data_3D8Z # _model_server_result.job_id '_U8TgrkSR1yd55pQ24x1KA' _model_server_result.datetime_utc '2024-12-21 12:38:12' _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 3d8z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":125}' # _entry.id 3D8Z # _exptl.entry_id 3D8Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.51 _cell.angle_gamma 90 _cell.entry_id 3D8Z _cell.length_a 100.102 _cell.length_b 32.678 _cell.length_c 72.562 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D8Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? # _chem_comp.formula 'C14 H21 N3 O4' _chem_comp.formula_weight 295.334 _chem_comp.id TXS _chem_comp.mon_nstd_flag . _chem_comp.name 1-(2,5-dideoxy-5-pyrrolidin-1-yl-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "5'-deoxy-5'-pyrrolidin-1-ylthymidine" # 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 C21 C22 TXS sing 323 n n C21 N25 TXS sing 324 n n C22 C23 TXS sing 325 n n C23 C24 TXS sing 326 n n C24 N25 TXS sing 327 n n N25 C5' TXS sing 328 n n C5' C4' TXS sing 329 n n C4' O4' TXS sing 330 n n C4' C3' TXS sing 331 n n O4' C1' TXS sing 332 n n C3' O3' TXS sing 333 n n C3' C2' TXS sing 334 n n C2' C1' TXS sing 335 n n C1' N1 TXS sing 336 n n N1 C6 TXS sing 337 n n N1 C2 TXS sing 338 n n C6 C5 TXS doub 339 n n C5 C5M TXS sing 340 n n C5 C4 TXS sing 341 n n C4 O4 TXS doub 342 n n C4 N3 TXS sing 343 n n N3 C2 TXS sing 344 n n C2 O2 TXS doub 345 n n C21 H21 TXS sing 346 n n C21 H21A TXS sing 347 n n C22 H22 TXS sing 348 n n C22 H22A TXS sing 349 n n C23 H23 TXS sing 350 n n C23 H23A TXS sing 351 n n C24 H24 TXS sing 352 n n C24 H24A TXS sing 353 n n C5' H5' TXS sing 354 n n C5' "H5'A" TXS sing 355 n n C4' H4' TXS sing 356 n n C3' H3' TXS sing 357 n n O3' HO3' TXS sing 358 n n C2' H2' TXS sing 359 n n C2' "H2'A" TXS sing 360 n n C1' H1' TXS sing 361 n n C6 H6 TXS sing 362 n n C5M H5M TXS sing 363 n n C5M H5MA TXS sing 364 n n C5M H5MB TXS sing 365 n n N3 HN3 TXS sing 366 n n # _atom_sites.entry_id 3D8Z _atom_sites.fract_transf_matrix[1][1] 0.00999 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000088 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.030602 _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] 0.013782 _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 TXS A 1 125 1 TXS T4S . D 3 FLC B 1 125 1 FLC FLC . E 4 HOH A 1 126 8 HOH HOH . E 4 HOH A 2 127 11 HOH HOH . E 4 HOH A 3 128 12 HOH HOH . E 4 HOH A 4 129 13 HOH HOH . E 4 HOH A 5 130 14 HOH HOH . E 4 HOH A 6 131 18 HOH HOH . E 4 HOH A 7 132 19 HOH HOH . E 4 HOH A 8 133 21 HOH HOH . E 4 HOH A 9 134 22 HOH HOH . E 4 HOH A 10 135 23 HOH HOH . E 4 HOH A 11 136 24 HOH HOH . E 4 HOH A 12 137 25 HOH HOH . E 4 HOH A 13 138 31 HOH HOH . E 4 HOH A 14 139 32 HOH HOH . E 4 HOH A 15 140 37 HOH HOH . E 4 HOH A 16 141 46 HOH HOH . E 4 HOH A 17 142 47 HOH HOH . E 4 HOH A 18 143 49 HOH HOH . E 4 HOH A 19 144 53 HOH HOH . E 4 HOH A 20 145 54 HOH HOH . E 4 HOH A 21 146 56 HOH HOH . E 4 HOH A 22 147 61 HOH HOH . E 4 HOH A 23 148 62 HOH HOH . E 4 HOH A 24 149 64 HOH HOH . E 4 HOH A 25 150 65 HOH HOH . E 4 HOH A 26 151 67 HOH HOH . E 4 HOH A 27 152 71 HOH HOH . E 4 HOH A 28 153 73 HOH HOH . E 4 HOH A 29 154 74 HOH HOH . E 4 HOH A 30 155 76 HOH HOH . E 4 HOH A 31 156 77 HOH HOH . E 4 HOH A 32 157 78 HOH HOH . E 4 HOH A 33 158 80 HOH HOH . E 4 HOH A 34 159 81 HOH HOH . E 4 HOH A 35 160 84 HOH HOH . E 4 HOH A 36 161 85 HOH HOH . E 4 HOH A 37 162 89 HOH HOH . E 4 HOH A 38 163 92 HOH HOH . E 4 HOH A 39 164 93 HOH HOH . E 4 HOH A 40 165 96 HOH HOH . E 4 HOH A 41 166 97 HOH HOH . E 4 HOH A 42 167 98 HOH HOH . E 4 HOH A 43 168 101 HOH HOH . E 4 HOH A 44 169 107 HOH HOH . E 4 HOH A 45 170 109 HOH HOH . E 4 HOH A 46 171 110 HOH HOH . E 4 HOH A 47 172 111 HOH HOH . E 4 HOH A 48 173 112 HOH HOH . E 4 HOH A 49 174 113 HOH HOH . E 4 HOH A 50 175 121 HOH HOH . E 4 HOH A 51 176 122 HOH HOH . E 4 HOH A 52 177 123 HOH HOH . E 4 HOH A 53 178 125 HOH HOH . E 4 HOH A 54 179 126 HOH HOH . E 4 HOH A 55 180 127 HOH HOH . E 4 HOH A 56 181 128 HOH HOH . E 4 HOH A 57 182 129 HOH HOH . E 4 HOH A 58 183 130 HOH HOH . E 4 HOH A 59 184 131 HOH HOH . E 4 HOH A 60 185 132 HOH HOH . E 4 HOH A 61 186 133 HOH HOH . E 4 HOH A 62 187 134 HOH HOH . E 4 HOH A 63 188 135 HOH HOH . E 4 HOH A 64 189 136 HOH HOH . E 4 HOH A 65 190 137 HOH HOH . E 4 HOH A 66 191 138 HOH HOH . E 4 HOH A 67 192 139 HOH HOH . E 4 HOH A 68 193 140 HOH HOH . E 4 HOH A 69 194 156 HOH HOH . E 4 HOH A 70 195 158 HOH HOH . E 4 HOH A 71 196 159 HOH HOH . E 4 HOH A 72 197 163 HOH HOH . E 4 HOH A 73 199 166 HOH HOH . F 4 HOH B 1 198 164 HOH HOH . F 4 HOH B 2 199 1 HOH HOH . F 4 HOH B 3 200 2 HOH HOH . F 4 HOH B 4 201 3 HOH HOH . F 4 HOH B 5 202 4 HOH HOH . F 4 HOH B 6 203 5 HOH HOH . F 4 HOH B 7 204 6 HOH HOH . F 4 HOH B 8 205 7 HOH HOH . F 4 HOH B 9 206 9 HOH HOH . F 4 HOH B 10 207 10 HOH HOH . F 4 HOH B 11 208 15 HOH HOH . F 4 HOH B 12 209 16 HOH HOH . F 4 HOH B 13 210 17 HOH HOH . F 4 HOH B 14 211 20 HOH HOH . F 4 HOH B 15 212 26 HOH HOH . F 4 HOH B 16 213 27 HOH HOH . F 4 HOH B 17 214 28 HOH HOH . F 4 HOH B 18 215 29 HOH HOH . F 4 HOH B 19 216 30 HOH HOH . F 4 HOH B 20 217 33 HOH HOH . F 4 HOH B 21 218 34 HOH HOH . F 4 HOH B 22 219 35 HOH HOH . F 4 HOH B 23 220 36 HOH HOH . F 4 HOH B 24 221 38 HOH HOH . F 4 HOH B 25 222 39 HOH HOH . F 4 HOH B 26 223 40 HOH HOH . F 4 HOH B 27 224 41 HOH HOH . F 4 HOH B 28 225 42 HOH HOH . F 4 HOH B 29 226 43 HOH HOH . F 4 HOH B 30 227 44 HOH HOH . F 4 HOH B 31 228 45 HOH HOH . F 4 HOH B 32 229 48 HOH HOH . F 4 HOH B 33 230 50 HOH HOH . F 4 HOH B 34 231 51 HOH HOH . F 4 HOH B 35 232 52 HOH HOH . F 4 HOH B 36 233 55 HOH HOH . F 4 HOH B 37 234 57 HOH HOH . F 4 HOH B 38 235 58 HOH HOH . F 4 HOH B 39 236 59 HOH HOH . F 4 HOH B 40 237 60 HOH HOH . F 4 HOH B 41 238 63 HOH HOH . F 4 HOH B 42 239 66 HOH HOH . F 4 HOH B 43 240 68 HOH HOH . F 4 HOH B 44 241 69 HOH HOH . F 4 HOH B 45 242 70 HOH HOH . F 4 HOH B 46 243 72 HOH HOH . F 4 HOH B 47 244 75 HOH HOH . F 4 HOH B 48 245 79 HOH HOH . F 4 HOH B 49 246 82 HOH HOH . F 4 HOH B 50 247 83 HOH HOH . F 4 HOH B 51 248 86 HOH HOH . F 4 HOH B 52 249 87 HOH HOH . F 4 HOH B 53 250 88 HOH HOH . F 4 HOH B 54 251 90 HOH HOH . F 4 HOH B 55 252 91 HOH HOH . F 4 HOH B 56 253 94 HOH HOH . F 4 HOH B 57 254 95 HOH HOH . F 4 HOH B 58 255 99 HOH HOH . F 4 HOH B 59 256 100 HOH HOH . F 4 HOH B 60 257 102 HOH HOH . F 4 HOH B 61 258 103 HOH HOH . F 4 HOH B 62 259 104 HOH HOH . F 4 HOH B 63 260 105 HOH HOH . F 4 HOH B 64 261 106 HOH HOH . F 4 HOH B 65 262 108 HOH HOH . F 4 HOH B 66 263 114 HOH HOH . F 4 HOH B 67 264 115 HOH HOH . F 4 HOH B 68 265 116 HOH HOH . F 4 HOH B 69 266 117 HOH HOH . F 4 HOH B 70 267 118 HOH HOH . F 4 HOH B 71 268 119 HOH HOH . F 4 HOH B 72 269 120 HOH HOH . F 4 HOH B 73 270 124 HOH HOH . F 4 HOH B 74 271 141 HOH HOH . F 4 HOH B 75 272 142 HOH HOH . F 4 HOH B 76 273 143 HOH HOH . F 4 HOH B 77 274 144 HOH HOH . F 4 HOH B 78 275 145 HOH HOH . F 4 HOH B 79 276 146 HOH HOH . F 4 HOH B 80 277 147 HOH HOH . F 4 HOH B 81 278 148 HOH HOH . F 4 HOH B 82 279 149 HOH HOH . F 4 HOH B 83 280 150 HOH HOH . F 4 HOH B 84 281 151 HOH HOH . F 4 HOH B 85 282 152 HOH HOH . F 4 HOH B 86 283 153 HOH HOH . F 4 HOH B 87 284 154 HOH HOH . F 4 HOH B 88 285 155 HOH HOH . F 4 HOH B 89 286 157 HOH HOH . F 4 HOH B 90 287 160 HOH HOH . F 4 HOH B 91 288 161 HOH HOH . F 4 HOH B 92 289 162 HOH HOH . F 4 HOH B 93 290 165 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 C C21 TXS . . . C 2 41.988 0.383 15.087 1 43.57 ? C21 TXS 125 A 1 HETATM 2 C C22 TXS . . . C 2 42.903 -0.417 16.033 1 43.45 ? C22 TXS 125 A 1 HETATM 3 C C23 TXS . . . C 2 42.68 -1.888 15.654 1 42.82 ? C23 TXS 125 A 1 HETATM 4 C C24 TXS . . . C 2 41.829 -1.833 14.385 1 43.42 ? C24 TXS 125 A 1 HETATM 5 N N25 TXS . . . C 2 41.032 -0.604 14.552 1 42.83 ? N25 TXS 125 A 1 HETATM 6 C C5' TXS . . . C 2 40.549 -0.141 13.245 1 41.47 ? C5' TXS 125 A 1 HETATM 7 C C4' TXS . . . C 2 39.059 -0.475 13.182 1 38.7 ? C4' TXS 125 A 1 HETATM 8 O O4' TXS . . . C 2 38.653 -1.403 12.145 1 35.35 ? O4' TXS 125 A 1 HETATM 9 C C3' TXS . . . C 2 38.145 0.751 12.936 1 38.76 ? C3' TXS 125 A 1 HETATM 10 O O3' TXS . . . C 2 37.688 1.201 14.216 1 40.61 ? O3' TXS 125 A 1 HETATM 11 C C2' TXS . . . C 2 36.972 0.142 12.146 1 36.22 ? C2' TXS 125 A 1 HETATM 12 C C1' TXS . . . C 2 37.272 -1.306 12.522 1 33.15 ? C1' TXS 125 A 1 HETATM 13 N N1 TXS . . . C 2 36.38 -2.479 12.341 1 31.12 ? N1 TXS 125 A 1 HETATM 14 C C6 TXS . . . C 2 36.735 -3.575 13.139 1 29.96 ? C6 TXS 125 A 1 HETATM 15 C C5 TXS . . . C 2 35.984 -4.738 13.121 1 29.24 ? C5 TXS 125 A 1 HETATM 16 C C5M TXS . . . C 2 36.439 -5.896 13.999 1 30.05 ? C5M TXS 125 A 1 HETATM 17 C C4 TXS . . . C 2 34.851 -4.815 12.311 1 29.72 ? C4 TXS 125 A 1 HETATM 18 O O4 TXS . . . C 2 34.176 -5.842 12.285 1 30.32 ? O4 TXS 125 A 1 HETATM 19 N N3 TXS . . . C 2 34.471 -3.717 11.515 1 28.22 ? N3 TXS 125 A 1 HETATM 20 C C2 TXS . . . C 2 35.229 -2.529 11.526 1 29.87 ? C2 TXS 125 A 1 HETATM 21 O O2 TXS . . . C 2 34.885 -1.578 10.83 1 28.2 ? O2 TXS 125 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #