data_3H6M # _model_server_result.job_id djeKJoCTZYDX_OjdwOQevg _model_server_result.datetime_utc '2024-10-11 10:23:38' _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 3h6m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3H6M # _exptl.entry_id 3H6M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 93.96 _cell.angle_gamma 90 _cell.entry_id 3H6M _cell.length_a 31.026 _cell.length_b 60.461 _cell.length_c 38.296 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H6M _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna 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 P2 O4P THP doub 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 3H6M _atom_sites.fract_transf_matrix[1][1] 0.032231 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002231 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01654 _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] 0.026175 _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 B 2 THP A 1 150 1 THP THP . C 3 CA A 1 151 1 CA CA . D 4 HOH A 1 44 44 HOH HOH . D 4 HOH A 2 45 45 HOH HOH . D 4 HOH A 3 46 46 HOH HOH . D 4 HOH A 4 47 47 HOH HOH . D 4 HOH A 5 48 48 HOH HOH . D 4 HOH A 6 49 49 HOH HOH . D 4 HOH A 7 152 2 HOH HOH . D 4 HOH A 8 153 3 HOH HOH . D 4 HOH A 9 154 4 HOH HOH . D 4 HOH A 10 155 5 HOH HOH . D 4 HOH A 11 156 6 HOH HOH . D 4 HOH A 12 157 7 HOH HOH . D 4 HOH A 13 158 8 HOH HOH . D 4 HOH A 14 159 9 HOH HOH . D 4 HOH A 15 160 10 HOH HOH . D 4 HOH A 16 161 11 HOH HOH . D 4 HOH A 17 162 12 HOH HOH . D 4 HOH A 18 163 13 HOH HOH . D 4 HOH A 19 164 14 HOH HOH . D 4 HOH A 20 165 15 HOH HOH . D 4 HOH A 21 166 16 HOH HOH . D 4 HOH A 22 167 17 HOH HOH . D 4 HOH A 23 168 18 HOH HOH . D 4 HOH A 24 169 19 HOH HOH . D 4 HOH A 25 170 20 HOH HOH . D 4 HOH A 26 171 21 HOH HOH . D 4 HOH A 27 172 22 HOH HOH . D 4 HOH A 28 173 23 HOH HOH . D 4 HOH A 29 174 24 HOH HOH . D 4 HOH A 30 175 25 HOH HOH . D 4 HOH A 31 176 26 HOH HOH . D 4 HOH A 32 177 27 HOH HOH . D 4 HOH A 33 178 28 HOH HOH . D 4 HOH A 34 179 29 HOH HOH . D 4 HOH A 35 180 30 HOH HOH . D 4 HOH A 36 181 31 HOH HOH . D 4 HOH A 37 182 32 HOH HOH . D 4 HOH A 38 183 33 HOH HOH . D 4 HOH A 39 184 34 HOH HOH . D 4 HOH A 40 185 35 HOH HOH . D 4 HOH A 41 186 36 HOH HOH . D 4 HOH A 42 187 37 HOH HOH . D 4 HOH A 43 188 38 HOH HOH . D 4 HOH A 44 189 39 HOH HOH . D 4 HOH A 45 190 40 HOH HOH . D 4 HOH A 46 191 41 HOH HOH . D 4 HOH A 47 192 42 HOH HOH . D 4 HOH A 48 193 43 HOH HOH . D 4 HOH A 49 194 1 HOH HOH . D 4 HOH A 50 195 2 HOH HOH . D 4 HOH A 51 196 3 HOH HOH . D 4 HOH A 52 197 4 HOH HOH . D 4 HOH A 53 198 5 HOH HOH . D 4 HOH A 54 199 6 HOH HOH . D 4 HOH A 55 200 7 HOH HOH . D 4 HOH A 56 201 8 HOH HOH . D 4 HOH A 57 202 9 HOH HOH . D 4 HOH A 58 203 10 HOH HOH . D 4 HOH A 59 204 11 HOH HOH . D 4 HOH A 60 205 12 HOH HOH . D 4 HOH A 61 206 13 HOH HOH . D 4 HOH A 62 207 14 HOH HOH . D 4 HOH A 63 208 15 HOH HOH . D 4 HOH A 64 209 16 HOH HOH . D 4 HOH A 65 210 17 HOH HOH . D 4 HOH A 66 211 18 HOH HOH . D 4 HOH A 67 212 19 HOH HOH . D 4 HOH A 68 213 21 HOH HOH . D 4 HOH A 69 214 22 HOH HOH . D 4 HOH A 70 215 23 HOH HOH . D 4 HOH A 71 216 24 HOH HOH . D 4 HOH A 72 217 25 HOH HOH . D 4 HOH A 73 218 26 HOH HOH . D 4 HOH A 74 219 27 HOH HOH . D 4 HOH A 75 220 28 HOH HOH . D 4 HOH A 76 221 29 HOH HOH . D 4 HOH A 77 222 30 HOH HOH . D 4 HOH A 78 223 31 HOH HOH . D 4 HOH A 79 224 32 HOH HOH . D 4 HOH A 80 225 33 HOH HOH . D 4 HOH A 81 226 34 HOH HOH . D 4 HOH A 82 227 35 HOH HOH . D 4 HOH A 83 228 36 HOH HOH . D 4 HOH A 84 229 37 HOH HOH . D 4 HOH A 85 230 38 HOH HOH . D 4 HOH A 86 231 39 HOH HOH . D 4 HOH A 87 232 40 HOH HOH . D 4 HOH A 88 233 41 HOH HOH . D 4 HOH A 89 234 42 HOH HOH . D 4 HOH A 90 235 43 HOH HOH . D 4 HOH A 91 236 44 HOH HOH . D 4 HOH A 92 237 45 HOH HOH . D 4 HOH A 93 238 46 HOH HOH . D 4 HOH A 94 239 1 HOH HOH . D 4 HOH A 95 240 2 HOH HOH . D 4 HOH A 96 241 3 HOH HOH . D 4 HOH A 97 242 4 HOH HOH . D 4 HOH A 98 243 5 HOH HOH . D 4 HOH A 99 244 6 HOH HOH . D 4 HOH A 100 245 7 HOH HOH . D 4 HOH A 101 246 8 HOH HOH . D 4 HOH A 102 247 9 HOH HOH . D 4 HOH A 103 248 1 HOH HOH . D 4 HOH A 104 249 2 HOH HOH . D 4 HOH A 105 250 3 HOH HOH . D 4 HOH A 106 251 4 HOH HOH . D 4 HOH A 107 252 6 HOH HOH . D 4 HOH A 108 253 7 HOH HOH . D 4 HOH A 109 254 8 HOH HOH . D 4 HOH A 110 255 9 HOH HOH . D 4 HOH A 111 256 10 HOH HOH . D 4 HOH A 112 257 11 HOH HOH . D 4 HOH A 113 258 12 HOH HOH . D 4 HOH A 114 259 13 HOH HOH . D 4 HOH A 115 260 14 HOH HOH . D 4 HOH A 116 261 15 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 P2 THP . . . B 2 17.757 11.116 4.846 1 13.35 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 16.527 11.777 5.409 1 14.13 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 17.715 9.607 5.156 1 11.83 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 19.048 11.878 5.38 1 15.45 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 21.006 14.622 1.033 1 15.84 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 21.713 13.533 1.8 1 20.16 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 22.047 15.206 0.002 1 17.78 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 20.325 15.629 1.983 1 18.05 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 17.697 11.159 3.252 1 14.73 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 17.825 12.478 2.697 1 16.26 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 18.76 12.391 1.467 1 13.88 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.351 11.288 0.635 1 12.97 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.663 13.674 0.589 1 14 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 19.979 13.852 0.029 1 13.86 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 17.774 13.179 -0.594 1 11.71 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 18.064 11.66 -0.704 1 13.52 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 16.765 11.035 -1.091 1 12.13 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.499 10.812 -2.409 1 13.8 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.385 11.144 -3.272 1 14.03 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.303 10.289 -2.835 1 13.02 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.323 9.995 -1.894 1 12.47 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.255 9.598 -2.321 1 13.27 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.61 10.202 -0.533 1 12.27 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.559 9.873 0.491 1 12.97 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 15.826 10.712 -0.148 1 10.31 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #