data_5KYM # _model_server_result.job_id sC07DiTMXi2AIjfX0Yyp9w _model_server_result.datetime_utc '2024-11-05 01:01:39' _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 5kym # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":305}' # _entry.id 5KYM # _exptl.entry_id 5KYM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 128.255 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description nonane _entity.pdbx_number_of_molecules 2 _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 5KYM _cell.length_a 173.836 _cell.length_b 173.836 _cell.length_c 173.836 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KYM _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,L 1 1 B,G,H,I,J,K 2 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 F N N ? 3 K N N # _chem_comp.formula 'C9 H20' _chem_comp.formula_weight 128.255 _chem_comp.id DD9 _chem_comp.mon_nstd_flag . _chem_comp.name nonane _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 C2 C1 DD9 sing 70 n n C1 H1 DD9 sing 71 n n C1 H1A DD9 sing 72 n n C1 H1B DD9 sing 73 n n C3 C2 DD9 sing 74 n n C2 H2 DD9 sing 75 n n C2 H2A DD9 sing 76 n n C4 C3 DD9 sing 77 n n C3 H3 DD9 sing 78 n n C3 H3A DD9 sing 79 n n C5 C4 DD9 sing 80 n n C4 H4 DD9 sing 81 n n C4 H4A DD9 sing 82 n n C6 C5 DD9 sing 83 n n C5 H5 DD9 sing 84 n n C5 H5A DD9 sing 85 n n C7 C6 DD9 sing 86 n n C6 H6 DD9 sing 87 n n C6 H6A DD9 sing 88 n n C8 C7 DD9 sing 89 n n C7 H7 DD9 sing 90 n n C7 H7A DD9 sing 91 n n C9 C8 DD9 sing 92 n n C8 H8 DD9 sing 93 n n C8 H8A DD9 sing 94 n n C9 H9 DD9 sing 95 n n C9 H9A DD9 sing 96 n n C9 H9B DD9 sing 97 n n # _atom_sites.entry_id 5KYM _atom_sites.fract_transf_matrix[1][1] 0.005753 _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] 0.005753 _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] 0.005753 _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 2 HGX A 1 301 1 HGX HGX . D 2 HGX A 1 302 2 HGX HGX . E 2 HGX A 1 303 3 HGX HGX . F 3 DD9 A 1 304 1 DD9 GK2 . G 2 HGX B 1 301 4 HGX HGX . H 2 HGX B 1 302 5 HGX HGX . I 2 HGX B 1 303 6 HGX HGX . J 4 LMT B 1 304 1 LMT LMT . K 3 DD9 B 1 305 2 DD9 GK2 . L 5 HOH A 1 401 1 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 DD9 . . . K 3 55.74 51.62 33.374 1 64.37 ? C1 DD9 305 B 1 HETATM 2 C C2 DD9 . . . K 3 56.64 51.83 32.154 1 67.76 ? C2 DD9 305 B 1 HETATM 3 C C3 DD9 . . . K 3 56.208 52.991 31.238 1 66.04 ? C3 DD9 305 B 1 HETATM 4 C C4 DD9 . . . K 3 57.366 53.433 30.335 1 68.5 ? C4 DD9 305 B 1 HETATM 5 C C5 DD9 . . . K 3 56.938 54.581 29.425 1 76.8 ? C5 DD9 305 B 1 HETATM 6 C C6 DD9 . . . K 3 58.142 55.099 28.629 1 84.64 ? C6 DD9 305 B 1 HETATM 7 C C7 DD9 . . . K 3 57.826 56.457 27.969 1 88.23 ? C7 DD9 305 B 1 HETATM 8 C C8 DD9 . . . K 3 58.736 56.665 26.744 1 93.54 ? C8 DD9 305 B 1 HETATM 9 C C9 DD9 . . . K 3 58.599 58.081 26.182 1 95.49 ? C9 DD9 305 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #