data_5Y6K # _model_server_result.job_id 0c2TN6Oflb-kBaGoveDypQ _model_server_result.datetime_utc '2025-01-11 20:47:43' _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 5y6k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":701}' # _entry.id 5Y6K # _exptl.entry_id 5Y6K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.046 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONATE ION' _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 5Y6K _cell.length_a 138.012 _cell.length_b 155.752 _cell.length_c 107.554 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y6K _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,C,D,E,F,G _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 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 9 A CYS 9 1_555 A SG CYS 48 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? disulf ? disulf2 A SG CYS 19 A CYS 19 1_555 A SG CYS 39 A CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? disulf ? disulf3 A SG CYS 118 A CYS 118 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 137 A CYS 137 1_555 A SG CYS 331 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? disulf ? disulf5 A SG CYS 158 A CYS 158 1_555 A SG CYS 174 A CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf6 A SG CYS 161 A CYS 161 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? disulf ? disulf7 A SG CYS 171 A CYS 171 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 A SG CYS 227 A CYS 227 1_555 A SG CYS 241 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf9 A SG CYS 339 A CYS 339 1_555 A SG CYS 596 A CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf10 A SG CYS 345 A CYS 345 1_555 A SG CYS 377 A CYS 377 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 A SG CYS 355 A CYS 355 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 A SG CYS 402 A CYS 402 1_555 A SG CYS 674 A CYS 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf13 A SG CYS 450 A CYS 450 1_555 A SG CYS 523 A CYS 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf14 A SG CYS 474 A CYS 474 1_555 A SG CYS 665 A CYS 665 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf15 A SG CYS 484 A CYS 484 1_555 A SG CYS 498 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf16 A SG CYS 495 A CYS 495 1_555 A SG CYS 506 A CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf17 A SG CYS 563 A CYS 563 1_555 A SG CYS 577 A CYS 577 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc1 A OH TYR 188 A TYR 188 1_555 D FE FE . A FE 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc2 A OD1 ASP 392 A ASP 392 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc3 A OH TYR 426 A TYR 426 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 A OH TYR 517 A TYR 517 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc5 A NE2 HIS 585 A HIS 585 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc6 B O7 MLI . A MLI 701 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc7 B O9 MLI . A MLI 701 1_555 C FE FE . A FE 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? metalc ? metalc8 D FE FE . A FE 703 1_555 E N1 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc9 D FE FE . A FE 703 1_555 E O5 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc10 D FE FE . A FE 703 1_555 E O13 8R6 . A 8R6 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? # _chem_comp.formula 'C3 H2 O4 -2' _chem_comp.formula_weight 102.046 _chem_comp.id MLI _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONATE ION' _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 MLI sing 299 n n C1 C3 MLI sing 300 n n C1 H11 MLI sing 301 n n C1 H12 MLI sing 302 n n C2 O6 MLI doub 303 n n C2 O7 MLI sing 304 n n C3 O8 MLI doub 305 n n C3 O9 MLI sing 306 n n # _atom_sites.entry_id 5Y6K _atom_sites.fract_transf_matrix[1][1] 0.007246 _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] 0.00642 _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] 0.009298 _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 MLI A 1 701 702 MLI MLI . C 3 FE A 1 702 1 FE FE . D 3 FE A 1 703 2 FE FE . E 4 8R6 A 1 704 3 8R6 NAC . F 4 8R6 A 1 705 4 8R6 NAC . G 5 HOH A 1 801 5 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 C C1 MLI . . . B 2 36.737 48.114 -7.435 1 64.06 ? C1 MLI 701 A 1 HETATM 2 C C2 MLI . . . B 2 35.663 48.963 -6.803 1 65.77 ? C2 MLI 701 A 1 HETATM 3 C C3 MLI . . . B 2 37.183 46.969 -6.55 1 65.34 ? C3 MLI 701 A 1 HETATM 4 O O6 MLI . . . B 2 34.852 49.535 -7.551 1 59.7 ? O6 MLI 701 A 1 HETATM 5 O O7 MLI . . . B 2 35.619 49.083 -5.551 1 67.79 ? O7 MLI 701 A 1 HETATM 6 O O8 MLI . . . B 2 37.367 45.866 -7.077 1 60.55 ? O8 MLI 701 A 1 HETATM 7 O O9 MLI . . . B 2 37.364 47.155 -5.321 1 69.32 ? O9 MLI 701 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 7 #