data_5YKO # _model_server_result.job_id 2JrNiuqeyh7YZtlvCfLnqQ _model_server_result.datetime_utc '2024-11-05 00:18:02' _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 5yko # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":803}' # _entry.id 5YKO # _exptl.entry_id 5YKO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 147.086 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-OXALYLGLYCINE _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 5YKO _cell.length_a 68.639 _cell.length_b 100.113 _cell.length_c 109.405 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 5 _struct_asym.id F _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 B C THR 3 P THR 3 1_555 B N M3L 4 P M3L 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 B C M3L 4 P M3L 4 1_555 B N GLN 5 P GLN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? metalc ? metalc1 A NE2 HIS 276 A HIS 309 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc2 A OE1 GLU 278 A GLU 311 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc3 A NE2 HIS 364 A HIS 397 1_555 C NI NI . A NI 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 A SG CYS 486 A CYS 519 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc5 A SG CYS 489 A CYS 522 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc6 A SG CYS 500 A CYS 533 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc7 A SG CYS 502 A CYS 535 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc8 A SG CYS 509 A CYS 542 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc9 A SG CYS 517 A CYS 550 1_555 E ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc10 C NI NI . A NI 800 1_555 F O2' OGA . A OGA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 C NI NI . A NI 800 1_555 F O1 OGA . A OGA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? # _chem_comp.formula 'C4 H5 N O5' _chem_comp.formula_weight 147.086 _chem_comp.id OGA _chem_comp.mon_nstd_flag . _chem_comp.name N-OXALYLGLYCINE _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 C1 C2 OGA sing 268 n n C1 O1 OGA doub 269 n n C1 O2 OGA sing 270 n n C2 O2' OGA doub 271 n n C2 N1 OGA sing 272 n n C4 C5 OGA sing 273 n n C4 N1 OGA sing 274 n n C4 H4C1 OGA sing 275 n n C4 H4C2 OGA sing 276 n n C5 O3 OGA sing 277 n n C5 O4 OGA doub 278 n n O2 H2 OGA sing 279 n n O3 H3 OGA sing 280 n n N1 H1 OGA sing 281 n n # _atom_sites.entry_id 5YKO _atom_sites.fract_transf_matrix[1][1] 0.014569 _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] 0.009989 _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] 0.00914 _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 C 3 NI A 1 800 800 NI NI . D 4 ZN A 1 801 801 ZN ZN . E 4 ZN A 1 802 802 ZN ZN . F 5 OGA A 1 803 803 OGA OGA . # 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 C1 OGA . . . F 5 28.293 -11.431 -12.504 1 45.49 ? C1 OGA 803 A 1 HETATM 2 C C2 OGA . . . F 5 26.985 -11.956 -12.883 1 57.57 ? C2 OGA 803 A 1 HETATM 3 C C4 OGA . . . F 5 25.378 -13.774 -12.864 1 46.38 ? C4 OGA 803 A 1 HETATM 4 C C5 OGA . . . F 5 25.241 -15.179 -12.329 1 50.49 ? C5 OGA 803 A 1 HETATM 5 O O1 OGA . . . F 5 28.602 -10.269 -12.848 1 43.67 ? O1 OGA 803 A 1 HETATM 6 O O2 OGA . . . F 5 29.07 -12.156 -11.847 1 33.72 ? O2 OGA 803 A 1 HETATM 7 O O2' OGA . . . F 5 26.221 -11.254 -13.525 1 66.34 ? O2' OGA 803 A 1 HETATM 8 O O3 OGA . . . F 5 26.28 -15.813 -12.044 1 50 ? O3 OGA 803 A 1 HETATM 9 N N1 OGA . . . F 5 26.659 -13.192 -12.515 1 50.79 ? N1 OGA 803 A 1 HETATM 10 O O4 OGA . . . F 5 24.093 -15.655 -12.19 1 51.49 ? O4 OGA 803 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #