data_8PKA
#
_model_server_result.job_id            hU4wjtTPC-Ffdp-jErKnZg 
_model_server_result.datetime_utc      '2024-10-15 13:21:04' 
_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          8pka 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":501}' 
#
_entry.id    8PKA 
#
_exptl.entry_id    8PKA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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            8PKA 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PKA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J 
_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    ? 
_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 
#
_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 205 A LYS 258 1_555 E C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale2 C OG SER 37 C SER 37 1_555 F P24 8Q1 . C 8Q1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? 
metalc ? metalc1 A SG CYS 328 A CYS 381 1_555 G FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc2 D OD1 ASP 39 D ASP 71 1_555 G FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc3 D OD2 ASP 39 D ASP 71 1_555 G FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
metalc ? metalc4 D SG CYS 63 D CYS 95 1_555 G FE FE2 . D FE2 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc5 G FE FE2 . D FE2 201 1_555 J O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_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 339 n y 
N1 C6 PLP sing 340 n y 
C2 C2A PLP sing 341 n n 
C2 C3 PLP sing 342 n y 
C2A H2A1 PLP sing 343 n n 
C2A H2A2 PLP sing 344 n n 
C2A H2A3 PLP sing 345 n n 
C3 O3 PLP sing 346 n n 
C3 C4 PLP doub 347 n y 
O3 HO3 PLP sing 348 n n 
C4 C4A PLP sing 349 n n 
C4 C5 PLP sing 350 n y 
C4A O4A PLP doub 351 n n 
C4A H4A PLP sing 352 n n 
C5 C6 PLP doub 353 n y 
C5 C5A PLP sing 354 n n 
C6 H6 PLP sing 355 n n 
C5A O4P PLP sing 356 n n 
C5A H5A1 PLP sing 357 n n 
C5A H5A2 PLP sing 358 n n 
O4P P PLP sing 359 n n 
P O1P PLP doub 360 n n 
P O2P PLP sing 361 n n 
P O3P PLP sing 362 n n 
O2P HOP2 PLP sing 363 n n 
O3P HOP3 PLP sing 364 n n 
#
_atom_sites.entry_id                     8PKA 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 5 PLP A 1 501 501 PLP PLP . 
F 6 8Q1 C 1 101 101 8Q1 8Q1 . 
G 7 FE2 D 1 201 201 FE2 FE2 . 
H 8 HOH A 1 601 73 HOH HOH . 
H 8 HOH A 2 602 141 HOH HOH . 
H 8 HOH A 3 603 61 HOH HOH . 
H 8 HOH A 4 604 194 HOH HOH . 
H 8 HOH A 5 605 193 HOH HOH . 
H 8 HOH A 6 606 165 HOH HOH . 
H 8 HOH A 7 607 42 HOH HOH . 
H 8 HOH A 8 608 134 HOH HOH . 
H 8 HOH A 9 609 94 HOH HOH . 
H 8 HOH A 10 610 192 HOH HOH . 
H 8 HOH A 11 611 95 HOH HOH . 
H 8 HOH A 12 612 72 HOH HOH . 
H 8 HOH A 13 613 156 HOH HOH . 
H 8 HOH A 14 614 153 HOH HOH . 
H 8 HOH A 15 615 41 HOH HOH . 
H 8 HOH A 16 616 121 HOH HOH . 
H 8 HOH A 17 617 145 HOH HOH . 
H 8 HOH A 18 618 99 HOH HOH . 
H 8 HOH A 19 619 50 HOH HOH . 
H 8 HOH A 20 620 109 HOH HOH . 
H 8 HOH A 21 621 195 HOH HOH . 
H 8 HOH A 22 622 78 HOH HOH . 
H 8 HOH A 23 623 189 HOH HOH . 
H 8 HOH A 24 624 39 HOH HOH . 
H 8 HOH A 25 625 63 HOH HOH . 
H 8 HOH A 26 626 64 HOH HOH . 
H 8 HOH A 27 627 53 HOH HOH . 
H 8 HOH A 28 628 129 HOH HOH . 
H 8 HOH A 29 629 110 HOH HOH . 
H 8 HOH A 30 630 75 HOH HOH . 
H 8 HOH A 31 631 22 HOH HOH . 
H 8 HOH A 32 632 51 HOH HOH . 
H 8 HOH A 33 633 101 HOH HOH . 
H 8 HOH A 34 634 154 HOH HOH . 
H 8 HOH A 35 635 146 HOH HOH . 
H 8 HOH A 36 636 135 HOH HOH . 
H 8 HOH A 37 637 80 HOH HOH . 
H 8 HOH A 38 638 155 HOH HOH . 
H 8 HOH A 39 639 190 HOH HOH . 
H 8 HOH A 40 640 68 HOH HOH . 
H 8 HOH A 41 641 123 HOH HOH . 
H 8 HOH A 42 642 143 HOH HOH . 
H 8 HOH A 43 643 102 HOH HOH . 
H 8 HOH A 44 644 93 HOH HOH . 
H 8 HOH A 45 645 74 HOH HOH . 
H 8 HOH A 46 646 90 HOH HOH . 
H 8 HOH A 47 647 142 HOH HOH . 
H 8 HOH A 48 648 127 HOH HOH . 
H 8 HOH A 49 649 65 HOH HOH . 
H 8 HOH A 50 650 56 HOH HOH . 
H 8 HOH A 51 651 96 HOH HOH . 
H 8 HOH A 52 652 197 HOH HOH . 
H 8 HOH A 53 653 149 HOH HOH . 
H 8 HOH A 54 654 148 HOH HOH . 
H 8 HOH A 55 655 16 HOH HOH . 
H 8 HOH A 56 656 57 HOH HOH . 
H 8 HOH A 57 657 118 HOH HOH . 
I 8 HOH B 1 101 111 HOH HOH . 
I 8 HOH B 2 102 172 HOH HOH . 
I 8 HOH B 3 103 174 HOH HOH . 
I 8 HOH B 4 104 18 HOH HOH . 
J 8 HOH D 1 301 1 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 98.59 117.53 114.577 1 11.28 ? N1 PLP 501 A 1 
HETATM 2 C C2 PLP . . . E 5 97.736 118.235 113.84 1 11.28 ? C2 PLP 501 A 1 
HETATM 3 C C2A PLP . . . E 5 97.349 119.603 114.295 1 11.28 ? C2A PLP 501 A 1 
HETATM 4 C C3 PLP . . . E 5 97.21 117.707 112.656 1 11.28 ? C3 PLP 501 A 1 
HETATM 5 O O3 PLP . . . E 5 96.346 118.466 111.942 1 11.28 ? O3 PLP 501 A 1 
HETATM 6 C C4 PLP . . . E 5 97.591 116.417 112.243 1 11.28 ? C4 PLP 501 A 1 
HETATM 7 C C4A PLP . . . E 5 97.045 115.861 111.004 1 11.28 ? C4A PLP 501 A 1 
HETATM 8 C C5 PLP . . . E 5 98.491 115.699 113.043 1 11.28 ? C5 PLP 501 A 1 
HETATM 9 C C6 PLP . . . E 5 98.954 116.292 114.185 1 11.28 ? C6 PLP 501 A 1 
HETATM 10 C C5A PLP . . . E 5 98.947 114.316 112.676 1 11.28 ? C5A PLP 501 A 1 
HETATM 11 O O4P PLP . . . E 5 100.079 114.39 111.755 1 11.28 ? O4P PLP 501 A 1 
HETATM 12 P P PLP . . . E 5 100.754 113.071 111.123 1 11.28 ? P PLP 501 A 1 
HETATM 13 O O1P PLP . . . E 5 101.848 113.573 110.205 1 11.28 ? O1P PLP 501 A 1 
HETATM 14 O O2P PLP . . . E 5 101.284 112.272 112.291 1 11.28 ? O2P PLP 501 A 1 
HETATM 15 O O3P PLP . . . E 5 99.643 112.36 110.381 1 11.28 ? O3P PLP 501 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           15 
#