data_7GPB
#
_model_server_result.job_id            ouqz-qk1PeFnWF3m5nQVzQ 
_model_server_result.datetime_utc      '2024-11-26 18:07:59' 
_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          7gpb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":999}' 
#
_entry.id    7GPB 
#
_exptl.entry_id    7GPB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              247.142 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "PYRIDOXAL-5'-PHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.35 
_cell.angle_gamma         90 
_cell.entry_id            7GPB 
_cell.length_a            119 
_cell.length_b            190 
_cell.length_c            88.2 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7GPB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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,G,H,I,J,K,L,M,N,O,P,Q,R,S 
_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
? 3 G N N 
? 3 K N N 
? 3 O N N 
? 3 R 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 680 A LYS 680 1_555 G C4A PLP . A PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? 
covale ? covale2 B NZ LYS 680 B LYS 680 1_555 K C4A PLP . B PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? 
covale ? covale3 C NZ LYS 680 C LYS 680 1_555 O C4A PLP . C PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 ? 
covale ? covale4 D NZ LYS 680 D LYS 680 1_555 R C4A PLP . D PLP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
#
_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' 
#
_atom_sites.entry_id                     7GPB 
_atom_sites.fract_transf_matrix[1][1]    0.008403 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002951 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005263 
_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]    0.012017 
_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 2 SO4 A 1 900 900 SO4 SO4 . 
F 2 SO4 A 1 901 901 SO4 SO4 . 
G 3 PLP A 1 999 999 PLP PLP . 
H 4 AMP A 1 920 920 AMP AMP . 
I 2 SO4 B 1 900 900 SO4 SO4 . 
J 2 SO4 B 1 901 901 SO4 SO4 . 
K 3 PLP B 1 999 999 PLP PLP . 
L 4 AMP B 1 920 920 AMP AMP . 
M 2 SO4 C 1 900 900 SO4 SO4 . 
N 2 SO4 C 1 901 901 SO4 SO4 . 
O 3 PLP C 1 999 999 PLP PLP . 
P 4 AMP C 1 920 920 AMP AMP . 
Q 2 SO4 D 1 900 900 SO4 SO4 . 
R 3 PLP D 1 999 999 PLP PLP . 
S 4 AMP D 1 920 920 AMP AMP . 
#
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 . . . R 3 64.272 46.251 8.787 1 42.76 ? N1 PLP 999 D 1 
HETATM 2 C C2 PLP . . . R 3 65.173 47.255 8.805 1 38.26 ? C2 PLP 999 D 1 
HETATM 3 C C2A PLP . . . R 3 66.572 46.907 9.134 1 38.1 ? C2A PLP 999 D 1 
HETATM 4 C C3 PLP . . . R 3 64.78 48.564 8.584 1 37.48 ? C3 PLP 999 D 1 
HETATM 5 O O3 PLP . . . R 3 65.697 49.595 8.625 1 35.3 ? O3 PLP 999 D 1 
HETATM 6 C C4 PLP . . . R 3 63.464 48.818 8.275 1 40.38 ? C4 PLP 999 D 1 
HETATM 7 C C4A PLP . . . R 3 62.999 50.228 7.981 1 32.53 ? C4A PLP 999 D 1 
HETATM 8 C C5 PLP . . . R 3 62.536 47.759 8.272 1 42.79 ? C5 PLP 999 D 1 
HETATM 9 C C6 PLP . . . R 3 62.965 46.489 8.5 1 43.11 ? C6 PLP 999 D 1 
HETATM 10 C C5A PLP . . . R 3 61.073 48.003 8.008 1 41.95 ? C5A PLP 999 D 1 
HETATM 11 O O4P PLP . . . R 3 60.073 46.952 8.022 1 36.44 ? O4P PLP 999 D 1 
HETATM 12 P P PLP . . . R 3 58.519 47.347 7.688 1 37.2 ? P PLP 999 D 1 
HETATM 13 O O1P PLP . . . R 3 58.166 48.512 8.53 1 26.18 ? O1P PLP 999 D 1 
HETATM 14 O O2P PLP . . . R 3 58.47 47.663 6.24 1 32.52 ? O2P PLP 999 D 1 
HETATM 15 O O3P PLP . . . R 3 57.71 46.152 7.954 1 43.51 ? O3P PLP 999 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           15 
#