data_2VXA # _model_server_result.job_id 0Ym2Mkbb8zVhZr2oPC32CA _model_server_result.datetime_utc '2024-11-08 06:54:23' _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 2vxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":200}' # _entry.id 2VXA # _exptl.entry_id 2VXA _exptl.method 'X-RAY DIFFRACTION' # _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 12 _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 2VXA _cell.length_a 85.76 _cell.length_b 100.51 _cell.length_c 100.47 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VXA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 M N N ? 2 P N N ? 2 S N N ? 2 V N N ? 2 Z N N ? 2 DA N N ? 2 FA N N ? 2 KA N N ? 2 MA N N ? 2 PA N N ? 2 SA N N ? 2 VA N 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 262 n n N1 C10 RBF doub 263 n n C2 O2 RBF doub 264 n n C2 N3 RBF sing 265 n n N3 C4 RBF sing 266 n n N3 HN3 RBF sing 267 n n C4 O4 RBF doub 268 n n C4 C4A RBF sing 269 n n C4A N5 RBF doub 270 n n C4A C10 RBF sing 271 n n N5 C5A RBF sing 272 n n C5A C6 RBF doub 273 n y C5A C9A RBF sing 274 n y C6 C7 RBF sing 275 n y C6 HC6 RBF sing 276 n n C7 C7M RBF sing 277 n n C7 C8 RBF doub 278 n y C7M HC71 RBF sing 279 n n C7M HC72 RBF sing 280 n n C7M HC73 RBF sing 281 n n C8 C8M RBF sing 282 n n C8 C9 RBF sing 283 n y C8M HC81 RBF sing 284 n n C8M HC82 RBF sing 285 n n C8M HC83 RBF sing 286 n n C9 C9A RBF doub 287 n y C9 HC9 RBF sing 288 n n C9A N10 RBF sing 289 n n N10 C10 RBF sing 290 n n N10 C1' RBF sing 291 n n C1' C2' RBF sing 292 n n C1' HC11 RBF sing 293 n n C1' HC12 RBF sing 294 n n C2' O2' RBF sing 295 n n C2' C3' RBF sing 296 n n C2' HC2' RBF sing 297 n n O2' HO2' RBF sing 298 n n C3' O3' RBF sing 299 n n C3' C4' RBF sing 300 n n C3' HC3' RBF sing 301 n n O3' HO3' RBF sing 302 n n C4' O4' RBF sing 303 n n C4' C5' RBF sing 304 n n C4' HC4' RBF sing 305 n n O4' HO4' RBF sing 306 n n C5' O5' RBF sing 307 n n C5' HC51 RBF sing 308 n n C5' HC52 RBF sing 309 n n O5' HO5' RBF sing 310 n n # _atom_sites.entry_id 2VXA _atom_sites.fract_transf_matrix[1][1] 0.01166 _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] 0.009949 _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] 0.009953 _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 M 2 RBF A 1 200 200 RBF RBF . N 3 CL A 1 1069 1069 CL CL . O 3 CL A 1 1070 1070 CL CL . P 2 RBF B 1 200 200 RBF RBF . Q 3 CL B 1 1069 1069 CL CL . R 3 CL B 1 1070 1070 CL CL . S 2 RBF C 1 200 200 RBF RBF . T 3 CL C 1 1069 1069 CL CL . U 3 CL C 1 1070 1070 CL CL . V 2 RBF D 1 200 200 RBF RBF . W 3 CL D 1 1069 1069 CL CL . X 3 CL D 1 1070 1070 CL CL . Y 3 CL D 1 1071 1071 CL CL . Z 2 RBF E 1 200 200 RBF RBF . AA 3 CL E 1 1069 1069 CL CL . BA 3 CL E 1 1070 1070 CL CL . CA 3 CL E 1 1071 1071 CL CL . DA 2 RBF F 1 200 200 RBF RBF . EA 3 CL F 1 1069 1069 CL CL . FA 2 RBF G 1 200 200 RBF RBF . GA 3 CL G 1 1069 1069 CL CL . HA 3 CL G 1 1070 1070 CL CL . IA 3 CL G 1 1071 1071 CL CL . JA 3 CL G 1 1072 1072 CL CL . KA 2 RBF H 1 200 200 RBF RBF . LA 3 CL H 1 1069 1069 CL CL . MA 2 RBF I 1 200 200 RBF RBF . NA 3 CL I 1 1069 1069 CL CL . OA 3 CL I 1 1070 1070 CL CL . PA 2 RBF J 1 200 200 RBF RBF . QA 3 CL J 1 1069 1069 CL CL . RA 3 CL J 1 1070 1070 CL CL . SA 2 RBF K 1 200 200 RBF RBF . TA 3 CL K 1 1069 1069 CL CL . UA 3 CL K 1 1070 1070 CL CL . VA 2 RBF L 1 200 200 RBF RBF . # 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 . . . S 2 2.249 -27.877 12.42 1 36.37 ? N1 RBF 200 C 1 HETATM 2 C C2 RBF . . . S 2 2.254 -29.22 12.504 1 36.65 ? C2 RBF 200 C 1 HETATM 3 O O2 RBF . . . S 2 3.25 -29.863 12.089 1 36.83 ? O2 RBF 200 C 1 HETATM 4 N N3 RBF . . . S 2 1.22 -29.9 13.008 1 36.82 ? N3 RBF 200 C 1 HETATM 5 C C4 RBF . . . S 2 0.118 -29.303 13.448 1 36.57 ? C4 RBF 200 C 1 HETATM 6 O O4 RBF . . . S 2 -0.798 -29.969 13.904 1 36.27 ? O4 RBF 200 C 1 HETATM 7 C C4A RBF . . . S 2 0.028 -27.83 13.385 1 36.5 ? C4A RBF 200 C 1 HETATM 8 N N5 RBF . . . S 2 -1.051 -27.142 13.814 1 36.42 ? N5 RBF 200 C 1 HETATM 9 C C5A RBF . . . S 2 -1.092 -25.826 13.733 1 36.11 ? C5A RBF 200 C 1 HETATM 10 C C6 RBF . . . S 2 -2.213 -25.178 14.179 1 36.7 ? C6 RBF 200 C 1 HETATM 11 C C7 RBF . . . S 2 -2.299 -23.792 14.109 1 36.74 ? C7 RBF 200 C 1 HETATM 12 C C7M RBF . . . S 2 -3.559 -23.14 14.594 1 36.33 ? C7M RBF 200 C 1 HETATM 13 C C8 RBF . . . S 2 -1.145 -23.009 13.54 1 36.72 ? C8 RBF 200 C 1 HETATM 14 C C8M RBF . . . S 2 -1.184 -21.509 13.431 1 36.78 ? C8M RBF 200 C 1 HETATM 15 C C9 RBF . . . S 2 -0.016 -23.663 13.095 1 36.54 ? C9 RBF 200 C 1 HETATM 16 C C9A RBF . . . S 2 0.052 -25.056 13.18 1 36.81 ? C9A RBF 200 C 1 HETATM 17 N N10 RBF . . . S 2 1.189 -25.77 12.728 1 37.21 ? N10 RBF 200 C 1 HETATM 18 C C10 RBF . . . S 2 1.207 -27.156 12.825 1 36.67 ? C10 RBF 200 C 1 HETATM 19 C C1' RBF . . . S 2 2.351 -25.099 12.204 1 37.78 ? C1' RBF 200 C 1 HETATM 20 C C2' RBF . . . S 2 2.21 -24.755 10.747 1 44.13 ? C2' RBF 200 C 1 HETATM 21 O O2' RBF . . . S 2 2.731 -25.864 9.997 1 43.54 ? O2' RBF 200 C 1 HETATM 22 C C3' RBF . . . S 2 2.977 -23.427 10.633 1 46.83 ? C3' RBF 200 C 1 HETATM 23 O O3' RBF . . . S 2 2.229 -22.439 9.919 1 48.77 ? O3' RBF 200 C 1 HETATM 24 C C4' RBF . . . S 2 4.333 -23.572 9.981 1 49.63 ? C4' RBF 200 C 1 HETATM 25 O O4' RBF . . . S 2 4.937 -24.795 10.429 1 50.46 ? O4' RBF 200 C 1 HETATM 26 C C5' RBF . . . S 2 5.169 -22.339 10.338 1 51.9 ? C5' RBF 200 C 1 HETATM 27 O O5' RBF . . . S 2 4.475 -21.161 9.882 1 53.02 ? O5' RBF 200 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #