data_7LIK # _model_server_result.job_id 1aUJDeFkzEcdnGL0DMSO8w _model_server_result.datetime_utc '2024-11-26 05:31:51' _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 7lik # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7LIK # _exptl.entry_id 7LIK _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 376.364 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RIBOFLAVIN _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 7LIK _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LIK _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 60-meric 60 'complete icosahedral assembly' 1 ? monomeric 1 'icosahedral asymmetric unit' 2 ? pentameric 5 'icosahedral pentamer' 3 ? hexameric 6 'icosahedral 23 hexamer' 4 ? monomeric 1 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 (1-60) A,B 2 1 A,B 3 (1-5) A,B 4 (1,2,6,10,23,24) A,B 5 P # 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] P 'transform to point frame' ? ? -0.500001 0.309018 0.809016 -0.309016 0.809017 -0.500001 -0.809017 -0.5 -0.309017 -116.28939 -0.00027 304.44923 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.809016 0.500001 0.309018 -0.500001 0.309017 0.809016 0.309017 -0.809017 0.500001 -116.28954 71.8711 188.16003 3 'point symmetry operation' ? ? 0.499998 0.309017 0.809018 -0.309018 -0.809017 0.499999 0.809018 -0.5 -0.309015 -116.28931 304.44993 188.15981 4 'point symmetry operation' ? ? 0.499998 -0.309018 0.809018 0.309017 -0.809017 -0.5 0.809018 0.499999 -0.309015 0.00037 376.32045 -0.00036 5 'point symmetry operation' ? ? 0.809016 -0.500001 0.309017 0.500001 0.309017 -0.809017 0.309018 0.809016 0.500001 71.87112 188.16004 -116.28951 6 'point symmetry operation' ? ? 0.309017 0.809016 0.500001 0.809016 -0.500001 0.309017 0.500001 0.309017 -0.809016 -116.28969 71.87149 188.15973 7 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 -0.00012 0.00041 -0.00029 8 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 0.809016 0.500001 0.309018 -0.500001 0.309017 0.809016 188.15991 -116.28911 71.87085 9 'point symmetry operation' ? ? 0.809018 -0.5 -0.309016 0.499998 0.309017 0.809018 -0.309018 -0.809017 0.499999 188.15963 -116.2889 304.44968 10 'point symmetry operation' ? ? 0.809018 0.5 -0.309015 0.499998 -0.309018 0.809018 0.309017 -0.809017 -0.5 -0.00057 0.00075 376.32016 11 'point symmetry operation' ? ? -0.809019 -0.499998 0.309016 -0.499998 0.309017 -0.809018 0.309016 -0.809018 -0.499998 376.31975 376.31999 376.32025 12 'point symmetry operation' ? ? -0.309018 -0.809017 -0.499999 -0.809016 0.500001 -0.309018 0.500001 0.309015 -0.809017 492.60928 304.44894 188.16019 13 'point symmetry operation' ? ? 0 -0.000002 -1 -1 0.000002 0 0.000002 1 -0.000002 376.32011 376.31971 -0.00019 14 'point symmetry operation' ? ? -0.309016 0.809016 -0.500002 -0.809017 -0.5 -0.309016 -0.5 0.309019 0.809016 188.15992 492.60935 71.87035 15 'point symmetry operation' ? ? -0.809017 0.500002 0.309014 -0.499999 -0.309018 -0.809017 -0.309019 -0.809016 0.500001 188.1597 492.60952 304.44917 16 'point symmetry operation' ? ? -0.499999 -0.309018 -0.809017 -0.309018 -0.809016 0.500001 -0.809017 0.500001 0.309014 492.60911 304.44937 188.15998 17 'point symmetry operation' ? ? -0.499998 0.309017 -0.809019 0.309017 -0.809018 -0.499998 -0.809019 -0.499998 0.309016 376.31955 376.32041 376.32003 18 'point symmetry operation' ? ? -0.809015 0.500002 -0.309018 0.500002 0.309015 -0.809017 -0.309018 -0.809017 -0.499999 304.44846 188.16033 492.6095 19 'point symmetry operation' ? ? -1 0.000002 0 0.000002 1 -0.000002 0 -0.000002 -1 376.31924 -0.00003 376.32029 20 'point symmetry operation' ? ? -0.809017 -0.5 -0.309016 -0.5 0.309019 0.809016 -0.309016 0.809016 -0.500002 492.60891 71.87055 188.16014 21 'point symmetry operation' ? ? 0.809016 -0.5 0.30902 -0.500002 -0.309016 0.809016 -0.309016 -0.809017 -0.5 71.87047 188.1606 492.60925 22 'point symmetry operation' ? ? 1 -0.000002 0.000002 -0.000002 -1 0 0.000002 0 -1 -0.00006 376.32077 376.31958 23 'point symmetry operation' ? ? 0.809018 0.499998 0.309017 0.5 -0.309018 -0.809017 -0.309015 0.809018 -0.5 -116.28933 304.44988 188.1593 24 'point symmetry operation' ? ? 0.500001 0.309017 0.809016 0.309017 0.809016 -0.500001 -0.809017 0.500001 0.309017 -116.28953 71.87106 188.15952 25 'point symmetry operation' ? ? 0.499999 -0.309015 0.809018 -0.309018 0.809018 0.499999 -0.809017 -0.5 0.309017 -0.00038 0.00033 376.31993 26 'point symmetry operation' ? ? 0.000002 1 -0.000002 0 -0.000002 -1 -1 0.000002 0 -0.00047 376.32049 376.31945 27 'point symmetry operation' ? ? -0.5 0.309019 0.809016 -0.309016 0.809016 -0.500002 -0.809017 -0.5 -0.309016 71.87007 188.1603 492.6091 28 'point symmetry operation' ? ? -0.309018 -0.809016 0.500001 -0.809017 0.500001 0.309015 -0.499999 -0.309018 -0.809017 304.4489 188.16012 492.60933 29 'point symmetry operation' ? ? 0.309017 -0.809018 -0.499998 -0.809018 -0.499998 0.309016 -0.499998 0.309016 -0.809019 376.31997 376.32019 376.31983 30 'point symmetry operation' ? ? 0.500002 0.309015 -0.809017 -0.309018 -0.809017 -0.499999 -0.809015 0.500001 -0.309019 188.15991 492.60969 304.44874 31 'point symmetry operation' ? ? -0.309018 -0.809017 0.499999 0.809018 -0.5 -0.309015 0.499998 0.309017 0.809018 304.44955 188.1601 -116.2891 32 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809018 0.499999 -0.309015 0.499999 -0.309018 0.809018 376.32004 -0.0001 0.00055 33 'point symmetry operation' ? ? 0.500001 0.309017 -0.809017 0.309017 0.809016 0.500001 0.809016 -0.500001 0.309017 188.15961 -116.28926 71.87124 34 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 -0.00041 0.00029 0.00012 35 'point symmetry operation' ? ? -0.500001 0.309017 0.809016 0.309017 -0.809017 0.500001 0.809016 0.500001 0.309018 71.87073 188.16034 -116.28937 36 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309016 0.809018 0.499999 0.809018 0.499999 -0.309018 376.31962 -0.00033 0.00036 37 'point symmetry operation' ? ? -0.809017 0.499999 -0.309018 -0.5 -0.309016 0.809017 0.309017 0.809018 0.499999 304.44912 188.15989 -116.28926 38 'point symmetry operation' ? ? -1 0 -0.000002 0 -1 0.000002 -0.000002 0.000002 1 376.31999 376.32012 0.00009 39 'point symmetry operation' ? ? -0.809017 -0.499999 -0.309019 0.500002 -0.309018 -0.809016 0.309014 -0.809017 0.500001 492.60913 304.44933 188.16049 40 'point symmetry operation' ? ? -0.5 -0.309016 -0.809017 0.309019 0.809016 -0.5 0.809016 -0.500002 -0.309016 492.6089 71.8705 188.16066 41 'point symmetry operation' ? ? 0.809016 -0.500002 -0.309016 -0.5 -0.309016 -0.809017 0.30902 0.809016 -0.5 188.16043 492.60933 71.8703 42 'point symmetry operation' ? ? 0.809018 0.499998 -0.309018 -0.5 0.309017 -0.809017 -0.309016 0.809018 0.499999 0.00018 376.32003 -0.00058 43 'point symmetry operation' ? ? 0.309017 0.809018 0.499999 -0.809017 0.499999 -0.309018 -0.5 -0.309015 0.809018 -116.28948 304.44949 188.15959 44 'point symmetry operation' ? ? -0.000002 0.000002 1 -1 0 -0.000002 0 -1 0.000002 -0.00018 376.32037 376.31986 45 'point symmetry operation' ? ? 0.309014 -0.809017 0.500002 -0.809017 -0.499999 -0.309019 0.500002 -0.309019 -0.809015 188.16021 492.60954 304.44913 46 'point symmetry operation' ? ? -0.309018 0.809018 0.499998 -0.809017 -0.5 0.309017 0.499999 -0.309015 0.809018 -0.00005 376.32022 -0.00016 47 'point symmetry operation' ? ? -0.500002 -0.309016 0.809016 -0.309016 -0.809017 -0.5 0.809016 -0.5 0.30902 188.16022 492.6095 71.87074 48 'point symmetry operation' ? ? -0.000002 -1 0 0.000002 0 -1 1 -0.000002 0.000002 376.3204 376.31983 0.00021 49 'point symmetry operation' ? ? 0.499999 -0.309018 -0.809017 -0.309016 0.809018 -0.5 0.809018 0.499999 0.309017 304.44951 188.15959 -116.28912 50 'point symmetry operation' ? ? 0.309017 0.809016 -0.500001 -0.809017 0.500001 0.309017 0.5 0.309018 0.809016 71.87068 188.15983 -116.28935 51 'point symmetry operation' ? ? -0.5 -0.309016 0.809018 0.309017 0.809018 0.499999 -0.809017 0.499999 -0.309018 188.15942 -116.28907 304.44924 52 'point symmetry operation' ? ? 0 -1 0.000002 -0.000002 0.000002 1 -1 0 -0.000002 376.31965 0.00026 376.32017 53 'point symmetry operation' ? ? 0.500002 -0.309018 -0.809015 0.309015 -0.809017 0.500001 -0.809017 -0.499999 -0.309019 304.44885 188.16063 492.60935 54 'point symmetry operation' ? ? 0.30902 0.809016 -0.5 0.809016 -0.500002 -0.309016 -0.5 -0.309016 -0.809018 71.87003 188.16081 492.60908 55 'point symmetry operation' ? ? -0.309016 0.809018 0.5 0.809018 0.499999 -0.309018 -0.5 0.309017 -0.809017 -0.0008 0.00055 376.31974 56 'point symmetry operation' ? ? 0.000002 0 -1 1 -0.000002 0.000002 -0.000002 -1 0 376.31936 0.00038 376.32058 57 'point symmetry operation' ? ? -0.309016 0.809018 -0.5 0.809018 0.499999 0.309017 0.5 -0.309018 -0.809017 188.15912 -116.28892 304.44963 58 'point symmetry operation' ? ? -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0.309017 0.809017 -0.500001 188.1594 -116.28909 71.87081 59 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 0.499999 -0.309016 0.809018 -0.309018 0.809017 0.499999 376.31981 0.00009 0.00013 60 'point symmetry operation' ? ? -0.309016 -0.809017 -0.5 0.809016 -0.5 0.309019 -0.500002 -0.309016 0.809016 492.60906 71.87094 188.16044 # _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 # _chem_comp.formula 'C17 H20 N4 O6' _chem_comp.formula_weight 376.364 _chem_comp.id RBF _chem_comp.mon_nstd_flag . _chem_comp.name RIBOFLAVIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'RIBOFLAVINE;VITAMIN B2' # 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 N1 C2 RBF sing 275 n n N1 C10 RBF doub 276 n n C2 O2 RBF doub 277 n n C2 N3 RBF sing 278 n n N3 C4 RBF sing 279 n n N3 HN3 RBF sing 280 n n C4 O4 RBF doub 281 n n C4 C4A RBF sing 282 n n C4A N5 RBF doub 283 n n C4A C10 RBF sing 284 n n N5 C5A RBF sing 285 n n C5A C6 RBF doub 286 n y C5A C9A RBF sing 287 n y C6 C7 RBF sing 288 n y C6 HC6 RBF sing 289 n n C7 C7M RBF sing 290 n n C7 C8 RBF doub 291 n y C7M HC71 RBF sing 292 n n C7M HC72 RBF sing 293 n n C7M HC73 RBF sing 294 n n C8 C8M RBF sing 295 n n C8 C9 RBF sing 296 n y C8M HC81 RBF sing 297 n n C8M HC82 RBF sing 298 n n C8M HC83 RBF sing 299 n n C9 C9A RBF doub 300 n y C9 HC9 RBF sing 301 n n C9A N10 RBF sing 302 n n N10 C10 RBF sing 303 n n N10 C1' RBF sing 304 n n C1' C2' RBF sing 305 n n C1' HC11 RBF sing 306 n n C1' HC12 RBF sing 307 n n C2' O2' RBF sing 308 n n C2' C3' RBF sing 309 n n C2' HC2' RBF sing 310 n n O2' HO2' RBF sing 311 n n C3' O3' RBF sing 312 n n C3' C4' RBF sing 313 n n C3' HC3' RBF sing 314 n n O3' HO3' RBF sing 315 n n C4' O4' RBF sing 316 n n C4' C5' RBF sing 317 n n C4' HC4' RBF sing 318 n n O4' HO4' RBF sing 319 n n C5' O5' RBF sing 320 n n C5' HC51 RBF sing 321 n n C5' HC52 RBF sing 322 n n O5' HO5' RBF sing 323 n n # _atom_sites.entry_id 7LIK _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id RBF _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 298 _pdbx_nonpoly_scheme.pdb_mon_id RBF _pdbx_nonpoly_scheme.auth_mon_id RBF _pdbx_nonpoly_scheme.pdb_ins_code . # 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 N N1 RBF . . . B 2 127.196 135.201 112.025 1 25.58 ? N1 RBF 301 A 1 HETATM 2 C C2 RBF . . . B 2 127.117 135.828 113.194 1 25.58 ? C2 RBF 301 A 1 HETATM 3 O O2 RBF . . . B 2 126.389 135.357 114.047 1 25.58 ? O2 RBF 301 A 1 HETATM 4 N N3 RBF . . . B 2 127.783 136.947 113.492 1 25.58 ? N3 RBF 301 A 1 HETATM 5 C C4 RBF . . . B 2 128.608 137.533 112.6 1 25.58 ? C4 RBF 301 A 1 HETATM 6 O O4 RBF . . . B 2 129.215 138.549 112.869 1 25.58 ? O4 RBF 301 A 1 HETATM 7 C C4A RBF . . . B 2 128.742 136.884 111.283 1 25.58 ? C4A RBF 301 A 1 HETATM 8 N N5 RBF . . . B 2 129.514 137.367 110.349 1 25.58 ? N5 RBF 301 A 1 HETATM 9 C C5A RBF . . . B 2 129.614 136.757 109.168 1 25.58 ? C5A RBF 301 A 1 HETATM 10 C C6 RBF . . . B 2 130.453 137.298 108.178 1 25.58 ? C6 RBF 301 A 1 HETATM 11 C C7 RBF . . . B 2 130.559 136.678 106.97 1 25.58 ? C7 RBF 301 A 1 HETATM 12 C C7M RBF . . . B 2 131.461 137.262 105.915 1 25.58 ? C7M RBF 301 A 1 HETATM 13 C C8 RBF . . . B 2 129.845 135.514 106.703 1 25.58 ? C8 RBF 301 A 1 HETATM 14 C C8M RBF . . . B 2 129.978 134.846 105.36 1 25.58 ? C8M RBF 301 A 1 HETATM 15 C C9 RBF . . . B 2 129.017 134.965 107.655 1 25.58 ? C9 RBF 301 A 1 HETATM 16 C C9A RBF . . . B 2 128.892 135.577 108.895 1 25.58 ? C9A RBF 301 A 1 HETATM 17 N N10 RBF . . . B 2 128.066 135.035 109.85 1 25.58 ? N10 RBF 301 A 1 HETATM 18 C C10 RBF . . . B 2 127.966 135.656 111.054 1 25.58 ? C10 RBF 301 A 1 HETATM 19 C C1' RBF . . . B 2 127.314 133.815 109.575 1 25.58 ? C1' RBF 301 A 1 HETATM 20 C C2' RBF . . . B 2 128.045 132.623 110.183 1 25.58 ? C2' RBF 301 A 1 HETATM 21 O O2' RBF . . . B 2 129.372 132.557 109.66 1 25.58 ? O2' RBF 301 A 1 HETATM 22 C C3' RBF . . . B 2 127.305 131.339 109.808 1 25.58 ? C3' RBF 301 A 1 HETATM 23 O O3' RBF . . . B 2 125.933 131.452 110.182 1 25.58 ? O3' RBF 301 A 1 HETATM 24 C C4' RBF . . . B 2 127.928 130.138 110.524 1 25.58 ? C4' RBF 301 A 1 HETATM 25 O O4' RBF . . . B 2 129.327 130.355 110.731 1 25.58 ? O4' RBF 301 A 1 HETATM 26 C C5' RBF . . . B 2 127.72 128.891 109.662 1 25.58 ? C5' RBF 301 A 1 HETATM 27 O O5' RBF . . . B 2 128.455 127.788 110.199 1 25.58 ? O5' RBF 301 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #