data_3LI0 # _model_server_result.job_id 2luZQivkDmej60H0S0zypg _model_server_result.datetime_utc '2024-10-17 11:30:22' _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 3li0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":229}' # _entry.id 3LI0 # _exptl.entry_id 3LI0 _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 90 _cell.angle_gamma 90 _cell.entry_id 3LI0 _cell.length_a 79.997 _cell.length_b 64.003 _cell.length_c 73.305 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LI0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 3LI0 _atom_sites.fract_transf_matrix[1][1] 0.0125 _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] 0.015624 _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] 0.013642 _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 8 HOH HOH . E 3 HOH A 2 231 11 HOH HOH . E 3 HOH A 3 232 12 HOH HOH . E 3 HOH A 4 233 15 HOH HOH . E 3 HOH A 5 234 16 HOH HOH . E 3 HOH A 6 235 17 HOH HOH . E 3 HOH A 7 236 18 HOH HOH . E 3 HOH A 8 237 20 HOH HOH . E 3 HOH A 9 238 21 HOH HOH . E 3 HOH A 10 239 22 HOH HOH . E 3 HOH A 11 240 25 HOH HOH . E 3 HOH A 12 241 29 HOH HOH . E 3 HOH A 13 242 32 HOH HOH . E 3 HOH A 14 243 34 HOH HOH . E 3 HOH A 15 244 35 HOH HOH . E 3 HOH A 16 245 38 HOH HOH . E 3 HOH A 17 246 40 HOH HOH . E 3 HOH A 18 247 43 HOH HOH . E 3 HOH A 19 248 47 HOH HOH . E 3 HOH A 20 249 53 HOH HOH . E 3 HOH A 21 250 55 HOH HOH . E 3 HOH A 22 251 58 HOH HOH . E 3 HOH A 23 252 59 HOH HOH . E 3 HOH A 24 253 61 HOH HOH . E 3 HOH A 25 254 63 HOH HOH . E 3 HOH A 26 255 64 HOH HOH . E 3 HOH A 27 256 65 HOH HOH . E 3 HOH A 28 257 70 HOH HOH . E 3 HOH A 29 258 71 HOH HOH . E 3 HOH A 30 259 73 HOH HOH . E 3 HOH A 31 260 74 HOH HOH . E 3 HOH A 32 261 75 HOH HOH . E 3 HOH A 33 262 78 HOH HOH . E 3 HOH A 34 263 79 HOH HOH . E 3 HOH A 35 264 80 HOH HOH . E 3 HOH A 36 265 81 HOH HOH . E 3 HOH A 37 266 84 HOH HOH . E 3 HOH A 38 267 85 HOH HOH . E 3 HOH A 39 268 86 HOH HOH . E 3 HOH A 40 269 87 HOH HOH . E 3 HOH A 41 270 88 HOH HOH . E 3 HOH A 42 271 89 HOH HOH . E 3 HOH A 43 272 91 HOH HOH . E 3 HOH A 44 273 93 HOH HOH . E 3 HOH A 45 274 95 HOH HOH . E 3 HOH A 46 275 96 HOH HOH . E 3 HOH A 47 276 102 HOH HOH . E 3 HOH A 48 277 103 HOH HOH . E 3 HOH A 49 278 104 HOH HOH . E 3 HOH A 50 279 108 HOH HOH . E 3 HOH A 51 280 109 HOH HOH . E 3 HOH A 52 281 110 HOH HOH . E 3 HOH A 53 282 117 HOH HOH . E 3 HOH A 54 283 118 HOH HOH . E 3 HOH A 55 284 121 HOH HOH . E 3 HOH A 56 285 122 HOH HOH . E 3 HOH A 57 286 124 HOH HOH . E 3 HOH A 58 287 126 HOH HOH . E 3 HOH A 59 288 131 HOH HOH . E 3 HOH A 60 289 133 HOH HOH . E 3 HOH A 61 290 135 HOH HOH . E 3 HOH A 62 291 139 HOH HOH . E 3 HOH A 63 292 142 HOH HOH . E 3 HOH A 64 293 147 HOH HOH . E 3 HOH A 65 294 148 HOH HOH . E 3 HOH A 66 295 149 HOH HOH . E 3 HOH A 67 296 150 HOH HOH . E 3 HOH A 68 297 151 HOH HOH . E 3 HOH A 69 298 152 HOH HOH . E 3 HOH A 70 299 157 HOH HOH . E 3 HOH A 71 300 161 HOH HOH . E 3 HOH A 72 301 163 HOH HOH . E 3 HOH A 73 302 165 HOH HOH . E 3 HOH A 74 303 169 HOH HOH . E 3 HOH A 75 304 171 HOH HOH . E 3 HOH A 76 305 173 HOH HOH . E 3 HOH A 77 306 174 HOH HOH . E 3 HOH A 78 307 175 HOH HOH . E 3 HOH A 79 308 177 HOH HOH . E 3 HOH A 80 309 178 HOH HOH . E 3 HOH A 81 310 179 HOH HOH . E 3 HOH A 82 311 98 HOH HOH . E 3 HOH A 83 312 130 HOH HOH . F 3 HOH B 1 230 9 HOH HOH . F 3 HOH B 2 231 13 HOH HOH . F 3 HOH B 3 232 19 HOH HOH . F 3 HOH B 4 233 23 HOH HOH . F 3 HOH B 5 234 26 HOH HOH . F 3 HOH B 6 235 30 HOH HOH . F 3 HOH B 7 236 31 HOH HOH . F 3 HOH B 8 237 33 HOH HOH . F 3 HOH B 9 238 36 HOH HOH . F 3 HOH B 10 239 37 HOH HOH . F 3 HOH B 11 240 39 HOH HOH . F 3 HOH B 12 241 41 HOH HOH . F 3 HOH B 13 242 42 HOH HOH . F 3 HOH B 14 243 44 HOH HOH . F 3 HOH B 15 244 45 HOH HOH . F 3 HOH B 16 245 46 HOH HOH . F 3 HOH B 17 246 48 HOH HOH . F 3 HOH B 18 247 49 HOH HOH . F 3 HOH B 19 248 50 HOH HOH . F 3 HOH B 20 249 51 HOH HOH . F 3 HOH B 21 250 52 HOH HOH . F 3 HOH B 22 251 54 HOH HOH . F 3 HOH B 23 252 56 HOH HOH . F 3 HOH B 24 253 57 HOH HOH . F 3 HOH B 25 254 60 HOH HOH . F 3 HOH B 26 255 66 HOH HOH . F 3 HOH B 27 256 67 HOH HOH . F 3 HOH B 28 257 68 HOH HOH . F 3 HOH B 29 258 72 HOH HOH . F 3 HOH B 30 259 76 HOH HOH . F 3 HOH B 31 260 83 HOH HOH . F 3 HOH B 32 261 90 HOH HOH . F 3 HOH B 33 262 92 HOH HOH . F 3 HOH B 34 264 99 HOH HOH . F 3 HOH B 35 265 100 HOH HOH . F 3 HOH B 36 266 101 HOH HOH . F 3 HOH B 37 267 106 HOH HOH . F 3 HOH B 38 268 107 HOH HOH . F 3 HOH B 39 269 111 HOH HOH . F 3 HOH B 40 270 112 HOH HOH . F 3 HOH B 41 271 114 HOH HOH . F 3 HOH B 42 272 115 HOH HOH . F 3 HOH B 43 273 116 HOH HOH . F 3 HOH B 44 274 119 HOH HOH . F 3 HOH B 45 275 125 HOH HOH . F 3 HOH B 46 276 127 HOH HOH . F 3 HOH B 47 277 128 HOH HOH . F 3 HOH B 48 278 129 HOH HOH . F 3 HOH B 49 280 132 HOH HOH . F 3 HOH B 50 281 137 HOH HOH . F 3 HOH B 51 282 140 HOH HOH . F 3 HOH B 52 283 141 HOH HOH . F 3 HOH B 53 284 144 HOH HOH . F 3 HOH B 54 285 153 HOH HOH . F 3 HOH B 55 286 154 HOH HOH . F 3 HOH B 56 287 155 HOH HOH . F 3 HOH B 57 288 156 HOH HOH . F 3 HOH B 58 289 160 HOH HOH . F 3 HOH B 59 290 162 HOH HOH . F 3 HOH B 60 291 170 HOH HOH . F 3 HOH B 61 292 172 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 -13.66 11.748 -35.072 1 18.19 ? P BMQ 229 B 1 HETATM 2 O O1P BMQ . . . D 2 -12.595 10.723 -35.215 1 17.7 ? O1P BMQ 229 B 1 HETATM 3 O O2P BMQ . . . D 2 -13.645 12.653 -36.408 1 17.58 ? O2P BMQ 229 B 1 HETATM 4 O O3P BMQ . . . D 2 -14.982 11.096 -34.795 1 17.63 ? O3P BMQ 229 B 1 HETATM 5 O O5' BMQ . . . D 2 -13.165 12.704 -33.897 1 18.88 ? O5' BMQ 229 B 1 HETATM 6 C C5' BMQ . . . D 2 -14.05 13.614 -33.267 1 19.19 ? C5' BMQ 229 B 1 HETATM 7 C C4' BMQ . . . D 2 -13.279 14.344 -32.194 1 17.27 ? C4' BMQ 229 B 1 HETATM 8 O O4' BMQ . . . D 2 -14.164 15.308 -31.616 1 16.92 ? O4' BMQ 229 B 1 HETATM 9 C C3' BMQ . . . D 2 -12.745 13.543 -31.01 1 17.11 ? C3' BMQ 229 B 1 HETATM 10 O O3' BMQ . . . D 2 -11.502 14.076 -30.53 1 18.87 ? O3' BMQ 229 B 1 HETATM 11 C C2' BMQ . . . D 2 -13.849 13.671 -29.977 1 16.47 ? C2' BMQ 229 B 1 HETATM 12 O O2' BMQ . . . D 2 -13.409 13.465 -28.624 1 16.82 ? O2' BMQ 229 B 1 HETATM 13 C C1' BMQ . . . D 2 -14.382 15.068 -30.261 1 16.29 ? C1' BMQ 229 B 1 HETATM 14 N N1 BMQ . . . D 2 -15.811 15.342 -29.957 1 14.53 ? N1 BMQ 229 B 1 HETATM 15 C C2 BMQ . . . D 2 -16.833 14.525 -30.539 1 15.51 ? C2 BMQ 229 B 1 HETATM 16 O O2 BMQ . . . D 2 -16.567 13.605 -31.306 1 17.1 ? O2 BMQ 229 B 1 HETATM 17 N N3 BMQ . . . D 2 -18.113 14.857 -30.175 1 14.02 ? N3 BMQ 229 B 1 HETATM 18 C C4 BMQ . . . D 2 -18.514 15.878 -29.293 1 13.8 ? C4 BMQ 229 B 1 HETATM 19 O O4 BMQ . . . D 2 -19.708 16.007 -29.105 1 13.91 ? O4 BMQ 229 B 1 HETATM 20 C C5 BMQ . . . D 2 -17.429 16.659 -28.714 1 13.73 ? C5 BMQ 229 B 1 HETATM 21 C C6 BMQ . . . D 2 -16.144 16.438 -29.085 1 14.89 ? C6 BMQ 229 B 1 HETATM 22 O O1 BMQ . . . D 2 -15.192 17.172 -28.691 1 14.55 ? O1 BMQ 229 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #