data_3LHY # _model_server_result.job_id DNkJhN3TkaZnM-AEO3F7Og _model_server_result.datetime_utc '2024-10-17 13:25:09' _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 3lhy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":229}' # _entry.id 3LHY # _exptl.entry_id 3LHY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.67 _cell.angle_gamma 90 _cell.entry_id 3LHY _cell.length_a 59.758 _cell.length_b 64.042 _cell.length_c 61.917 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LHY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 D N N # _chem_comp.formula 'C9 H13 N2 O10 P' _chem_comp.formula_weight 340.181 _chem_comp.id BMQ _chem_comp.mon_nstd_flag . _chem_comp.name "1-(5'-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC ACID" _chem_comp.type 'rna linking' _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 P O1P BMQ doub 70 n n P O2P BMQ sing 71 n n P O3P BMQ sing 72 n n P O5' BMQ sing 73 n n O2P HOP2 BMQ sing 74 n n O3P HOP3 BMQ sing 75 n n O5' C5' BMQ sing 76 n n C5' C4' BMQ sing 77 n n C5' "H5'1" BMQ sing 78 n n C5' "H5'2" BMQ sing 79 n n C4' O4' BMQ sing 80 n n C4' C3' BMQ sing 81 n n C4' H4' BMQ sing 82 n n O4' C1' BMQ sing 83 n n C3' O3' BMQ sing 84 n n C3' C2' BMQ sing 85 n n C3' H3' BMQ sing 86 n n O3' HO3' BMQ sing 87 n n C2' O2' BMQ sing 88 n n C2' C1' BMQ sing 89 n n C2' H2' BMQ sing 90 n n O2' HO2' BMQ sing 91 n n C1' N1 BMQ sing 92 n n C1' H1' BMQ sing 93 n n N1 C2 BMQ sing 94 n n N1 C6 BMQ sing 95 n n C2 O2 BMQ doub 96 n n C2 N3 BMQ sing 97 n n N3 C4 BMQ sing 98 n n N3 HN3 BMQ sing 99 n n C4 O4 BMQ doub 100 n n C4 C5 BMQ sing 101 n n C5 C6 BMQ sing 102 n n C5 H51 BMQ sing 103 n n C5 H52 BMQ sing 104 n n C6 O1 BMQ doub 105 n n # _atom_sites.entry_id 3LHY _atom_sites.fract_transf_matrix[1][1] 0.016734 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008042 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015615 _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] 0.017919 _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 C 2 BMQ A 1 229 1 BMQ BMQ . D 2 BMQ B 1 229 2 BMQ BMQ . E 3 HOH A 1 230 1 HOH HOH . E 3 HOH A 2 231 6 HOH HOH . E 3 HOH A 3 232 232 HOH HOH . E 3 HOH A 4 233 233 HOH HOH . E 3 HOH A 5 234 16 HOH HOH . E 3 HOH A 6 235 235 HOH HOH . E 3 HOH A 7 236 236 HOH HOH . E 3 HOH A 8 237 20 HOH HOH . E 3 HOH A 9 238 238 HOH HOH . E 3 HOH A 10 239 239 HOH HOH . E 3 HOH A 11 240 21 HOH HOH . E 3 HOH A 12 241 23 HOH HOH . E 3 HOH A 13 242 242 HOH HOH . E 3 HOH A 14 243 188 HOH HOH . E 3 HOH A 15 244 24 HOH HOH . E 3 HOH A 16 245 245 HOH HOH . E 3 HOH A 17 246 28 HOH HOH . E 3 HOH A 18 247 29 HOH HOH . E 3 HOH A 19 248 248 HOH HOH . E 3 HOH A 20 249 249 HOH HOH . E 3 HOH A 21 250 250 HOH HOH . E 3 HOH A 22 251 251 HOH HOH . E 3 HOH A 23 252 31 HOH HOH . E 3 HOH A 24 253 253 HOH HOH . E 3 HOH A 25 254 33 HOH HOH . E 3 HOH A 26 255 34 HOH HOH . E 3 HOH A 27 256 256 HOH HOH . E 3 HOH A 28 257 37 HOH HOH . E 3 HOH A 29 258 38 HOH HOH . E 3 HOH A 30 259 259 HOH HOH . E 3 HOH A 31 260 40 HOH HOH . E 3 HOH A 32 261 261 HOH HOH . E 3 HOH A 33 262 46 HOH HOH . E 3 HOH A 34 263 48 HOH HOH . E 3 HOH A 35 264 264 HOH HOH . E 3 HOH A 36 265 265 HOH HOH . E 3 HOH A 37 266 52 HOH HOH . E 3 HOH A 38 267 267 HOH HOH . E 3 HOH A 39 268 57 HOH HOH . E 3 HOH A 40 269 61 HOH HOH . E 3 HOH A 41 270 63 HOH HOH . E 3 HOH A 42 271 65 HOH HOH . E 3 HOH A 43 272 67 HOH HOH . E 3 HOH A 44 273 68 HOH HOH . E 3 HOH A 45 274 72 HOH HOH . E 3 HOH A 46 275 74 HOH HOH . E 3 HOH A 47 276 75 HOH HOH . E 3 HOH A 48 277 79 HOH HOH . E 3 HOH A 49 278 80 HOH HOH . E 3 HOH A 50 279 82 HOH HOH . E 3 HOH A 51 280 83 HOH HOH . E 3 HOH A 52 281 85 HOH HOH . E 3 HOH A 53 282 88 HOH HOH . E 3 HOH A 54 283 90 HOH HOH . E 3 HOH A 55 284 92 HOH HOH . E 3 HOH A 56 285 96 HOH HOH . E 3 HOH A 57 286 97 HOH HOH . E 3 HOH A 58 287 98 HOH HOH . E 3 HOH A 59 288 99 HOH HOH . E 3 HOH A 60 289 102 HOH HOH . E 3 HOH A 61 290 105 HOH HOH . E 3 HOH A 62 291 106 HOH HOH . E 3 HOH A 63 292 107 HOH HOH . E 3 HOH A 64 293 108 HOH HOH . E 3 HOH A 65 294 113 HOH HOH . E 3 HOH A 66 295 115 HOH HOH . E 3 HOH A 67 296 116 HOH HOH . E 3 HOH A 68 297 118 HOH HOH . E 3 HOH A 69 298 120 HOH HOH . E 3 HOH A 70 299 123 HOH HOH . E 3 HOH A 71 300 124 HOH HOH . E 3 HOH A 72 301 126 HOH HOH . E 3 HOH A 73 302 127 HOH HOH . E 3 HOH A 74 303 128 HOH HOH . E 3 HOH A 75 304 130 HOH HOH . E 3 HOH A 76 305 131 HOH HOH . E 3 HOH A 77 306 132 HOH HOH . E 3 HOH A 78 307 135 HOH HOH . E 3 HOH A 79 308 136 HOH HOH . E 3 HOH A 80 309 140 HOH HOH . E 3 HOH A 81 310 144 HOH HOH . E 3 HOH A 82 311 145 HOH HOH . E 3 HOH A 83 312 146 HOH HOH . E 3 HOH A 84 313 147 HOH HOH . E 3 HOH A 85 314 149 HOH HOH . E 3 HOH A 86 315 150 HOH HOH . E 3 HOH A 87 316 152 HOH HOH . E 3 HOH A 88 317 153 HOH HOH . E 3 HOH A 89 318 155 HOH HOH . E 3 HOH A 90 319 156 HOH HOH . E 3 HOH A 91 320 158 HOH HOH . E 3 HOH A 92 321 161 HOH HOH . E 3 HOH A 93 322 162 HOH HOH . E 3 HOH A 94 323 163 HOH HOH . E 3 HOH A 95 324 167 HOH HOH . E 3 HOH A 96 325 168 HOH HOH . E 3 HOH A 97 326 170 HOH HOH . E 3 HOH A 98 327 171 HOH HOH . E 3 HOH A 99 328 172 HOH HOH . E 3 HOH A 100 329 176 HOH HOH . E 3 HOH A 101 330 180 HOH HOH . E 3 HOH A 102 331 182 HOH HOH . E 3 HOH A 103 332 183 HOH HOH . E 3 HOH A 104 333 184 HOH HOH . E 3 HOH A 105 334 185 HOH HOH . E 3 HOH A 106 335 187 HOH HOH . E 3 HOH A 107 336 198 HOH HOH . E 3 HOH A 108 337 201 HOH HOH . E 3 HOH A 109 338 202 HOH HOH . E 3 HOH A 110 339 204 HOH HOH . E 3 HOH A 111 340 205 HOH HOH . E 3 HOH A 112 341 206 HOH HOH . E 3 HOH A 113 342 207 HOH HOH . E 3 HOH A 114 343 208 HOH HOH . E 3 HOH A 115 344 209 HOH HOH . E 3 HOH A 116 345 212 HOH HOH . E 3 HOH A 117 346 213 HOH HOH . E 3 HOH A 118 347 215 HOH HOH . E 3 HOH A 119 348 222 HOH HOH . E 3 HOH A 120 349 225 HOH HOH . E 3 HOH A 121 350 227 HOH HOH . E 3 HOH A 122 351 228 HOH HOH . F 3 HOH B 1 230 230 HOH HOH . F 3 HOH B 2 231 231 HOH HOH . F 3 HOH B 3 232 3 HOH HOH . F 3 HOH B 4 233 11 HOH HOH . F 3 HOH B 5 234 234 HOH HOH . F 3 HOH B 6 235 13 HOH HOH . F 3 HOH B 7 236 15 HOH HOH . F 3 HOH B 8 237 17 HOH HOH . F 3 HOH B 9 238 18 HOH HOH . F 3 HOH B 10 239 19 HOH HOH . F 3 HOH B 11 240 240 HOH HOH . F 3 HOH B 12 241 22 HOH HOH . F 3 HOH B 13 242 25 HOH HOH . F 3 HOH B 14 243 243 HOH HOH . F 3 HOH B 15 244 244 HOH HOH . F 3 HOH B 16 245 30 HOH HOH . F 3 HOH B 17 246 36 HOH HOH . F 3 HOH B 18 247 247 HOH HOH . F 3 HOH B 19 248 42 HOH HOH . F 3 HOH B 20 249 43 HOH HOH . F 3 HOH B 21 250 45 HOH HOH . F 3 HOH B 22 251 47 HOH HOH . F 3 HOH B 23 252 252 HOH HOH . F 3 HOH B 24 253 49 HOH HOH . F 3 HOH B 25 254 254 HOH HOH . F 3 HOH B 26 255 50 HOH HOH . F 3 HOH B 27 256 51 HOH HOH . F 3 HOH B 28 257 53 HOH HOH . F 3 HOH B 29 258 258 HOH HOH . F 3 HOH B 30 259 54 HOH HOH . F 3 HOH B 31 260 260 HOH HOH . F 3 HOH B 32 261 55 HOH HOH . F 3 HOH B 33 262 262 HOH HOH . F 3 HOH B 34 263 263 HOH HOH . F 3 HOH B 35 264 56 HOH HOH . F 3 HOH B 36 265 58 HOH HOH . F 3 HOH B 37 266 266 HOH HOH . F 3 HOH B 38 267 59 HOH HOH . F 3 HOH B 39 268 60 HOH HOH . F 3 HOH B 40 269 62 HOH HOH . F 3 HOH B 41 270 64 HOH HOH . F 3 HOH B 42 271 66 HOH HOH . F 3 HOH B 43 272 69 HOH HOH . F 3 HOH B 44 273 70 HOH HOH . F 3 HOH B 45 274 71 HOH HOH . F 3 HOH B 46 275 73 HOH HOH . F 3 HOH B 47 276 76 HOH HOH . F 3 HOH B 48 277 77 HOH HOH . F 3 HOH B 49 278 78 HOH HOH . F 3 HOH B 50 279 81 HOH HOH . F 3 HOH B 51 280 84 HOH HOH . F 3 HOH B 52 281 87 HOH HOH . F 3 HOH B 53 282 89 HOH HOH . F 3 HOH B 54 283 91 HOH HOH . F 3 HOH B 55 284 93 HOH HOH . F 3 HOH B 56 285 100 HOH HOH . F 3 HOH B 57 286 101 HOH HOH . F 3 HOH B 58 287 103 HOH HOH . F 3 HOH B 59 288 104 HOH HOH . F 3 HOH B 60 289 109 HOH HOH . F 3 HOH B 61 290 110 HOH HOH . F 3 HOH B 62 291 111 HOH HOH . F 3 HOH B 63 292 112 HOH HOH . F 3 HOH B 64 293 114 HOH HOH . F 3 HOH B 65 294 117 HOH HOH . F 3 HOH B 66 295 122 HOH HOH . F 3 HOH B 67 296 125 HOH HOH . F 3 HOH B 68 297 129 HOH HOH . F 3 HOH B 69 298 133 HOH HOH . F 3 HOH B 70 299 134 HOH HOH . F 3 HOH B 71 300 137 HOH HOH . F 3 HOH B 72 301 138 HOH HOH . F 3 HOH B 73 302 139 HOH HOH . F 3 HOH B 74 303 141 HOH HOH . F 3 HOH B 75 304 143 HOH HOH . F 3 HOH B 76 305 148 HOH HOH . F 3 HOH B 77 306 151 HOH HOH . F 3 HOH B 78 307 154 HOH HOH . F 3 HOH B 79 308 157 HOH HOH . F 3 HOH B 80 309 159 HOH HOH . F 3 HOH B 81 310 164 HOH HOH . F 3 HOH B 82 311 165 HOH HOH . F 3 HOH B 83 312 166 HOH HOH . F 3 HOH B 84 313 169 HOH HOH . F 3 HOH B 85 314 173 HOH HOH . F 3 HOH B 86 315 174 HOH HOH . F 3 HOH B 87 316 175 HOH HOH . F 3 HOH B 88 317 177 HOH HOH . F 3 HOH B 89 318 179 HOH HOH . F 3 HOH B 90 319 181 HOH HOH . F 3 HOH B 91 320 186 HOH HOH . F 3 HOH B 92 321 27 HOH HOH . F 3 HOH B 93 322 189 HOH HOH . F 3 HOH B 94 323 190 HOH HOH . F 3 HOH B 95 324 191 HOH HOH . F 3 HOH B 96 325 192 HOH HOH . F 3 HOH B 97 326 193 HOH HOH . F 3 HOH B 98 327 194 HOH HOH . F 3 HOH B 99 328 195 HOH HOH . F 3 HOH B 100 329 196 HOH HOH . F 3 HOH B 101 330 199 HOH HOH . F 3 HOH B 102 331 203 HOH HOH . F 3 HOH B 103 332 210 HOH HOH . F 3 HOH B 104 333 211 HOH HOH . F 3 HOH B 105 334 216 HOH HOH . F 3 HOH B 106 335 218 HOH HOH . F 3 HOH B 107 336 219 HOH HOH . F 3 HOH B 108 337 220 HOH HOH . F 3 HOH B 109 338 221 HOH HOH . F 3 HOH B 110 339 223 HOH HOH . F 3 HOH B 111 340 224 HOH HOH . F 3 HOH B 112 341 226 HOH HOH . F 3 HOH B 113 342 229 HOH HOH . # 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 P P BMQ . . . D 2 -4.893 1.974 25.252 1 10.99 ? P BMQ 229 B 1 HETATM 2 O O1P BMQ . . . D 2 -4.488 2.905 26.326 1 12.54 ? O1P BMQ 229 B 1 HETATM 3 O O2P BMQ . . . D 2 -5.948 0.922 25.87 1 10.79 ? O2P BMQ 229 B 1 HETATM 4 O O3P BMQ . . . D 2 -5.418 2.726 24.056 1 11.07 ? O3P BMQ 229 B 1 HETATM 5 O O5' BMQ . . . D 2 -3.578 1.145 24.908 1 11.13 ? O5' BMQ 229 B 1 HETATM 6 C C5' BMQ . . . D 2 -3.456 0.403 23.702 1 10.73 ? C5' BMQ 229 B 1 HETATM 7 C C4' BMQ . . . D 2 -2.088 -0.242 23.719 1 9.35 ? C4' BMQ 229 B 1 HETATM 8 O O4' BMQ . . . D 2 -1.979 -1.103 22.569 1 9.64 ? O4' BMQ 229 B 1 HETATM 9 C C3' BMQ . . . D 2 -0.868 0.667 23.634 1 9.47 ? C3' BMQ 229 B 1 HETATM 10 O O3' BMQ . . . D 2 0.245 0.146 24.374 1 11.32 ? O3' BMQ 229 B 1 HETATM 11 C C2' BMQ . . . D 2 -0.575 0.722 22.149 1 9.7 ? C2' BMQ 229 B 1 HETATM 12 O O2' BMQ . . . D 2 0.781 1.084 21.837 1 8.81 ? O2' BMQ 229 B 1 HETATM 13 C C1' BMQ . . . D 2 -0.98 -0.674 21.691 1 8.09 ? C1' BMQ 229 B 1 HETATM 14 N N1 BMQ . . . D 2 -1.48 -0.835 20.296 1 8.49 ? N1 BMQ 229 B 1 HETATM 15 C C2 BMQ . . . D 2 -2.571 -0.027 19.828 1 9.01 ? C2 BMQ 229 B 1 HETATM 16 O O2 BMQ . . . D 2 -3.127 0.776 20.554 1 10.2 ? O2 BMQ 229 B 1 HETATM 17 N N3 BMQ . . . D 2 -2.942 -0.251 18.521 1 7.68 ? N3 BMQ 229 B 1 HETATM 18 C C4 BMQ . . . D 2 -2.366 -1.16 17.618 1 8.9 ? C4 BMQ 229 B 1 HETATM 19 O O4 BMQ . . . D 2 -2.848 -1.226 16.508 1 10.75 ? O4 BMQ 229 B 1 HETATM 20 C C5 BMQ . . . D 2 -1.248 -1.925 18.143 1 7.43 ? C5 BMQ 229 B 1 HETATM 21 C C6 BMQ . . . D 2 -0.896 -1.826 19.454 1 8.06 ? C6 BMQ 229 B 1 HETATM 22 O O1 BMQ . . . D 2 -0.058 -2.606 19.99 1 11.01 ? O1 BMQ 229 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #