HOH A 22 459 459 HOH WAT . 
F 6 HOH A 23 460 460 HOH WAT . 
F 6 HOH A 24 461 461 HOH WAT . 
F 6 HOH A 25 462 462 HOH WAT . 
F 6 HOH A 26 463 463 HOH WAT . 
F 6 HOH A 27 464 464 HOH WAT . 
F 6 HOH A 28 465 465 HOH WAT . 
F 6 HOH A 29 466 466 HOH WAT . 
F 6 HOH A 30 467 467 HOH WAT . 
F 6 HOH A 31 468 468 HOH WAT . 
F 6 HOH A 32 469 469 HOH WAT . 
F 6 HOH A 33 470 470 HOH WAT . 
F 6 HOH A 34 471 471 HOH WAT . 
F 6 HOH A 35 472 472 HOH WAT . 
F 6 HOH A 36 473 473 HOH WAT . 
F 6 HOH A 37 474 474 HOH WAT . 
F 6 HOH A 38 475 475 HOH WAT . 
F 6 HOH A 39 476 476 HOH WAT . 
F 6 HOH A 40 477 477 HOH WAT . 
F 6 HOH A 41 478 478 HOH WAT . 
F 6 HOH A 42 479 479 HOH WAT . 
F 6 HOH A 43 480 480 HOH WAT . 
F 6 HOH A 44 481 481 HOH WAT . 
F 6 HOH A 45 482 482 HOH WAT . 
F 6 HOH A 46 483 483 HOH WAT . 
F 6 HOH A 47 484 484 HOH WAT . 
F 6 HOH A 48 485 485 HOH WAT . 
F 6 HOH A 49 486 486 HOH WAT . 
F 6 HOH A 50 487 487 HOH WAT . 
F 6 HOH A 51 488 488 HOH WAT . 
F 6 HOH A 52 489 489 HOH WAT . 
F 6 HOH A 53 490 490 HOH WAT . 
F 6 HOH A 54 491 491 HOH WAT . 
F 6 HOH A 55 492 492 HOH WAT . 
F 6 HOH A 56 493 493 HOH WAT . 
F 6 HOH A 57 494 494 HOH WAT . 
F 6 HOH A 58 495 495 HOH WAT . 
F 6 HOH A 59 496 496 HOH WAT . 
F 6 HOH A 60 497 497 HOH WAT . 
F 6 HOH A 61 498 498 HOH WAT . 
F 6 HOH A 62 499 499 HOH WAT . 
F 6 HOH A 63 500 500 HOH WAT . 
F 6 HOH A 64 501 501 HOH WAT . 
#
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 4 17.699 52.565 13.214 1 57.04 ? N1 PLP 434 A 1 
HETATM 2 C C2 PLP . . . D 4 16.446 52.734 13.697 1 57.32 ? C2 PLP 434 A 1 
HETATM 3 C C2A PLP . . . D 4 15.521 53.721 13.049 1 57.91 ? C2A PLP 434 A 1 
HETATM 4 C C3 PLP . . . D 4 16.008 51.995 14.819 1 57.03 ? C3 PLP 434 A 1 
HETATM 5 O O3 PLP . . . D 4 14.719 52.174 15.306 1 55.94 ? O3 PLP 434 A 1 
HETATM 6 C C4 PLP . . . D 4 16.89 51.059 15.427 1 57.42 ? C4 PLP 434 A 1 
HETATM 7 C C4A PLP . . . D 4 16.389 50.281 16.623 1 56.16 ? C4A PLP 434 A 1 
HETATM 8 C C5 PLP . . . D 4 18.224 50.913 14.885 1 58.01 ? C5 PLP 434 A 1 
HETATM 9 C C6 PLP . . . D 4 18.571 51.692 13.762 1 57.58 ? C6 PLP 434 A 1 
HETATM 10 C C5A PLP . . . D 4 19.289 49.965 15.453 1 60.59 ? C5A PLP 434 A 1 
HETATM 11 O O4P PLP . . . D 4 19.117 48.572 15.174 1 64.13 ? O4P PLP 434 A 1 
HETATM 12 P P PLP . . . D 4 20.25 47.742 15.885 1 64.11 ? P PLP 434 A 1 
HETATM 13 O O1P PLP . . . D 4 20.029 46.245 15.564 1 64.11 ? O1P PLP 434 A 1 
HETATM 14 O O2P PLP . . . D 4 21.651 48.186 15.369 1 63.13 ? O2P PLP 434 A 1 
HETATM 15 O O3P PLP . . . D 4 20.175 47.956 17.429 1 63.5 ? O3P PLP 434 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           15 
#