data_3NKA # _model_server_result.job_id kw92tWz0Bl9eisADi31lSg _model_server_result.datetime_utc '2025-08-31 00:01:41' _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 3nka # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":233}' # _entry.id 3NKA # _exptl.entry_id 3NKA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 3NKA _cell.length_a 92.784 _cell.length_b 92.784 _cell.length_c 78.919 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NKA _symmetry.cell_setting ? _symmetry.Int_Tables_number 75 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 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,G,J 1 1,2,3,4 B,H,I,K 2 1,5,6,7 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 92.784 92.784 0 6 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 92.784 0 0 7 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 92.784 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 G N N ? 3 I N N # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 O1 GOL sing 177 n n C1 C2 GOL sing 178 n n C1 H11 GOL sing 179 n n C1 H12 GOL sing 180 n n O1 HO1 GOL sing 181 n n C2 O2 GOL sing 182 n n C2 C3 GOL sing 183 n n C2 H2 GOL sing 184 n n O2 HO2 GOL sing 185 n n C3 O3 GOL sing 186 n n C3 H31 GOL sing 187 n n C3 H32 GOL sing 188 n n O3 HO3 GOL sing 189 n n # _atom_sites.entry_id 3NKA _atom_sites.fract_transf_matrix[1][1] 0.010778 _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] 0.010778 _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] 0.012671 _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 BOG A 1 232 1 BOG BOG . D 2 BOG A 1 233 2 BOG BOG . E 2 BOG A 1 234 4 BOG BOG . F 3 GOL A 1 235 1 GOL CRY . G 3 GOL A 1 236 2 GOL CRY . H 2 BOG B 1 232 3 BOG BOG . I 3 GOL B 1 233 3 GOL CRY . J 4 HOH A 1 237 1 HOH HOH . J 4 HOH A 2 238 3 HOH HOH . J 4 HOH A 3 239 4 HOH HOH . J 4 HOH A 4 240 5 HOH HOH . J 4 HOH A 5 241 6 HOH HOH . J 4 HOH A 6 242 8 HOH HOH . J 4 HOH A 7 243 9 HOH HOH . J 4 HOH A 8 244 10 HOH HOH . J 4 HOH A 9 245 11 HOH HOH . J 4 HOH A 10 246 12 HOH HOH . J 4 HOH A 11 247 13 HOH HOH . J 4 HOH A 12 248 14 HOH HOH . J 4 HOH A 13 249 15 HOH HOH . J 4 HOH A 14 250 16 HOH HOH . J 4 HOH A 15 251 20 HOH HOH . J 4 HOH A 16 252 21 HOH HOH . J 4 HOH A 17 253 22 HOH HOH . J 4 HOH A 18 254 24 HOH HOH . J 4 HOH A 19 255 25 HOH HOH . J 4 HOH A 20 256 29 HOH HOH . J 4 HOH A 21 257 31 HOH HOH . J 4 HOH A 22 258 34 HOH HOH . J 4 HOH A 23 259 35 HOH HOH . J 4 HOH A 24 260 36 HOH HOH . J 4 HOH A 25 261 37 HOH HOH . J 4 HOH A 26 262 38 HOH HOH . J 4 HOH A 27 263 39 HOH HOH . J 4 HOH A 28 264 40 HOH HOH . J 4 HOH A 29 265 41 HOH HOH . J 4 HOH A 30 266 42 HOH HOH . J 4 HOH A 31 267 50 HOH HOH . J 4 HOH A 32 268 52 HOH HOH . J 4 HOH A 33 269 53 HOH HOH . J 4 HOH A 34 270 54 HOH HOH . J 4 HOH A 35 271 56 HOH HOH . J 4 HOH A 36 272 57 HOH HOH . J 4 HOH A 37 273 59 HOH HOH . J 4 HOH A 38 274 60 HOH HOH . J 4 HOH A 39 275 61 HOH HOH . J 4 HOH A 40 276 64 HOH HOH . J 4 HOH A 41 277 67 HOH HOH . J 4 HOH A 42 278 70 HOH HOH . J 4 HOH A 43 279 71 HOH HOH . J 4 HOH A 44 280 72 HOH HOH . J 4 HOH A 45 281 73 HOH HOH . J 4 HOH A 46 282 74 HOH HOH . J 4 HOH A 47 283 75 HOH HOH . J 4 HOH A 48 284 76 HOH HOH . J 4 HOH A 49 285 77 HOH HOH . J 4 HOH A 50 286 78 HOH HOH . J 4 HOH A 51 287 79 HOH HOH . J 4 HOH A 52 288 80 HOH HOH . J 4 HOH A 53 289 81 HOH HOH . K 4 HOH B 1 234 2 HOH HOH . K 4 HOH B 2 235 7 HOH HOH . K 4 HOH B 3 236 17 HOH HOH . K 4 HOH B 4 237 18 HOH HOH . K 4 HOH B 5 238 19 HOH HOH . K 4 HOH B 6 239 23 HOH HOH . K 4 HOH B 7 240 26 HOH HOH . K 4 HOH B 8 241 27 HOH HOH . K 4 HOH B 9 242 28 HOH HOH . K 4 HOH B 10 243 30 HOH HOH . K 4 HOH B 11 244 32 HOH HOH . K 4 HOH B 12 245 33 HOH HOH . K 4 HOH B 13 246 44 HOH HOH . K 4 HOH B 14 247 48 HOH HOH . K 4 HOH B 15 248 51 HOH HOH . K 4 HOH B 16 249 55 HOH HOH . K 4 HOH B 17 250 58 HOH HOH . K 4 HOH B 18 251 62 HOH HOH . K 4 HOH B 19 252 63 HOH HOH . K 4 HOH B 20 253 66 HOH HOH . K 4 HOH B 21 254 68 HOH HOH . K 4 HOH B 22 255 69 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 GOL . . . I 3 37.779 35.483 -44.591 1 88.59 ? C1 GOL 233 B 1 HETATM 2 O O1 GOL . . . I 3 36.721 36.045 -45.394 1 88.38 ? O1 GOL 233 B 1 HETATM 3 C C2 GOL . . . I 3 37.404 35.397 -43.106 1 87.57 ? C2 GOL 233 B 1 HETATM 4 O O2 GOL . . . I 3 36.297 34.5 -42.959 1 88.17 ? O2 GOL 233 B 1 HETATM 5 C C3 GOL . . . I 3 38.581 34.915 -42.241 1 87.08 ? C3 GOL 233 B 1 HETATM 6 O O3 GOL . . . I 3 38.194 34.45 -40.925 1 86.22 ? O3 GOL 233 B 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 604 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #