data_6G8H # _model_server_result.job_id TzwmAx2XuKxWWMqgd_SLzA _model_server_result.datetime_utc '2024-11-25 21:58:15' _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 6g8h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1001}' # _entry.id 6G8H # _exptl.entry_id 6G8H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 272.253 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NARINGENIN _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 6G8H _cell.length_a 118.709 _cell.length_b 118.709 _cell.length_c 78.354 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G8H _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,H 1 1 C,D,I,J,K,L,M 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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id L _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 A C LYS 4 CCC LYS 22 1_555 A N MSE 5 CCC MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C MSE 5 CCC MSE 23 1_555 A N ASP 6 CCC ASP 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C SER 25 CCC SER 43 1_555 A N MSE 26 CCC MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale4 A C MSE 26 CCC MSE 44 1_555 A N ASP 27 CCC ASP 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C PRO 146 CCC PRO 164 1_555 A N MSE 147 CCC MSE 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale6 A C MSE 147 CCC MSE 165 1_555 A N GLU 148 CCC GLU 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale7 B C LYS 4 DDD LYS 22 1_555 B N MSE 5 DDD MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 B C MSE 5 DDD MSE 23 1_555 B N ASP 6 DDD ASP 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale9 B C SER 25 DDD SER 43 1_555 B N MSE 26 DDD MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale10 B C MSE 26 DDD MSE 44 1_555 B N ASP 27 DDD ASP 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale11 B C PRO 146 DDD PRO 164 1_555 B N MSE 147 DDD MSE 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale12 B C MSE 147 DDD MSE 165 1_555 B N GLU 148 DDD GLU 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale13 C C LYS 4 AAA LYS 22 1_555 C N MSE 5 AAA MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale14 C C MSE 5 AAA MSE 23 1_555 C N ASP 6 AAA ASP 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale15 C C SER 25 AAA SER 43 1_555 C N MSE 26 AAA MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale16 C C MSE 26 AAA MSE 44 1_555 C N ASP 27 AAA ASP 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale17 C C PRO 146 AAA PRO 164 1_555 C N MSE 147 AAA MSE 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale18 C C MSE 147 AAA MSE 165 1_555 C N GLU 148 AAA GLU 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale19 D C LYS 4 BBB LYS 22 1_555 D N MSE 5 BBB MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale20 D C MSE 5 BBB MSE 23 1_555 D N ASP 6 BBB ASP 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale21 D C SER 25 BBB SER 43 1_555 D N MSE 26 BBB MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale22 D C MSE 26 BBB MSE 44 1_555 D N ASP 27 BBB ASP 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale23 D C PRO 146 BBB PRO 164 1_555 D N MSE 147 BBB MSE 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale24 D C MSE 147 BBB MSE 165 1_555 D N GLU 148 BBB GLU 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _chem_comp.formula 'C15 H12 O5' _chem_comp.formula_weight 272.253 _chem_comp.id NAR _chem_comp.mon_nstd_flag . _chem_comp.name NARINGENIN _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 NAR doub 269 n y C1 C6 NAR sing 270 n y C1 H11 NAR sing 271 n n C2 C3 NAR sing 272 n y C2 O4 NAR sing 273 n n C3 C4 NAR doub 274 n y C3 H31 NAR sing 275 n n C4 C5 NAR sing 276 n y C4 O5 NAR sing 277 n n C5 C6 NAR doub 278 n y C5 C7 NAR sing 279 n n C6 O1 NAR sing 280 n n C7 C8 NAR sing 281 n n C7 O2 NAR doub 282 n n C8 C9 NAR sing 283 n n C8 H81 NAR sing 284 n n C8 H82 NAR sing 285 n n C9 O1 NAR sing 286 n n C9 C10 NAR sing 287 n n C9 H9 NAR sing 288 n n C10 C11 NAR sing 289 n y C10 C15 NAR doub 290 n y C11 C12 NAR doub 291 n y C11 H111 NAR sing 292 n n C12 C13 NAR sing 293 n y C12 H121 NAR sing 294 n n C13 C14 NAR doub 295 n y C13 O3 NAR sing 296 n n C14 C15 NAR sing 297 n y C14 H141 NAR sing 298 n n C15 H151 NAR sing 299 n n O3 HO3 NAR sing 300 n n O4 H41 NAR sing 301 n n O5 H51 NAR sing 302 n n # _atom_sites.entry_id 6G8H _atom_sites.fract_transf_matrix[1][1] 0.008424 _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] 0.008424 _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] 0.012763 _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 E 2 NHE CCC 1 301 1005 NHE NHE . F 3 CWE DDD 1 301 1002 CWE NAR . G 2 NHE DDD 1 302 1003 NHE NHE . H 2 NHE DDD 1 303 1007 NHE NHE . I 2 NHE AAA 1 1001 1001 NHE NHE . J 2 NHE AAA 1 1002 1002 NHE NHE . K 2 NHE AAA 1 1003 1004 NHE NHE . L 4 NAR BBB 1 1001 1001 NAR NAR . M 2 NHE BBB 1 1002 1006 NHE NHE . # 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 NAR . . . L 4 35.051 37.139 0.949 1 92.29 0 C1 NAR 1001 BBB 1 HETATM 2 C C2 NAR . . . L 4 33.82 36.513 1.142 1 94.84 0 C2 NAR 1001 BBB 1 HETATM 3 C C3 NAR . . . L 4 33.739 35.247 1.719 1 92.42 0 C3 NAR 1001 BBB 1 HETATM 4 C C4 NAR . . . L 4 34.893 34.602 2.103 1 91.79 0 C4 NAR 1001 BBB 1 HETATM 5 C C5 NAR . . . L 4 36.167 35.202 1.912 1 82.81 0 C5 NAR 1001 BBB 1 HETATM 6 C C6 NAR . . . L 4 36.207 36.488 1.347 1 91.5 0 C6 NAR 1001 BBB 1 HETATM 7 C C7 NAR . . . L 4 37.381 34.507 2.323 1 93.84 0 C7 NAR 1001 BBB 1 HETATM 8 C C8 NAR . . . L 4 38.67 35.25 2.043 1 95.58 0 C8 NAR 1001 BBB 1 HETATM 9 C C9 NAR . . . L 4 38.442 36.767 2.106 1 101.93 0 C9 NAR 1001 BBB 1 HETATM 10 O O1 NAR . . . L 4 37.4 37.164 1.156 1 101.47 0 O1 NAR 1001 BBB 1 HETATM 11 O O2 NAR . . . L 4 37.365 33.39 2.896 1 93.49 0 O2 NAR 1001 BBB 1 HETATM 12 C C10 NAR . . . L 4 39.692 37.596 1.937 1 112.04 0 C10 NAR 1001 BBB 1 HETATM 13 C C11 NAR . . . L 4 39.659 38.906 1.461 1 111.89 0 C11 NAR 1001 BBB 1 HETATM 14 C C12 NAR . . . L 4 40.828 39.655 1.362 1 117.74 0 C12 NAR 1001 BBB 1 HETATM 15 C C13 NAR . . . L 4 42.048 39.099 1.741 1 122.56 0 C13 NAR 1001 BBB 1 HETATM 16 C C14 NAR . . . L 4 42.093 37.804 2.227 1 119.66 0 C14 NAR 1001 BBB 1 HETATM 17 C C15 NAR . . . L 4 40.923 37.071 2.332 1 121.06 0 C15 NAR 1001 BBB 1 HETATM 18 O O3 NAR . . . L 4 43.231 39.779 1.668 1 110.49 0 O3 NAR 1001 BBB 1 HETATM 19 O O4 NAR . . . L 4 32.645 37.126 0.789 1 96.32 0 O4 NAR 1001 BBB 1 HETATM 20 O O5 NAR . . . L 4 34.788 33.366 2.675 1 98.22 0 O5 NAR 1001 BBB 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #