data_8K5C
#
_model_server_result.job_id            z3YX8ymfTLns49oprYmDpA 
_model_server_result.datetime_utc      '2025-04-08 01:17:59' 
_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          8k5c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    8K5C 
#
_exptl.entry_id    8K5C 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              155.131 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid' 
_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            8K5C 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K5C 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B 
_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                      2 
_struct_asym.id                             B 
_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
disulf ? disulf1 A SG CYS 131 A CYS 18 1_555 A SG CYS 296 A CYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 132 A CYS 19 1_555 A SG CYS 379 A CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 213 A CYS 100 1_555 A SG CYS 290 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_chem_comp.formula           'C6 H7 N2 O3 1' 
_chem_comp.formula_weight    155.131 
_chem_comp.id                OJX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic 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
C10 C06 OJX sing 235 n n 
O01 N04 OJX sing 236 n n 
C06 N04 OJX doub 237 n y 
C06 C09 OJX sing 238 n y 
N04 C07 OJX sing 239 n y 
C09 N05 OJX doub 240 n y 
C07 C08 OJX doub 241 n y 
N05 C08 OJX sing 242 n y 
C08 C11 OJX sing 243 n n 
C11 O02 OJX doub 244 n n 
C11 O03 OJX sing 245 n n 
C07 H1 OJX sing 246 n n 
C09 H2 OJX sing 247 n n 
C10 H3 OJX sing 248 n n 
C10 H4 OJX sing 249 n n 
C10 H5 OJX sing 250 n n 
O03 H7 OJX sing 251 n n 
O01 H6 OJX sing 252 n n 
#
_atom_sites.entry_id                     8K5C 
_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 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           OJX 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      401 
_pdbx_nonpoly_scheme.auth_seq_num     301 
_pdbx_nonpoly_scheme.pdb_mon_id       OJX 
_pdbx_nonpoly_scheme.auth_mon_id      ACP 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C06 OJX . . . B 2 117.154 114.475 162.955 1 38.65 ? C06 OJX 401 A 1 
HETATM 2 C C07 OJX . . . B 2 118.461 113.482 161.375 1 37.3 ? C07 OJX 401 A 1 
HETATM 3 C C08 OJX . . . B 2 118.787 114.736 160.891 1 33.42 ? C08 OJX 401 A 1 
HETATM 4 C C09 OJX . . . B 2 117.475 115.733 162.48 1 40.82 ? C09 OJX 401 A 1 
HETATM 5 C C10 OJX . . . B 2 116.211 114.349 164.143 1 41.35 ? C10 OJX 401 A 1 
HETATM 6 C C11 OJX . . . B 2 119.73 114.868 159.704 1 37.08 ? C11 OJX 401 A 1 
HETATM 7 N N04 OJX . . . B 2 117.644 113.383 162.405 1 39.89 ? N04 OJX 401 A 1 
HETATM 8 N N05 OJX . . . B 2 118.293 115.821 161.451 1 39.5 ? N05 OJX 401 A 1 
HETATM 9 O O01 OJX . . . B 2 117.296 112.125 162.914 1 49.46 ? O01 OJX 401 A 1 
HETATM 10 O O02 OJX . . . B 2 119.777 115.943 159.053 1 31.64 ? O02 OJX 401 A 1 
HETATM 11 O O03 OJX . . . B 2 120.463 113.902 159.374 1 53.19 ? O03 OJX 401 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           11 
#