data_2B99 # _model_server_result.job_id ICJ4P6tJX7pfpT5B87cYUg _model_server_result.datetime_utc '2025-03-04 16:16:00' _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 2b99 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1210}' # _entry.id 2B99 # _exptl.entry_id 2B99 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.251 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 68.5 _cell.angle_beta 74.39 _cell.angle_gamma 74.53 _cell.entry_id 2B99 _cell.length_a 41.94 _cell.length_b 72.912 _cell.length_c 72.782 _cell.Z_PDB 5 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2B99 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N # _chem_comp.formula 'C11 H14 N4 O8' _chem_comp.formula_weight 330.251 _chem_comp.id RDL _chem_comp.mon_nstd_flag . _chem_comp.name 6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE _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 O15 C15 RDL sing 277 n n O15 H15O RDL sing 278 n n C15 C14 RDL sing 279 n n C15 H151 RDL sing 280 n n C15 H152 RDL sing 281 n n C14 O14 RDL sing 282 n n C14 C13 RDL sing 283 n n C14 H141 RDL sing 284 n n O14 H14O RDL sing 285 n n C13 O13 RDL sing 286 n n C13 C12 RDL sing 287 n n C13 H131 RDL sing 288 n n O13 H13O RDL sing 289 n n C12 O12 RDL sing 290 n n C12 C11 RDL sing 291 n n C12 H121 RDL sing 292 n n O12 H12O RDL sing 293 n n C11 N9 RDL sing 294 n n C11 H111 RDL sing 295 n n C11 H112 RDL sing 296 n n N9 C8 RDL sing 297 n y N9 C10 RDL sing 298 n y C8 O8 RDL doub 299 n n C8 C7 RDL sing 300 n y C7 O7 RDL doub 301 n n C7 N6 RDL sing 302 n y C10 C5 RDL doub 303 n y C10 N1 RDL sing 304 n y C5 N6 RDL sing 305 n y C5 C4 RDL sing 306 n y N6 HN6 RDL sing 307 n n C4 O4 RDL doub 308 n n C4 N3 RDL sing 309 n y N3 C2 RDL sing 310 n y N3 HN3 RDL sing 311 n n C2 N1 RDL sing 312 n y C2 O2 RDL doub 313 n n N1 HN1 RDL sing 314 n n # _atom_sites.entry_id 2B99 _atom_sites.fract_transf_matrix[1][1] 0.023844 _atom_sites.fract_transf_matrix[1][2] -0.006599 _atom_sites.fract_transf_matrix[1][3] -0.004816 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014231 _atom_sites.fract_transf_matrix[2][3] -0.004765 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015044 _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 F 2 RDL A 1 1205 1201 RDL RDL . G 2 RDL A 1 1208 1201 RDL RDL . H 2 RDL B 1 1206 1201 RDL RDL . I 2 RDL B 1 1209 1201 RDL RDL . J 2 RDL B 1 1210 1201 RDL RDL . K 2 RDL C 1 1201 1201 RDL RDL . L 2 RDL C 1 1204 1201 RDL RDL . M 2 RDL D 1 1203 1201 RDL RDL . N 2 RDL E 1 1202 1201 RDL RDL . O 2 RDL E 1 1207 1201 RDL RDL . P 3 HOH A 1 1209 2 HOH TIP . P 3 HOH A 2 1210 8 HOH TIP . P 3 HOH A 3 1211 11 HOH TIP . P 3 HOH A 4 1212 13 HOH TIP . P 3 HOH A 5 1213 30 HOH TIP . P 3 HOH A 6 1214 33 HOH TIP . P 3 HOH A 7 1215 34 HOH TIP . P 3 HOH A 8 1216 38 HOH TIP . P 3 HOH A 9 1217 41 HOH TIP . P 3 HOH A 10 1218 42 HOH TIP . P 3 HOH A 11 1219 52 HOH TIP . P 3 HOH A 12 1220 55 HOH TIP . P 3 HOH A 13 1221 60 HOH TIP . P 3 HOH A 14 1222 63 HOH TIP . P 3 HOH A 15 1223 65 HOH TIP . P 3 HOH A 16 1224 73 HOH TIP . P 3 HOH A 17 1225 74 HOH TIP . P 3 HOH A 18 1226 77 HOH TIP . P 3 HOH A 19 1227 81 HOH TIP . P 3 HOH A 20 1228 87 HOH TIP . P 3 HOH A 21 1229 104 HOH TIP . P 3 HOH A 22 1230 113 HOH TIP . P 3 HOH A 23 1231 115 HOH TIP . P 3 HOH A 24 1232 118 HOH TIP . P 3 HOH A 25 1233 124 HOH TIP . P 3 HOH A 26 1234 129 HOH TIP . P 3 HOH A 27 1235 130 HOH TIP . P 3 HOH A 28 1236 134 HOH TIP . P 3 HOH A 29 1237 153 HOH TIP . P 3 HOH A 30 1238 156 HOH TIP . P 3 HOH A 31 1239 164 HOH TIP . P 3 HOH A 32 1240 167 HOH TIP . P 3 HOH A 33 1241 173 HOH TIP . P 3 HOH A 34 1242 180 HOH TIP . P 3 HOH A 35 1243 192 HOH TIP . P 3 HOH A 36 1244 222 HOH TIP . P 3 HOH A 37 1245 229 HOH TIP . P 3 HOH A 38 1246 231 HOH TIP . P 3 HOH A 39 1247 233 HOH TIP . Q 3 HOH B 1 1211 20 HOH TIP . Q 3 HOH B 2 1212 31 HOH TIP . Q 3 HOH B 3 1213 35 HOH TIP . Q 3 HOH B 4 1214 43 HOH TIP . Q 3 HOH B 5 1215 57 HOH TIP . Q 3 HOH B 6 1216 58 HOH TIP . Q 3 HOH B 7 1217 59 HOH TIP . Q 3 HOH B 8 1218 66 HOH TIP . Q 3 HOH B 9 1219 67 HOH TIP . Q 3 HOH B 10 1220 75 HOH TIP . Q 3 HOH B 11 1221 78 HOH TIP . Q 3 HOH B 12 1222 83 HOH TIP . Q 3 HOH B 13 1223 84 HOH TIP . Q 3 HOH B 14 1224 89 HOH TIP . Q 3 HOH B 15 1225 97 HOH TIP . Q 3 HOH B 16 1226 101 HOH TIP . Q 3 HOH B 17 1227 103 HOH TIP . Q 3 HOH B 18 1228 105 HOH TIP . Q 3 HOH B 19 1229 116 HOH TIP . Q 3 HOH B 20 1230 120 HOH TIP . Q 3 HOH B 21 1231 121 HOH TIP . Q 3 HOH B 22 1232 123 HOH TIP . Q 3 HOH B 23 1233 125 HOH TIP . Q 3 HOH B 24 1234 126 HOH TIP . Q 3 HOH B 25 1235 127 HOH TIP . Q 3 HOH B 26 1236 128 HOH TIP . Q 3 HOH B 27 1237 131 HOH TIP . Q 3 HOH B 28 1238 132 HOH TIP . Q 3 HOH B 29 1239 137 HOH TIP . Q 3 HOH B 30 1240 141 HOH TIP . Q 3 HOH B 31 1241 158 HOH TIP . Q 3 HOH B 32 1242 159 HOH TIP . Q 3 HOH B 33 1243 160 HOH TIP . Q 3 HOH B 34 1244 170 HOH TIP . Q 3 HOH B 35 1245 171 HOH TIP . Q 3 HOH B 36 1246 172 HOH TIP . Q 3 HOH B 37 1247 174 HOH TIP . Q 3 HOH B 38 1248 175 HOH TIP . Q 3 HOH B 39 1249 176 HOH TIP . Q 3 HOH B 40 1250 200 HOH TIP . Q 3 HOH B 41 1251 203 HOH TIP . Q 3 HOH B 42 1252 206 HOH TIP . Q 3 HOH B 43 1253 226 HOH TIP . Q 3 HOH B 44 1254 228 HOH TIP . R 3 HOH C 1 1205 1 HOH TIP . R 3 HOH C 2 1206 4 HOH TIP . R 3 HOH C 3 1207 6 HOH TIP . R 3 HOH C 4 1208 14 HOH TIP . R 3 HOH C 5 1209 15 HOH TIP . R 3 HOH C 6 1210 17 HOH TIP . R 3 HOH C 7 1211 19 HOH TIP . R 3 HOH C 8 1212 23 HOH TIP . R 3 HOH C 9 1213 25 HOH TIP . R 3 HOH C 10 1214 26 HOH TIP . R 3 HOH C 11 1215 27 HOH TIP . R 3 HOH C 12 1216 36 HOH TIP . R 3 HOH C 13 1217 37 HOH TIP . R 3 HOH C 14 1218 48 HOH TIP . R 3 HOH C 15 1219 49 HOH TIP . R 3 HOH C 16 1220 50 HOH TIP . R 3 HOH C 17 1221 56 HOH TIP . R 3 HOH C 18 1222 70 HOH TIP . R 3 HOH C 19 1223 76 HOH TIP . R 3 HOH C 20 1224 80 HOH TIP . R 3 HOH C 21 1225 86 HOH TIP . R 3 HOH C 22 1226 91 HOH TIP . R 3 HOH C 23 1227 93 HOH TIP . R 3 HOH C 24 1228 94 HOH TIP . R 3 HOH C 25 1229 100 HOH TIP . R 3 HOH C 26 1230 107 HOH TIP . R 3 HOH C 27 1231 108 HOH TIP . R 3 HOH C 28 1232 110 HOH TIP . R 3 HOH C 29 1233 112 HOH TIP . R 3 HOH C 30 1234 114 HOH TIP . R 3 HOH C 31 1235 133 HOH TIP . R 3 HOH C 32 1236 136 HOH TIP . R 3 HOH C 33 1237 138 HOH TIP . R 3 HOH C 34 1238 139 HOH TIP . R 3 HOH C 35 1239 142 HOH TIP . R 3 HOH C 36 1240 145 HOH TIP . R 3 HOH C 37 1241 146 HOH TIP . R 3 HOH C 38 1242 148 HOH TIP . R 3 HOH C 39 1243 151 HOH TIP . R 3 HOH C 40 1244 155 HOH TIP . R 3 HOH C 41 1245 169 HOH TIP . R 3 HOH C 42 1246 183 HOH TIP . R 3 HOH C 43 1247 195 HOH TIP . R 3 HOH C 44 1248 208 HOH TIP . R 3 HOH C 45 1249 212 HOH TIP . R 3 HOH C 46 1250 217 HOH TIP . R 3 HOH C 47 1251 220 HOH TIP . R 3 HOH C 48 1252 223 HOH TIP . R 3 HOH C 49 1253 224 HOH TIP . R 3 HOH C 50 1254 230 HOH TIP . S 3 HOH D 1 1204 3 HOH TIP . S 3 HOH D 2 1205 9 HOH TIP . S 3 HOH D 3 1206 10 HOH TIP . S 3 HOH D 4 1207 21 HOH TIP . S 3 HOH D 5 1208 24 HOH TIP . S 3 HOH D 6 1209 28 HOH TIP . S 3 HOH D 7 1210 32 HOH TIP . S 3 HOH D 8 1211 39 HOH TIP . S 3 HOH D 9 1212 46 HOH TIP . S 3 HOH D 10 1213 47 HOH TIP . S 3 HOH D 11 1214 64 HOH TIP . S 3 HOH D 12 1215 69 HOH TIP . S 3 HOH D 13 1216 79 HOH TIP . S 3 HOH D 14 1217 85 HOH TIP . S 3 HOH D 15 1218 98 HOH TIP . S 3 HOH D 16 1219 106 HOH TIP . S 3 HOH D 17 1220 111 HOH TIP . S 3 HOH D 18 1221 117 HOH TIP . S 3 HOH D 19 1222 122 HOH TIP . S 3 HOH D 20 1223 143 HOH TIP . S 3 HOH D 21 1224 147 HOH TIP . S 3 HOH D 22 1225 150 HOH TIP . S 3 HOH D 23 1226 154 HOH TIP . S 3 HOH D 24 1227 163 HOH TIP . S 3 HOH D 25 1228 184 HOH TIP . S 3 HOH D 26 1229 185 HOH TIP . S 3 HOH D 27 1230 189 HOH TIP . S 3 HOH D 28 1231 198 HOH TIP . S 3 HOH D 29 1232 199 HOH TIP . S 3 HOH D 30 1233 209 HOH TIP . S 3 HOH D 31 1234 210 HOH TIP . S 3 HOH D 32 1235 211 HOH TIP . S 3 HOH D 33 1236 227 HOH TIP . T 3 HOH E 1 1208 5 HOH TIP . T 3 HOH E 2 1209 7 HOH TIP . T 3 HOH E 3 1210 12 HOH TIP . T 3 HOH E 4 1211 16 HOH TIP . T 3 HOH E 5 1212 18 HOH TIP . T 3 HOH E 6 1213 22 HOH TIP . T 3 HOH E 7 1214 29 HOH TIP . T 3 HOH E 8 1215 40 HOH TIP . T 3 HOH E 9 1216 44 HOH TIP . T 3 HOH E 10 1217 51 HOH TIP . T 3 HOH E 11 1218 53 HOH TIP . T 3 HOH E 12 1219 54 HOH TIP . T 3 HOH E 13 1220 61 HOH TIP . T 3 HOH E 14 1221 62 HOH TIP . T 3 HOH E 15 1222 68 HOH TIP . T 3 HOH E 16 1223 71 HOH TIP . T 3 HOH E 17 1224 72 HOH TIP . T 3 HOH E 18 1225 90 HOH TIP . T 3 HOH E 19 1226 92 HOH TIP . T 3 HOH E 20 1227 95 HOH TIP . T 3 HOH E 21 1228 96 HOH TIP . T 3 HOH E 22 1229 99 HOH TIP . T 3 HOH E 23 1230 109 HOH TIP . T 3 HOH E 24 1231 135 HOH TIP . T 3 HOH E 25 1232 140 HOH TIP . T 3 HOH E 26 1233 157 HOH TIP . T 3 HOH E 27 1234 166 HOH TIP . T 3 HOH E 28 1235 177 HOH TIP . T 3 HOH E 29 1236 179 HOH TIP . T 3 HOH E 30 1237 186 HOH TIP . T 3 HOH E 31 1238 187 HOH TIP . T 3 HOH E 32 1239 188 HOH TIP . T 3 HOH E 33 1240 191 HOH TIP . T 3 HOH E 34 1241 193 HOH TIP . T 3 HOH E 35 1242 197 HOH TIP . T 3 HOH E 36 1243 201 HOH TIP . T 3 HOH E 37 1244 213 HOH TIP . T 3 HOH E 38 1245 215 HOH TIP . T 3 HOH E 39 1246 219 HOH TIP . T 3 HOH E 40 1247 221 HOH TIP . T 3 HOH E 41 1248 225 HOH TIP . # 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 O O15 RDL . . . J 2 -3.459 -12.291 13.746 1 29.45 ? O15 RDL 1210 B 1 HETATM 2 C C15 RDL . . . J 2 -4.449 -13.199 14.205 1 32.75 ? C15 RDL 1210 B 1 HETATM 3 C C14 RDL . . . J 2 -5.769 -12.997 13.422 1 32.73 ? C14 RDL 1210 B 1 HETATM 4 O O14 RDL . . . J 2 -6.105 -11.606 13.409 1 31.92 ? O14 RDL 1210 B 1 HETATM 5 C C13 RDL . . . J 2 -5.641 -13.492 11.978 1 32.64 ? C13 RDL 1210 B 1 HETATM 6 O O13 RDL . . . J 2 -5.314 -14.883 12.055 1 30.26 ? O13 RDL 1210 B 1 HETATM 7 C C12 RDL . . . J 2 -6.92 -13.311 11.108 1 34.92 ? C12 RDL 1210 B 1 HETATM 8 O O12 RDL . . . J 2 -6.736 -13.771 9.773 1 35.48 ? O12 RDL 1210 B 1 HETATM 9 C C11 RDL . . . J 2 -8.092 -14.082 11.607 1 34.05 ? C11 RDL 1210 B 1 HETATM 10 N N9 RDL . . . J 2 -9.395 -13.889 10.978 1 35.57 ? N9 RDL 1210 B 1 HETATM 11 C C8 RDL . . . J 2 -10.218 -12.938 11.489 1 38.08 ? C8 RDL 1210 B 1 HETATM 12 O O8 RDL . . . J 2 -9.879 -12.235 12.465 1 38.13 ? O8 RDL 1210 B 1 HETATM 13 C C7 RDL . . . J 2 -11.566 -12.72 10.872 1 39 ? C7 RDL 1210 B 1 HETATM 14 O O7 RDL . . . J 2 -12.322 -11.83 11.361 1 40.64 ? O7 RDL 1210 B 1 HETATM 15 C C10 RDL . . . J 2 -9.75 -14.659 9.908 1 37.54 ? C10 RDL 1210 B 1 HETATM 16 C C5 RDL . . . J 2 -11.084 -14.439 9.304 1 38.75 ? C5 RDL 1210 B 1 HETATM 17 N N6 RDL . . . J 2 -11.938 -13.481 9.812 1 38.31 ? N6 RDL 1210 B 1 HETATM 18 C C4 RDL . . . J 2 -11.432 -15.277 8.163 1 38.64 ? C4 RDL 1210 B 1 HETATM 19 O O4 RDL . . . J 2 -12.558 -15.145 7.603 1 37 ? O4 RDL 1210 B 1 HETATM 20 N N3 RDL . . . J 2 -10.517 -16.192 7.726 1 38.52 ? N3 RDL 1210 B 1 HETATM 21 C C2 RDL . . . J 2 -9.287 -16.351 8.325 1 38.02 ? C2 RDL 1210 B 1 HETATM 22 N N1 RDL . . . J 2 -8.934 -15.612 9.371 1 38.73 ? N1 RDL 1210 B 1 HETATM 23 O O2 RDL . . . J 2 -8.494 -17.2 7.877 1 35.49 ? O2 RDL 1210 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 23 #