data_1PKN
#
_model_server_result.job_id            O_di7jkUiz56JEXMuEknrA 
_model_server_result.datetime_utc      '2024-11-25 11:31:00' 
_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          1pkn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":533}' 
#
_entry.id    1PKN 
#
_exptl.entry_id    1PKN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              88.062 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PYRUVIC ACID' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         94.9 
_cell.angle_beta          93.6 
_cell.angle_gamma         112.3 
_cell.entry_id            1PKN 
_cell.length_a            83.6 
_cell.length_b            109.9 
_cell.length_c            146.8 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1PKN 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_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
metalc ? metalc1 A OD1 ASN 74 A ASN 74 1_555 B K K . A K 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.166 ? 
metalc ? metalc2 A OG SER 76 A SER 76 1_555 B K K . A K 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? 
metalc ? metalc3 A OD1 ASP 112 A ASP 112 1_555 B K K . A K 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? 
metalc ? metalc4 A O THR 113 A THR 113 1_555 B K K . A K 532 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? 
metalc ? metalc5 A OE2 GLU 271 A GLU 271 1_555 C MN MN . A MN 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc6 A OD2 ASP 295 A ASP 295 1_555 C MN MN . A MN 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc7 D OXT PYR . A PYR 533 1_555 C MN MN . A MN 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc8 D O3 PYR . A PYR 533 1_555 C MN MN . A MN 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
#
_chem_comp.formula           'C3 H4 O3' 
_chem_comp.formula_weight    88.062 
_chem_comp.id                PYR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PYRUVIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C O PYR doub 275 n n 
C OXT PYR sing 276 n n 
C CA PYR sing 277 n n 
OXT HXT PYR sing 278 n n 
CA O3 PYR doub 279 n n 
CA CB PYR sing 280 n n 
CB HB1 PYR sing 281 n n 
CB HB2 PYR sing 282 n n 
CB HB3 PYR sing 283 n n 
#
_atom_sites.entry_id                     1PKN 
_atom_sites.fract_transf_matrix[1][1]    0.011962 
_atom_sites.fract_transf_matrix[1][2]    0.004906 
_atom_sites.fract_transf_matrix[1][3]    0.001342 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009835 
_atom_sites.fract_transf_matrix[2][3]    0.001172 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.006874 
_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 K A 1 532 532 K K . 
C 3 MN A 1 534 534 MN MN . 
D 4 PYR A 1 533 533 PYR PYR . 
#
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 C C PYR . . . D 4 29.853 50.736 30.581 1 63.9 ? C PYR 533 A 1 
HETATM 2 O O PYR . . . D 4 30.92 51.328 31.1 1 17.68 ? O PYR 533 A 1 
HETATM 3 O OXT PYR . . . D 4 28.769 51.123 30.115 1 4.64 ? OXT PYR 533 A 1 
HETATM 4 C CA PYR . . . D 4 29.818 49.228 30.808 1 1 ? CA PYR 533 A 1 
HETATM 5 O O3 PYR . . . D 4 28.764 48.769 30.494 1 36.24 ? O3 PYR 533 A 1 
HETATM 6 C CB PYR . . . D 4 31.004 48.646 31.548 1 2.2 ? CB PYR 533 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           6 
#