data_7LIJ # _model_server_result.job_id vad7aynO4kMndP7g4uPrDw _model_server_result.datetime_utc '2024-11-22 17:44:56' _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 7lij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7LIJ # _exptl.entry_id 7LIJ _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 7LIJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LIJ _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' ? ? -0.5 0.309019 0.809016 -0.309015 0.809017 -0.500001 -0.809017 -0.499999 -0.309017 -116.28959 -0.00032 304.44917 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 0.5 0.309018 -0.500001 0.309017 0.809016 0.309017 -0.809017 0.500001 -116.28957 71.87108 188.16021 3 'point symmetry operation' ? ? 0.499999 0.309017 0.809018 -0.309018 -0.809017 0.499999 0.809017 -0.5 -0.309016 -116.28934 304.45005 188.16008 4 'point symmetry operation' ? ? 0.499999 -0.309018 0.809017 0.309017 -0.809017 -0.5 0.809018 0.499999 -0.309016 0.00038 376.32069 -0.00021 5 'point symmetry operation' ? ? 0.809016 -0.500001 0.309017 0.5 0.309017 -0.809017 0.309018 0.809016 0.500001 71.87114 188.16021 -116.28953 6 'point symmetry operation' ? ? 0.309018 0.809016 0.5 0.809016 -0.500001 0.309017 0.5 0.309017 -0.809017 -116.28985 71.8718 188.16001 7 'point symmetry operation' ? ? 0.000001 0 1 1 0 -0.000001 0 1 0 -0.0004 0.00064 -0.00024 8 'point symmetry operation' ? ? 0.309017 -0.809016 0.500001 0.809016 0.500001 0.309017 -0.500001 0.309017 0.809016 188.15976 -116.28904 71.87076 9 'point symmetry operation' ? ? 0.809018 -0.5 -0.309015 0.499998 0.309017 0.809018 -0.309018 -0.809017 0.499999 188.1597 -116.28886 304.44973 10 'point symmetry operation' ? ? 0.809018 0.499999 -0.309015 0.499998 -0.309018 0.809018 0.309016 -0.809017 -0.5 -0.00051 0.00093 376.32044 11 'point symmetry operation' ? ? -0.809019 -0.499997 0.309016 -0.499997 0.309017 -0.809019 0.309016 -0.809019 -0.499998 376.31971 376.32 376.32034 12 'point symmetry operation' ? ? -0.309019 -0.809017 -0.499999 -0.809015 0.500002 -0.309018 0.500002 0.309014 -0.809017 492.60936 304.44872 188.16027 13 'point symmetry operation' ? ? -0.000001 -0.000002 -1 -1 0.000002 0.000001 0.000002 1 -0.000002 376.32023 376.31946 -0.00034 14 'point symmetry operation' ? ? -0.309016 0.809016 -0.500002 -0.809018 -0.5 -0.309016 -0.5 0.30902 0.809016 188.15994 492.6093 71.87009 15 'point symmetry operation' ? ? -0.809017 0.500002 0.309014 -0.499999 -0.309019 -0.809017 -0.309019 -0.809015 0.500002 188.15962 492.60964 304.44906 16 'point symmetry operation' ? ? -0.499999 -0.309019 -0.809017 -0.309019 -0.809015 0.500002 -0.809017 0.500002 0.309015 492.60916 304.44923 188.15969 17 'point symmetry operation' ? ? -0.499998 0.309016 -0.809019 0.309016 -0.809019 -0.499997 -0.809019 -0.499997 0.309017 376.31964 376.32059 376.31982 18 'point symmetry operation' ? ? -0.809015 0.500002 -0.309019 0.500002 0.309014 -0.809017 -0.309019 -0.809017 -0.499999 304.44837 188.16056 492.60955 19 'point symmetry operation' ? ? -1 0.000003 0 0.000003 1 -0.000002 0 -0.000002 -1 376.319 -0.00009 376.32044 20 'point symmetry operation' ? ? -0.809018 -0.5 -0.309016 -0.5 0.30902 0.809016 -0.309016 0.809016 -0.500002 492.60877 71.87026 188.16007 21 'point symmetry operation' ? ? 0.809016 -0.5 0.30902 -0.500003 -0.309016 0.809016 -0.309016 -0.809017 -0.5 71.87063 188.16062 492.60936 22 'point symmetry operation' ? ? 1 -0.000003 0.000002 -0.000003 -1 0 0.000002 0 -1 0.00019 376.32102 376.31971 23 'point symmetry operation' ? ? 0.809018 0.499998 0.309016 0.499999 -0.309018 -0.809017 -0.309015 0.809018 -0.5 -116.28926 304.45026 188.15931 24 'point symmetry operation' ? ? 0.500001 0.309018 0.809016 0.309017 0.809016 -0.500001 -0.809016 0.500001 0.309017 -116.28965 71.87128 188.15944 25 'point symmetry operation' ? ? 0.499999 -0.309015 0.809018 -0.309018 0.809018 0.499998 -0.809017 -0.5 0.309017 -0.00044 0.00034 376.31992 26 'point symmetry operation' ? ? 0.000002 1 -0.000002 0 -0.000002 -1 -1 0.000002 0 -0.00045 376.32078 376.31931 27 'point symmetry operation' ? ? -0.5 0.30902 0.809016 -0.309016 0.809016 -0.500003 -0.809017 -0.5 -0.309016 71.86991 188.16043 492.60908 28 'point symmetry operation' ? ? -0.309019 -0.809015 0.500002 -0.809017 0.500002 0.309014 -0.499999 -0.309018 -0.809017 304.44888 188.15999 492.60936 29 'point symmetry operation' ? ? 0.309016 -0.809019 -0.499998 -0.809019 -0.499997 0.309017 -0.499998 0.309017 -0.809019 376.32023 376.32007 376.31975 30 'point symmetry operation' ? ? 0.500001 0.309014 -0.809017 -0.309019 -0.809017 -0.499999 -0.809015 0.500002 -0.309018 188.16019 492.60983 304.44855 31 'point symmetry operation' ? ? -0.309018 -0.809017 0.5 0.809018 -0.5 -0.309016 0.499999 0.309017 0.809018 304.44939 188.16021 -116.28914 32 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809018 0.499999 -0.309015 0.499998 -0.309018 0.809018 376.32004 -0.00006 0.00059 33 'point symmetry operation' ? ? 0.500001 0.309017 -0.809017 0.309018 0.809016 0.500001 0.809016 -0.500001 0.309017 188.15957 -116.28932 71.87148 34 'point symmetry operation' ? ? 0.000001 1 0 0 0 1 1 -0.000001 0 -0.00064 0.00024 0.0004 35 'point symmetry operation' ? ? -0.500001 0.309017 0.809017 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 71.87042 188.1604 -116.28925 36 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309015 0.809018 0.5 0.809018 0.499998 -0.309018 376.31944 -0.00058 0.00052 37 'point symmetry operation' ? ? -0.809017 0.5 -0.309018 -0.5 -0.309015 0.809018 0.309018 0.809018 0.499998 304.44887 188.15964 -116.28934 38 'point symmetry operation' ? ? -1 0 -0.000002 0 -1 0.000002 -0.000002 0.000002 1 376.31982 376.3201 -0.0001 39 'point symmetry operation' ? ? -0.809017 -0.499999 -0.309019 0.500002 -0.309019 -0.809015 0.309014 -0.809017 0.500002 492.60908 304.44944 188.16046 40 'point symmetry operation' ? ? -0.5 -0.309016 -0.809017 0.30902 0.809016 -0.5 0.809016 -0.500003 -0.309016 492.60885 71.87046 188.16084 41 'point symmetry operation' ? ? 0.809016 -0.500003 -0.309016 -0.5 -0.309016 -0.809017 0.30902 0.809016 -0.5 188.16071 492.60938 71.8703 42 'point symmetry operation' ? ? 0.809018 0.499998 -0.309018 -0.5 0.309017 -0.809017 -0.309015 0.809018 0.499999 0.00031 376.32009 -0.00073 43 'point symmetry operation' ? ? 0.309017 0.809018 0.499998 -0.809017 0.499999 -0.309018 -0.5 -0.309015 0.809018 -116.28954 304.44953 188.1595 44 'point symmetry operation' ? ? -0.000002 0.000002 1 -1 0 -0.000002 0 -1 0.000002 -0.00021 376.32038 376.31995 45 'point symmetry operation' ? ? 0.309014 -0.809017 0.500001 -0.809017 -0.499998 -0.309019 0.500001 -0.309019 -0.809015 188.16039 492.60956 304.44927 46 'point symmetry operation' ? ? -0.309018 0.809018 0.499999 -0.809017 -0.5 0.309017 0.5 -0.309016 0.809018 -0.00022 376.32016 -0.00014 47 'point symmetry operation' ? ? -0.500002 -0.309016 0.809016 -0.309016 -0.809017 -0.5 0.809016 -0.5 0.309019 188.16013 492.60958 71.87081 48 'point symmetry operation' ? ? -0.000002 -1 0 0.000002 0 -1 1 -0.000002 0.000002 376.32047 376.31986 0.00031 49 'point symmetry operation' ? ? 0.499999 -0.309018 -0.809017 -0.309015 0.809018 -0.5 0.809018 0.499998 0.309017 304.4496 188.15945 -116.28906 50 'point symmetry operation' ? ? 0.309017 0.809016 -0.500001 -0.809016 0.500001 0.309017 0.500001 0.309017 0.809016 71.87062 188.15963 -116.28933 51 'point symmetry operation' ? ? -0.5 -0.309015 0.809018 0.309017 0.809018 0.499998 -0.809017 0.5 -0.309018 188.15912 -116.28906 304.44921 52 'point symmetry operation' ? ? -0.000001 -1 0.000002 -0.000002 0.000002 1 -1 0.000001 -0.000002 376.31965 0.00015 376.32003 53 'point symmetry operation' ? ? 0.500001 -0.309019 -0.809015 0.309014 -0.809017 0.500002 -0.809017 -0.499999 -0.309018 304.44909 188.16076 492.60928 54 'point symmetry operation' ? ? 0.30902 0.809016 -0.5 0.809016 -0.500003 -0.309016 -0.5 -0.309016 -0.809017 71.87012 188.1612 492.60916 55 'point symmetry operation' ? ? -0.309015 0.809018 0.499999 0.809018 0.499998 -0.309018 -0.5 0.309017 -0.809017 -0.00104 0.00086 376.31985 56 'point symmetry operation' ? ? 0.000002 0 -1 1 -0.000002 0.000002 -0.000002 -1 0 376.31941 0.00055 376.32068 57 'point symmetry operation' ? ? -0.309015 0.809018 -0.5 0.809018 0.499998 0.309017 0.499999 -0.309018 -0.809017 188.15893 -116.28878 304.44994 58 'point symmetry operation' ? ? -0.809016 0.500001 0.309017 0.500001 0.309017 0.809016 0.309017 0.809016 -0.500001 188.159 -116.28912 71.87096 59 'point symmetry operation' ? ? -0.809017 -0.5 0.309018 0.5 -0.309015 0.809018 -0.309018 0.809018 0.499998 376.31951 0.00001 0 60 'point symmetry operation' ? ? -0.309016 -0.809018 -0.5 0.809016 -0.5 0.30902 -0.500002 -0.309016 0.809016 492.60904 71.87098 188.16027 # _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 7LIJ _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 2 126.997 134.815 111.733 1 17.3 ? N1 RBF 301 A 1 HETATM 2 C C2 RBF . . . B 2 126.778 135.334 112.94 1 17.3 ? C2 RBF 301 A 1 HETATM 3 O O2 RBF . . . B 2 126.005 134.759 113.68 1 17.3 ? O2 RBF 301 A 1 HETATM 4 N N3 RBF . . . B 2 127.352 136.451 113.399 1 17.3 ? N3 RBF 301 A 1 HETATM 5 C C4 RBF . . . B 2 128.222 137.15 112.639 1 17.3 ? C4 RBF 301 A 1 HETATM 6 O O4 RBF . . . B 2 128.743 138.163 113.054 1 17.3 ? O4 RBF 301 A 1 HETATM 7 C C4A RBF . . . B 2 128.508 136.626 111.286 1 17.3 ? C4A RBF 301 A 1 HETATM 8 N N5 RBF . . . B 2 129.336 137.229 110.474 1 17.3 ? N5 RBF 301 A 1 HETATM 9 C C5A RBF . . . B 2 129.577 136.732 109.258 1 17.3 ? C5A RBF 301 A 1 HETATM 10 C C6 RBF . . . B 2 130.471 137.391 108.395 1 17.3 ? C6 RBF 301 A 1 HETATM 11 C C7 RBF . . . B 2 130.714 136.88 107.154 1 17.3 ? C7 RBF 301 A 1 HETATM 12 C C7M RBF . . . B 2 131.671 137.582 106.228 1 17.3 ? C7M RBF 301 A 1 HETATM 13 C C8 RBF . . . B 2 130.088 135.713 106.729 1 17.3 ? C8 RBF 301 A 1 HETATM 14 C C8M RBF . . . B 2 130.371 135.166 105.355 1 17.3 ? C8M RBF 301 A 1 HETATM 15 C C9 RBF . . . B 2 129.21 135.049 107.553 1 17.3 ? C9 RBF 301 A 1 HETATM 16 C C9A RBF . . . B 2 128.947 135.547 108.821 1 17.3 ? C9A RBF 301 A 1 HETATM 17 N N10 RBF . . . B 2 128.074 134.874 109.639 1 17.3 ? N10 RBF 301 A 1 HETATM 18 C C10 RBF . . . B 2 127.824 135.385 110.876 1 17.3 ? C10 RBF 301 A 1 HETATM 19 C C1' RBF . . . B 2 127.431 133.655 109.141 1 17.3 ? C1' RBF 301 A 1 HETATM 20 C C2' RBF . . . B 2 127.972 132.377 109.775 1 17.3 ? C2' RBF 301 A 1 HETATM 21 O O2' RBF . . . B 2 129.234 132.063 109.185 1 17.3 ? O2' RBF 301 A 1 HETATM 22 C C3' RBF . . . B 2 126.994 131.244 109.48 1 17.3 ? C3' RBF 301 A 1 HETATM 23 O O3' RBF . . . B 2 126.112 131.664 108.44 1 17.3 ? O3' RBF 301 A 1 HETATM 24 C C4' RBF . . . B 2 126.175 130.92 110.724 1 17.3 ? C4' RBF 301 A 1 HETATM 25 O O4' RBF . . . B 2 126.825 131.46 111.875 1 17.3 ? O4' RBF 301 A 1 HETATM 26 C C5' RBF . . . B 2 126.059 129.404 110.852 1 17.3 ? C5' RBF 301 A 1 HETATM 27 O O5' RBF . . . B 2 125.81 128.844 109.561 1 17.3 ? O5' RBF 301 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #