data_1OV6 # _model_server_result.job_id 7M5EKXfNspa3hhFKI94tqg _model_server_result.datetime_utc '2024-11-08 06:52:47' _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 1ov6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":245}' # _entry.id 1OV6 # _exptl.entry_id 1OV6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 280.28 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-(6-DEOXY-BETA-D-ALLOFURANOSYL)-6-METHYLPURINE _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 1OV6 _cell.length_a 120.55 _cell.length_b 120.55 _cell.length_c 241.03 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OV6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 40.171667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C12 H16 N4 O4' _chem_comp.formula_weight 280.28 _chem_comp.id DBM _chem_comp.mon_nstd_flag . _chem_comp.name 9-(6-DEOXY-BETA-D-ALLOFURANOSYL)-6-METHYLPURINE _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 O5' C5' DBM sing 83 n n O5' H5' DBM sing 84 n n C5' C6' DBM sing 85 n n C5' C4' DBM sing 86 n n C5' H1 DBM sing 87 n n C6' "H6'1" DBM sing 88 n n C6' "H6'2" DBM sing 89 n n C6' "H6'3" DBM sing 90 n n C4' O4' DBM sing 91 n n C4' C3' DBM sing 92 n n C4' H4' DBM sing 93 n n O4' C1' DBM sing 94 n n C1' N9 DBM sing 95 n n C1' C2' DBM sing 96 n n C1' H1' DBM sing 97 n n N9 C8 DBM sing 98 n y N9 C4 DBM sing 99 n y C8 N7 DBM doub 100 n y C8 H8 DBM sing 101 n n N7 C5 DBM sing 102 n y C5 C4 DBM doub 103 n y C5 C6 DBM sing 104 n y C4 N3 DBM sing 105 n y N3 C2 DBM doub 106 n y C2 N1 DBM sing 107 n y C2 H2 DBM sing 108 n n N1 C6 DBM doub 109 n y C6 C7 DBM sing 110 n n C7 H71 DBM sing 111 n n C7 H72 DBM sing 112 n n C7 H73 DBM sing 113 n n C2' O2' DBM sing 114 n n C2' C3' DBM sing 115 n n C2' H2' DBM sing 116 n n O2' H3 DBM sing 117 n n C3' O3' DBM sing 118 n n C3' H3' DBM sing 119 n n O3' H4 DBM sing 120 n n # _atom_sites.entry_id 1OV6 _atom_sites.fract_transf_matrix[1][1] 0.008295 _atom_sites.fract_transf_matrix[1][2] 0.004789 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009579 _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] 0.004149 _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 D 2 PO4 A 1 248 247 PO4 PO4 . E 3 DBM A 1 245 245 DBM ALO . F 2 PO4 B 1 249 247 PO4 PO4 . G 3 DBM B 1 246 245 DBM ALO . H 2 PO4 C 1 250 247 PO4 PO4 . I 3 DBM C 1 247 245 DBM ALO . J 4 HOH A 1 249 4 HOH TIP . J 4 HOH A 2 250 6 HOH TIP . J 4 HOH A 3 251 9 HOH TIP . J 4 HOH A 4 252 14 HOH TIP . J 4 HOH A 5 253 15 HOH TIP . J 4 HOH A 6 254 20 HOH TIP . J 4 HOH A 7 255 21 HOH TIP . J 4 HOH A 8 256 25 HOH TIP . J 4 HOH A 9 257 26 HOH TIP . J 4 HOH A 10 258 27 HOH TIP . J 4 HOH A 11 259 28 HOH TIP . J 4 HOH A 12 260 30 HOH TIP . J 4 HOH A 13 261 34 HOH TIP . J 4 HOH A 14 262 38 HOH TIP . J 4 HOH A 15 263 43 HOH TIP . J 4 HOH A 16 264 45 HOH TIP . J 4 HOH A 17 265 51 HOH TIP . J 4 HOH A 18 266 54 HOH TIP . J 4 HOH A 19 267 61 HOH TIP . J 4 HOH A 20 268 63 HOH TIP . J 4 HOH A 21 269 64 HOH TIP . J 4 HOH A 22 270 65 HOH TIP . J 4 HOH A 23 271 66 HOH TIP . J 4 HOH A 24 272 67 HOH TIP . J 4 HOH A 25 273 71 HOH TIP . J 4 HOH A 26 274 72 HOH TIP . J 4 HOH A 27 275 77 HOH TIP . J 4 HOH A 28 276 79 HOH TIP . J 4 HOH A 29 277 89 HOH TIP . J 4 HOH A 30 278 90 HOH TIP . J 4 HOH A 31 279 93 HOH TIP . J 4 HOH A 32 280 94 HOH TIP . J 4 HOH A 33 281 95 HOH TIP . J 4 HOH A 34 282 96 HOH TIP . J 4 HOH A 35 283 99 HOH TIP . J 4 HOH A 36 284 106 HOH TIP . J 4 HOH A 37 285 107 HOH TIP . J 4 HOH A 38 286 111 HOH TIP . J 4 HOH A 39 287 113 HOH TIP . J 4 HOH A 40 288 114 HOH TIP . J 4 HOH A 41 289 121 HOH TIP . J 4 HOH A 42 290 123 HOH TIP . J 4 HOH A 43 291 126 HOH TIP . J 4 HOH A 44 292 128 HOH TIP . J 4 HOH A 45 293 129 HOH TIP . J 4 HOH A 46 294 137 HOH TIP . J 4 HOH A 47 295 140 HOH TIP . J 4 HOH A 48 296 147 HOH TIP . J 4 HOH A 49 297 149 HOH TIP . J 4 HOH A 50 298 155 HOH TIP . J 4 HOH A 51 299 156 HOH TIP . J 4 HOH A 52 300 168 HOH TIP . J 4 HOH A 53 301 169 HOH TIP . J 4 HOH A 54 302 170 HOH TIP . J 4 HOH A 55 303 171 HOH TIP . J 4 HOH A 56 304 172 HOH TIP . J 4 HOH A 57 305 174 HOH TIP . J 4 HOH A 58 306 183 HOH TIP . J 4 HOH A 59 307 184 HOH TIP . K 4 HOH B 1 250 1 HOH TIP . K 4 HOH B 2 251 5 HOH TIP . K 4 HOH B 3 252 8 HOH TIP . K 4 HOH B 4 253 10 HOH TIP . K 4 HOH B 5 254 13 HOH TIP . K 4 HOH B 6 255 16 HOH TIP . K 4 HOH B 7 256 17 HOH TIP . K 4 HOH B 8 257 18 HOH TIP . K 4 HOH B 9 258 19 HOH TIP . K 4 HOH B 10 259 24 HOH TIP . K 4 HOH B 11 260 31 HOH TIP . K 4 HOH B 12 261 32 HOH TIP . K 4 HOH B 13 262 33 HOH TIP . K 4 HOH B 14 263 35 HOH TIP . K 4 HOH B 15 264 36 HOH TIP . K 4 HOH B 16 265 37 HOH TIP . K 4 HOH B 17 266 40 HOH TIP . K 4 HOH B 18 267 44 HOH TIP . K 4 HOH B 19 268 46 HOH TIP . K 4 HOH B 20 269 48 HOH TIP . K 4 HOH B 21 270 49 HOH TIP . K 4 HOH B 22 271 53 HOH TIP . K 4 HOH B 23 272 58 HOH TIP . K 4 HOH B 24 273 59 HOH TIP . K 4 HOH B 25 274 60 HOH TIP . K 4 HOH B 26 275 62 HOH TIP . K 4 HOH B 27 276 69 HOH TIP . K 4 HOH B 28 277 73 HOH TIP . K 4 HOH B 29 278 74 HOH TIP . K 4 HOH B 30 279 75 HOH TIP . K 4 HOH B 31 280 76 HOH TIP . K 4 HOH B 32 281 78 HOH TIP . K 4 HOH B 33 282 80 HOH TIP . K 4 HOH B 34 283 82 HOH TIP . K 4 HOH B 35 284 83 HOH TIP . K 4 HOH B 36 285 85 HOH TIP . K 4 HOH B 37 286 87 HOH TIP . K 4 HOH B 38 287 91 HOH TIP . K 4 HOH B 39 288 98 HOH TIP . K 4 HOH B 40 289 100 HOH TIP . K 4 HOH B 41 290 101 HOH TIP . K 4 HOH B 42 291 102 HOH TIP . K 4 HOH B 43 292 103 HOH TIP . K 4 HOH B 44 293 104 HOH TIP . K 4 HOH B 45 294 105 HOH TIP . K 4 HOH B 46 295 108 HOH TIP . K 4 HOH B 47 296 109 HOH TIP . K 4 HOH B 48 297 110 HOH TIP . K 4 HOH B 49 298 112 HOH TIP . K 4 HOH B 50 299 115 HOH TIP . K 4 HOH B 51 300 116 HOH TIP . K 4 HOH B 52 301 117 HOH TIP . K 4 HOH B 53 302 122 HOH TIP . K 4 HOH B 54 303 124 HOH TIP . K 4 HOH B 55 304 130 HOH TIP . K 4 HOH B 56 305 131 HOH TIP . K 4 HOH B 57 306 133 HOH TIP . K 4 HOH B 58 307 136 HOH TIP . K 4 HOH B 59 308 143 HOH TIP . K 4 HOH B 60 309 146 HOH TIP . K 4 HOH B 61 310 152 HOH TIP . K 4 HOH B 62 311 154 HOH TIP . K 4 HOH B 63 312 158 HOH TIP . K 4 HOH B 64 313 159 HOH TIP . K 4 HOH B 65 314 160 HOH TIP . K 4 HOH B 66 315 162 HOH TIP . K 4 HOH B 67 316 165 HOH TIP . K 4 HOH B 68 317 166 HOH TIP . K 4 HOH B 69 318 173 HOH TIP . K 4 HOH B 70 319 176 HOH TIP . K 4 HOH B 71 320 177 HOH TIP . K 4 HOH B 72 321 178 HOH TIP . L 4 HOH C 1 251 2 HOH TIP . L 4 HOH C 2 252 3 HOH TIP . L 4 HOH C 3 253 7 HOH TIP . L 4 HOH C 4 254 11 HOH TIP . L 4 HOH C 5 255 12 HOH TIP . L 4 HOH C 6 256 22 HOH TIP . L 4 HOH C 7 257 23 HOH TIP . L 4 HOH C 8 258 29 HOH TIP . L 4 HOH C 9 259 39 HOH TIP . L 4 HOH C 10 260 41 HOH TIP . L 4 HOH C 11 261 42 HOH TIP . L 4 HOH C 12 262 47 HOH TIP . L 4 HOH C 13 263 50 HOH TIP . L 4 HOH C 14 264 52 HOH TIP . L 4 HOH C 15 265 55 HOH TIP . L 4 HOH C 16 266 56 HOH TIP . L 4 HOH C 17 267 57 HOH TIP . L 4 HOH C 18 268 68 HOH TIP . L 4 HOH C 19 269 70 HOH TIP . L 4 HOH C 20 270 81 HOH TIP . L 4 HOH C 21 271 84 HOH TIP . L 4 HOH C 22 272 86 HOH TIP . L 4 HOH C 23 273 88 HOH TIP . L 4 HOH C 24 274 92 HOH TIP . L 4 HOH C 25 275 97 HOH TIP . L 4 HOH C 26 276 118 HOH TIP . L 4 HOH C 27 277 119 HOH TIP . L 4 HOH C 28 278 120 HOH TIP . L 4 HOH C 29 279 125 HOH TIP . L 4 HOH C 30 280 127 HOH TIP . L 4 HOH C 31 281 132 HOH TIP . L 4 HOH C 32 282 134 HOH TIP . L 4 HOH C 33 283 135 HOH TIP . L 4 HOH C 34 284 138 HOH TIP . L 4 HOH C 35 285 139 HOH TIP . L 4 HOH C 36 286 141 HOH TIP . L 4 HOH C 37 287 142 HOH TIP . L 4 HOH C 38 288 144 HOH TIP . L 4 HOH C 39 289 145 HOH TIP . L 4 HOH C 40 290 148 HOH TIP . L 4 HOH C 41 291 150 HOH TIP . L 4 HOH C 42 292 151 HOH TIP . L 4 HOH C 43 293 153 HOH TIP . L 4 HOH C 44 294 157 HOH TIP . L 4 HOH C 45 295 161 HOH TIP . L 4 HOH C 46 296 163 HOH TIP . L 4 HOH C 47 297 164 HOH TIP . L 4 HOH C 48 298 167 HOH TIP . L 4 HOH C 49 299 175 HOH TIP . L 4 HOH C 50 300 179 HOH TIP . L 4 HOH C 51 301 180 HOH TIP . L 4 HOH C 52 302 181 HOH TIP . L 4 HOH C 53 303 182 HOH TIP . L 4 HOH C 54 304 185 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 O5' DBM . . . E 3 92.614 69.863 19.282 1 28.89 ? O5' DBM 245 A 1 HETATM 2 C C5' DBM . . . E 3 91.699 68.974 18.68 1 29.92 ? C5' DBM 245 A 1 HETATM 3 C C6' DBM . . . E 3 90.568 69.769 18.022 1 30.04 ? C6' DBM 245 A 1 HETATM 4 C C4' DBM . . . E 3 91.252 67.883 19.683 1 29.84 ? C4' DBM 245 A 1 HETATM 5 O O4' DBM . . . E 3 89.808 67.919 19.962 1 27.55 ? O4' DBM 245 A 1 HETATM 6 C C1' DBM . . . E 3 89.266 66.608 19.919 1 27.49 ? C1' DBM 245 A 1 HETATM 7 N N9 DBM . . . E 3 88.31 66.484 18.781 1 26.75 ? N9 DBM 245 A 1 HETATM 8 C C8 DBM . . . E 3 87.932 67.47 17.89 1 25.85 ? C8 DBM 245 A 1 HETATM 9 N N7 DBM . . . E 3 87.069 67.069 16.992 1 26.88 ? N7 DBM 245 A 1 HETATM 10 C C5 DBM . . . E 3 86.864 65.732 17.281 1 25.64 ? C5 DBM 245 A 1 HETATM 11 C C4 DBM . . . E 3 87.612 65.346 18.392 1 25.78 ? C4 DBM 245 A 1 HETATM 12 N N3 DBM . . . E 3 87.677 64.107 18.984 1 26.01 ? N3 DBM 245 A 1 HETATM 13 C C2 DBM . . . E 3 86.903 63.178 18.375 1 25.67 ? C2 DBM 245 A 1 HETATM 14 N N1 DBM . . . E 3 86.121 63.457 17.256 1 25.1 ? N1 DBM 245 A 1 HETATM 15 C C6 DBM . . . E 3 86.034 64.721 16.629 1 25.53 ? C6 DBM 245 A 1 HETATM 16 C C7 DBM . . . E 3 85.166 64.981 15.401 1 22.01 ? C7 DBM 245 A 1 HETATM 17 C C2' DBM . . . E 3 90.46 65.65 19.932 1 28.72 ? C2' DBM 245 A 1 HETATM 18 O O2' DBM . . . E 3 90.791 65.251 21.27 1 31.2 ? O2' DBM 245 A 1 HETATM 19 C C3' DBM . . . E 3 91.551 66.444 19.251 1 29.5 ? C3' DBM 245 A 1 HETATM 20 O O3' DBM . . . E 3 92.832 66.029 19.761 1 29.96 ? O3' DBM 245 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #