data_7LII # _model_server_result.job_id L1qd5WRqUR1mUDDAGnSKPg _model_server_result.datetime_utc '2024-10-19 17:20:08' _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 7lii # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7LII # _exptl.entry_id 7LII _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 7LII _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LII _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' ? ? -0.499993 0.30902 0.80902 -0.309017 0.809018 -0.499999 -0.809022 -0.499996 -0.30901 -116.29168 -0.00096 304.44752 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.809022 0.499992 0.309018 -0.499996 0.309017 0.809019 0.309011 -0.809022 0.499995 -116.28872 71.86974 188.16265 3 'point symmetry operation' ? ? 0.500012 0.309008 0.809013 -0.309019 -0.809017 0.499999 0.809009 -0.500006 -0.309029 -116.28885 304.44985 188.16438 4 'point symmetry operation' ? ? 0.500012 -0.309019 0.809009 0.309008 -0.809017 -0.500006 0.809013 0.499999 -0.309029 -0.00021 376.32252 0.0028 5 'point symmetry operation' ? ? 0.809022 -0.499996 0.309011 0.499992 0.309017 -0.809022 0.309018 0.809019 0.499995 71.87025 188.16217 -116.28918 6 'point symmetry operation' ? ? 0.309032 0.809016 0.499992 0.809016 -0.500007 0.309008 0.499992 0.309008 -0.809025 -116.29056 71.87454 188.1637 7 'point symmetry operation' ? ? 0.000012 0.000008 1 1 -0.000004 -0.000012 0.000004 1 -0.000008 -0.00384 0.00356 0.00028 8 'point symmetry operation' ? ? 0.309017 -0.809013 0.500006 0.80902 0.500001 0.309009 -0.499996 0.309026 0.809016 188.15801 -116.28769 71.86801 9 'point symmetry operation' ? ? 0.809012 -0.500009 -0.309015 0.500003 0.309017 0.809015 -0.309024 -0.809012 0.500005 188.16172 -116.28866 304.44812 10 'point symmetry operation' ? ? 0.809022 0.499988 -0.309023 0.500001 -0.309022 0.809015 0.309003 -0.809022 -0.5 0.00216 0.002 376.32281 11 'point symmetry operation' ? ? -0.809017 -0.5 0.309016 -0.5 0.30902 -0.809016 0.309016 -0.809016 -0.500003 376.3193 376.31838 376.31961 12 'point symmetry operation' ? ? -0.309025 -0.809011 -0.500004 -0.809015 0.500008 -0.30901 0.499999 0.309019 -0.809017 492.60927 304.44539 188.15897 13 'point symmetry operation' ? ? -0.000012 0.000006 -1 -1 0.000006 0.000012 0.000006 1 0.000006 376.3198 376.31592 -0.00291 14 'point symmetry operation' ? ? -0.309024 0.809018 -0.499994 -0.809021 -0.5 -0.309007 -0.499989 0.309015 0.809024 188.159 492.60735 71.86729 15 'point symmetry operation' ? ? -0.809017 0.499997 0.309022 -0.500004 -0.309019 -0.809014 -0.309011 -0.809018 0.500002 188.15869 492.60886 304.4474 16 'point symmetry operation' ? ? -0.500015 -0.309016 -0.809008 -0.309016 -0.809013 0.500007 -0.809008 0.500007 0.309028 492.60867 304.44694 188.154 17 'point symmetry operation' ? ? -0.500009 0.309011 -0.809014 0.309011 -0.809021 -0.499997 -0.809014 -0.499997 0.30903 376.32072 376.32117 376.3154 18 'point symmetry operation' ? ? -0.809017 0.499999 -0.309019 0.499999 0.30901 -0.80902 -0.309019 -0.80902 -0.499994 304.44846 188.16178 492.60783 19 'point symmetry operation' ? ? -1 0.00001 0 0.00001 1 -0.000002 0 -0.000002 -1 376.31691 -0.00135 376.3191 20 'point symmetry operation' ? ? -0.809026 -0.499989 -0.30901 -0.499989 0.309024 0.809021 -0.30901 0.809021 -0.499997 492.60632 71.86683 188.15628 21 'point symmetry operation' ? ? 0.809012 -0.500011 0.309012 -0.5 -0.309012 0.809019 -0.30903 -0.809012 -0.5 71.8747 188.15887 492.60953 22 'point symmetry operation' ? ? 1 -0.00001 -0.000015 -0.00001 -1 0 -0.000015 0 -1 0.00455 376.32173 376.3214 23 'point symmetry operation' ? ? 0.809022 0.500001 0.309003 0.499988 -0.309022 -0.809022 -0.309023 0.809015 -0.5 -116.28761 304.4531 188.16045 24 'point symmetry operation' ? ? 0.500003 0.309023 0.809013 0.309014 0.809014 -0.500007 -0.809016 0.500001 0.309017 -116.28996 71.87299 188.15872 25 'point symmetry operation' ? ? 0.499997 -0.309018 0.809018 -0.309013 0.80902 0.499998 -0.80902 -0.499994 0.309017 0.00074 -0.00079 376.3186 26 'point symmetry operation' ? ? -0.000003 1 -0.000006 -0.000008 -0.000006 -1 -1 -0.000003 0.000008 0.00099 376.32201 376.31756 27 'point symmetry operation' ? ? -0.5 0.309021 0.809016 -0.309015 0.809016 -0.500003 -0.809018 -0.5 -0.309016 71.8699 188.15992 492.6077 28 'point symmetry operation' ? ? -0.309025 -0.809015 0.499999 -0.809011 0.500008 0.309019 -0.500004 -0.30901 -0.809017 304.45001 188.1568 492.60724 29 'point symmetry operation' ? ? 0.309002 -0.809019 -0.500006 -0.809019 -0.499992 0.309025 -0.500006 0.309025 -0.80901 376.32351 376.31696 376.31682 30 'point symmetry operation' ? ? 0.499988 0.309013 -0.809026 -0.309028 -0.809017 -0.499993 -0.80902 0.500002 -0.309005 188.16367 492.60946 304.44584 31 'point symmetry operation' ? ? -0.30901 -0.809015 0.500008 0.809014 -0.5 -0.309024 0.500009 0.309022 0.80901 304.44556 188.16202 -116.29029 32 'point symmetry operation' ? ? 0.309017 -0.809019 -0.499997 0.809016 0.499999 -0.30902 0.500001 -0.309013 0.809018 376.31896 0.00117 -0.00092 33 'point symmetry operation' ? ? 0.500003 0.309014 -0.809016 0.309023 0.809014 0.500001 0.809013 -0.500007 0.309017 188.15906 -116.28953 71.87281 34 'point symmetry operation' ? ? 0.000012 1 0.000004 0.000008 -0.000004 1 1 -0.000012 -0.000008 -0.00356 -0.00028 0.00384 35 'point symmetry operation' ? ? -0.499985 0.30902 0.809025 0.30902 -0.809019 0.499995 0.809025 0.499995 0.309004 71.86545 188.16112 -116.28734 36 'point symmetry operation' ? ? -0.5 0.309026 -0.809014 -0.309006 0.809018 0.500005 0.809021 0.499993 -0.309018 376.31617 -0.00304 0.0005 37 'point symmetry operation' ? ? -0.809017 0.500008 -0.309004 -0.499991 -0.309015 0.809023 0.309031 0.809013 0.499998 304.44401 188.15704 -116.29088 38 'point symmetry operation' ? ? -1 0 0.000015 0 -1 0.000002 0.000015 0.000002 1 376.31596 376.31949 -0.00319 39 'point symmetry operation' ? ? -0.809017 -0.500004 -0.309011 0.499997 -0.309019 -0.809018 0.309022 -0.809014 0.500002 492.60743 304.45019 188.15792 40 'point symmetry operation' ? ? -0.5 -0.309015 -0.809018 0.309021 0.809016 -0.5 0.809016 -0.500003 -0.309016 492.60756 71.87008 188.16021 41 'point symmetry operation' ? ? 0.809012 -0.5 -0.30903 -0.500011 -0.309012 -0.809012 0.309012 0.809019 -0.5 188.16293 492.60859 71.87053 42 'point symmetry operation' ? ? 0.809012 0.500003 -0.309024 -0.500009 0.309017 -0.809012 -0.309015 0.809015 0.500005 0.0012 376.31973 -0.0014 43 'point symmetry operation' ? ? 0.309017 0.809016 0.500001 -0.809019 0.499999 -0.309013 -0.499997 -0.30902 0.809018 -116.28944 304.4483 188.15941 44 'point symmetry operation' ? ? 0.000003 -0.000006 1 -1 0.000004 0.000003 -0.000004 -1 -0.000006 0.00071 376.31817 376.32112 45 'point symmetry operation' ? ? 0.309017 -0.809023 0.499991 -0.809023 -0.499993 -0.309014 0.499991 -0.309014 -0.809024 188.16262 492.60762 304.45065 46 'point symmetry operation' ? ? -0.30901 0.809014 0.500009 -0.809015 -0.5 0.309022 0.500008 -0.309024 0.80901 -0.003 376.31832 0.00139 47 'point symmetry operation' ? ? -0.499991 -0.309021 0.809021 -0.309021 -0.809015 -0.5 0.809021 -0.5 0.309006 188.15795 492.60918 71.87209 48 'point symmetry operation' ? ? 0.000003 -1 -0.000004 -0.000006 0.000004 -1 1 0.000003 -0.000006 376.31952 376.31977 0.00065 49 'point symmetry operation' ? ? 0.499997 -0.309013 -0.80902 -0.309018 0.80902 -0.499994 0.809018 0.499998 0.309017 304.44881 188.15809 -116.28904 50 'point symmetry operation' ? ? 0.309017 0.80902 -0.499996 -0.809013 0.500001 0.309026 0.500006 0.309009 0.809016 71.8687 188.15719 -116.28859 51 'point symmetry operation' ? ? -0.5 -0.309006 0.809021 0.309026 0.809018 0.499993 -0.809014 0.500005 -0.309018 188.15674 -116.28925 304.44656 52 'point symmetry operation' ? ? -0.000012 -1 0.000006 0.000006 0.000006 1 -1 0.000012 0.000006 376.32047 -0.00163 376.31525 53 'point symmetry operation' ? ? 0.499988 -0.309028 -0.80902 0.309013 -0.809017 0.500002 -0.809026 -0.499993 -0.309005 304.45326 188.16073 492.606 54 'point symmetry operation' ? ? 0.309017 0.80901 -0.500011 0.80901 -0.500008 -0.309021 -0.500011 -0.309021 -0.809009 71.87315 188.16385 492.60894 55 'point symmetry operation' ? ? -0.309009 0.809024 0.499994 0.809018 0.499992 -0.309027 -0.500003 0.309012 -0.809017 -0.00205 0.00341 376.32001 56 'point symmetry operation' ? ? -0.000003 -0.000008 -1 1 -0.000006 -0.000003 -0.000006 -1 0.000008 376.32075 0.00221 376.31882 57 'point symmetry operation' ? ? -0.309009 0.809018 -0.500003 0.809024 0.499992 0.309012 0.499994 -0.309027 -0.809017 188.15779 -116.28742 304.45137 58 'point symmetry operation' ? ? -0.809008 0.500012 0.309023 0.500012 0.309014 0.809011 0.309023 0.809011 -0.500006 188.15408 -116.28893 71.87125 59 'point symmetry operation' ? ? -0.809017 -0.499991 0.309031 0.500008 -0.309015 0.809013 -0.309004 0.809023 0.499998 376.31476 -0.00025 -0.00371 60 'point symmetry operation' ? ? -0.309024 -0.809021 -0.499989 0.809018 -0.5 0.309015 -0.499994 -0.309007 0.809024 492.60815 71.87163 188.15523 # _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 7LII _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 2 128.436 135.748 113.335 1 40.47 ? N1 RBF 301 A 1 HETATM 2 C C2 RBF . . . B 2 128.375 136.232 114.573 1 40.47 ? C2 RBF 301 A 1 HETATM 3 O O2 RBF . . . B 2 127.615 135.692 115.356 1 40.47 ? O2 RBF 301 A 1 HETATM 4 N N3 RBF . . . B 2 129.093 137.273 115.016 1 40.47 ? N3 RBF 301 A 1 HETATM 5 C C4 RBF . . . B 2 129.963 137.917 114.206 1 40.47 ? C4 RBF 301 A 1 HETATM 6 O O4 RBF . . . B 2 130.613 138.865 114.596 1 40.47 ? O4 RBF 301 A 1 HETATM 7 C C4A RBF . . . B 2 130.062 137.428 112.785 1 40.47 ? C4A RBF 301 A 1 HETATM 8 N N5 RBF . . . B 2 130.862 137.935 111.859 1 40.47 ? N5 RBF 301 A 1 HETATM 9 C C5A RBF . . . B 2 130.922 137.431 110.6 1 40.47 ? C5A RBF 301 A 1 HETATM 10 C C6 RBF . . . B 2 131.775 137.989 109.619 1 40.47 ? C6 RBF 301 A 1 HETATM 11 C C7 RBF . . . B 2 131.828 137.479 108.343 1 40.47 ? C7 RBF 301 A 1 HETATM 12 C C7M RBF . . . B 2 132.757 138.12 107.348 1 40.47 ? C7M RBF 301 A 1 HETATM 13 C C8 RBF . . . B 2 131.046 136.388 107.95 1 40.47 ? C8 RBF 301 A 1 HETATM 14 C C8M RBF . . . B 2 131.117 135.841 106.55 1 40.47 ? C8M RBF 301 A 1 HETATM 15 C C9 RBF . . . B 2 130.203 135.826 108.902 1 40.47 ? C9 RBF 301 A 1 HETATM 16 C C9A RBF . . . B 2 130.129 136.328 110.214 1 40.47 ? C9A RBF 301 A 1 HETATM 17 N N10 RBF . . . B 2 129.283 135.762 111.148 1 40.47 ? N10 RBF 301 A 1 HETATM 18 C C10 RBF . . . B 2 129.231 136.267 112.417 1 40.47 ? C10 RBF 301 A 1 HETATM 19 C C1' RBF . . . B 2 128.447 134.617 110.792 1 40.47 ? C1' RBF 301 A 1 HETATM 20 C C2' RBF . . . B 2 128.96 133.353 111.494 1 40.47 ? C2' RBF 301 A 1 HETATM 21 O O2' RBF . . . B 2 130.384 133.396 111.621 1 40.47 ? O2' RBF 301 A 1 HETATM 22 C C3' RBF . . . B 2 128.558 132.112 110.693 1 40.47 ? C3' RBF 301 A 1 HETATM 23 O O3' RBF . . . B 2 127.569 132.477 109.731 1 40.47 ? O3' RBF 301 A 1 HETATM 24 C C4' RBF . . . B 2 127.993 131.062 111.646 1 40.47 ? C4' RBF 301 A 1 HETATM 25 O O4' RBF . . . B 2 127.609 129.896 110.915 1 40.47 ? O4' RBF 301 A 1 HETATM 26 C C5' RBF . . . B 2 126.776 131.638 112.372 1 40.47 ? C5' RBF 301 A 1 HETATM 27 O O5' RBF . . . B 2 126.427 130.786 113.466 1 40.47 ? O5' RBF 301 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 235 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #