data_3DDI # _model_server_result.job_id M0ErXEgUQWn1yX7qQp-WeA _model_server_result.datetime_utc '2024-12-09 08:09:21' _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 3ddi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 3DDI # _exptl.entry_id 3DDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 3DDI _cell.length_a 70.084 _cell.length_b 70.084 _cell.length_c 103.313 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 PISA dimeric 2 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,B,C,D,E,F,G,H 1 1,2,3 A,C,D,G 2 1 B,E,F,H 2 3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.084 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 35.042 60.694524 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N 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 metalc ? metalc1 E MG MG . B MG 142 1_555 F O1A TYD . B TYD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 E MG MG . B MG 142 1_555 H O HOH . B HOH 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc3 E MG MG . B MG 142 1_555 H O HOH . B HOH 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 3DDI _atom_sites.fract_transf_matrix[1][1] 0.014269 _atom_sites.fract_transf_matrix[1][2] 0.008238 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016476 _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] 0.009679 _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 MG A 1 142 1 MG MG . D 3 TYD A 1 201 201 TYD TYD . E 2 MG B 1 142 1 MG MG . F 3 TYD B 1 201 201 TYD TYD . G 4 HOH A 1 202 2 HOH HOH . G 4 HOH A 2 203 3 HOH HOH . G 4 HOH A 3 204 4 HOH HOH . G 4 HOH A 4 205 6 HOH HOH . G 4 HOH A 5 206 7 HOH HOH . G 4 HOH A 6 207 8 HOH HOH . G 4 HOH A 7 208 10 HOH HOH . G 4 HOH A 8 209 12 HOH HOH . G 4 HOH A 9 210 13 HOH HOH . G 4 HOH A 10 211 15 HOH HOH . G 4 HOH A 11 212 16 HOH HOH . G 4 HOH A 12 213 19 HOH HOH . G 4 HOH A 13 214 20 HOH HOH . G 4 HOH A 14 215 21 HOH HOH . G 4 HOH A 15 216 22 HOH HOH . G 4 HOH A 16 217 23 HOH HOH . G 4 HOH A 17 218 24 HOH HOH . G 4 HOH A 18 219 27 HOH HOH . G 4 HOH A 19 220 28 HOH HOH . G 4 HOH A 20 221 33 HOH HOH . G 4 HOH A 21 222 34 HOH HOH . G 4 HOH A 22 223 39 HOH HOH . G 4 HOH A 23 224 44 HOH HOH . G 4 HOH A 24 225 45 HOH HOH . G 4 HOH A 25 226 50 HOH HOH . G 4 HOH A 26 227 51 HOH HOH . G 4 HOH A 27 228 53 HOH HOH . G 4 HOH A 28 229 54 HOH HOH . G 4 HOH A 29 230 57 HOH HOH . G 4 HOH A 30 231 58 HOH HOH . G 4 HOH A 31 232 61 HOH HOH . G 4 HOH A 32 233 65 HOH HOH . G 4 HOH A 33 234 66 HOH HOH . G 4 HOH A 34 235 68 HOH HOH . G 4 HOH A 35 236 69 HOH HOH . G 4 HOH A 36 237 70 HOH HOH . G 4 HOH A 37 238 73 HOH HOH . G 4 HOH A 38 239 74 HOH HOH . G 4 HOH A 39 240 76 HOH HOH . G 4 HOH A 40 241 77 HOH HOH . G 4 HOH A 41 242 78 HOH HOH . G 4 HOH A 42 243 80 HOH HOH . G 4 HOH A 43 244 81 HOH HOH . G 4 HOH A 44 245 84 HOH HOH . G 4 HOH A 45 246 87 HOH HOH . G 4 HOH A 46 247 91 HOH HOH . G 4 HOH A 47 248 94 HOH HOH . G 4 HOH A 48 249 95 HOH HOH . G 4 HOH A 49 250 97 HOH HOH . G 4 HOH A 50 251 99 HOH HOH . G 4 HOH A 51 252 100 HOH HOH . G 4 HOH A 52 253 101 HOH HOH . G 4 HOH A 53 254 102 HOH HOH . G 4 HOH A 54 255 108 HOH HOH . G 4 HOH A 55 256 111 HOH HOH . G 4 HOH A 56 257 112 HOH HOH . G 4 HOH A 57 258 113 HOH HOH . G 4 HOH A 58 259 117 HOH HOH . G 4 HOH A 59 260 119 HOH HOH . G 4 HOH A 60 261 120 HOH HOH . G 4 HOH A 61 262 121 HOH HOH . G 4 HOH A 62 263 122 HOH HOH . G 4 HOH A 63 264 124 HOH HOH . G 4 HOH A 64 265 129 HOH HOH . G 4 HOH A 65 266 130 HOH HOH . G 4 HOH A 66 267 131 HOH HOH . G 4 HOH A 67 268 132 HOH HOH . G 4 HOH A 68 269 137 HOH HOH . G 4 HOH A 69 270 139 HOH HOH . G 4 HOH A 70 271 140 HOH HOH . G 4 HOH A 71 272 142 HOH HOH . G 4 HOH A 72 273 144 HOH HOH . G 4 HOH A 73 274 145 HOH HOH . G 4 HOH A 74 275 150 HOH HOH . G 4 HOH A 75 276 151 HOH HOH . G 4 HOH A 76 277 153 HOH HOH . G 4 HOH A 77 278 154 HOH HOH . G 4 HOH A 78 279 156 HOH HOH . G 4 HOH A 79 280 158 HOH HOH . G 4 HOH A 80 281 159 HOH HOH . G 4 HOH A 81 282 42 HOH HOH . G 4 HOH A 82 283 160 HOH HOH . H 4 HOH B 1 202 1 HOH HOH . H 4 HOH B 2 203 5 HOH HOH . H 4 HOH B 3 204 9 HOH HOH . H 4 HOH B 4 205 11 HOH HOH . H 4 HOH B 5 206 14 HOH HOH . H 4 HOH B 6 207 17 HOH HOH . H 4 HOH B 7 208 18 HOH HOH . H 4 HOH B 8 209 25 HOH HOH . H 4 HOH B 9 210 26 HOH HOH . H 4 HOH B 10 211 29 HOH HOH . H 4 HOH B 11 212 30 HOH HOH . H 4 HOH B 12 213 31 HOH HOH . H 4 HOH B 13 214 32 HOH HOH . H 4 HOH B 14 215 35 HOH HOH . H 4 HOH B 15 216 36 HOH HOH . H 4 HOH B 16 217 37 HOH HOH . H 4 HOH B 17 218 38 HOH HOH . H 4 HOH B 18 219 40 HOH HOH . H 4 HOH B 19 220 41 HOH HOH . H 4 HOH B 20 222 43 HOH HOH . H 4 HOH B 21 223 46 HOH HOH . H 4 HOH B 22 224 47 HOH HOH . H 4 HOH B 23 225 48 HOH HOH . H 4 HOH B 24 226 49 HOH HOH . H 4 HOH B 25 227 52 HOH HOH . H 4 HOH B 26 228 55 HOH HOH . H 4 HOH B 27 229 56 HOH HOH . H 4 HOH B 28 230 59 HOH HOH . H 4 HOH B 29 231 60 HOH HOH . H 4 HOH B 30 232 62 HOH HOH . H 4 HOH B 31 233 64 HOH HOH . H 4 HOH B 32 234 71 HOH HOH . H 4 HOH B 33 235 72 HOH HOH . H 4 HOH B 34 236 75 HOH HOH . H 4 HOH B 35 237 79 HOH HOH . H 4 HOH B 36 238 82 HOH HOH . H 4 HOH B 37 239 83 HOH HOH . H 4 HOH B 38 240 85 HOH HOH . H 4 HOH B 39 241 86 HOH HOH . H 4 HOH B 40 242 88 HOH HOH . H 4 HOH B 41 243 89 HOH HOH . H 4 HOH B 42 244 90 HOH HOH . H 4 HOH B 43 245 92 HOH HOH . H 4 HOH B 44 246 93 HOH HOH . H 4 HOH B 45 247 96 HOH HOH . H 4 HOH B 46 248 98 HOH HOH . H 4 HOH B 47 249 103 HOH HOH . H 4 HOH B 48 250 104 HOH HOH . H 4 HOH B 49 251 105 HOH HOH . H 4 HOH B 50 252 106 HOH HOH . H 4 HOH B 51 253 107 HOH HOH . H 4 HOH B 52 254 109 HOH HOH . H 4 HOH B 53 255 110 HOH HOH . H 4 HOH B 54 256 114 HOH HOH . H 4 HOH B 55 257 115 HOH HOH . H 4 HOH B 56 258 116 HOH HOH . H 4 HOH B 57 259 118 HOH HOH . H 4 HOH B 58 260 123 HOH HOH . H 4 HOH B 59 261 125 HOH HOH . H 4 HOH B 60 262 126 HOH HOH . H 4 HOH B 61 263 127 HOH HOH . H 4 HOH B 62 264 128 HOH HOH . H 4 HOH B 63 265 133 HOH HOH . H 4 HOH B 64 266 134 HOH HOH . H 4 HOH B 65 267 135 HOH HOH . H 4 HOH B 66 268 136 HOH HOH . H 4 HOH B 67 269 146 HOH HOH . H 4 HOH B 68 270 147 HOH HOH . H 4 HOH B 69 271 149 HOH HOH . H 4 HOH B 70 272 152 HOH HOH . H 4 HOH B 71 273 155 HOH HOH . H 4 HOH B 72 274 157 HOH HOH . H 4 HOH B 73 276 161 HOH HOH . H 4 HOH B 74 277 162 HOH HOH . H 4 HOH B 75 278 163 HOH HOH . H 4 HOH B 76 279 164 HOH HOH . H 4 HOH B 77 280 165 HOH HOH . H 4 HOH B 78 281 166 HOH HOH . H 4 HOH B 79 282 167 HOH HOH . H 4 HOH B 80 283 168 HOH HOH . H 4 HOH B 81 284 169 HOH HOH . H 4 HOH B 82 285 170 HOH HOH . H 4 HOH B 83 286 171 HOH HOH . H 4 HOH B 84 287 172 HOH HOH . H 4 HOH B 85 288 173 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 PA TYD . . . D 3 52.474 9.726 -9.008 1 28.02 ? PA TYD 201 A 1 HETATM 2 O O1A TYD . . . D 3 52.141 8.255 -8.947 1 28.19 ? O1A TYD 201 A 1 HETATM 3 O O2A TYD . . . D 3 52.532 10.452 -10.338 1 23.42 ? O2A TYD 201 A 1 HETATM 4 O O3A TYD . . . D 3 51.505 10.591 -8.043 1 22.41 ? O3A TYD 201 A 1 HETATM 5 P PB TYD . . . D 3 50.214 10.096 -7.203 1 24.19 ? PB TYD 201 A 1 HETATM 6 O O1B TYD . . . D 3 50.757 9.904 -5.806 1 24.44 ? O1B TYD 201 A 1 HETATM 7 O O2B TYD . . . D 3 49.708 8.826 -7.864 1 26.28 ? O2B TYD 201 A 1 HETATM 8 O O3B TYD . . . D 3 49.273 11.282 -7.317 1 22.26 ? O3B TYD 201 A 1 HETATM 9 O O5' TYD . . . D 3 53.883 9.986 -8.27 1 25.54 ? O5' TYD 201 A 1 HETATM 10 C C5' TYD . . . D 3 54.252 9.233 -7.12 1 19.36 ? C5' TYD 201 A 1 HETATM 11 C C4' TYD . . . D 3 54.896 10.168 -6.109 1 21.21 ? C4' TYD 201 A 1 HETATM 12 O O4' TYD . . . D 3 56.09 10.738 -6.65 1 20.64 ? O4' TYD 201 A 1 HETATM 13 C C3' TYD . . . D 3 54.016 11.36 -5.757 1 22.86 ? C3' TYD 201 A 1 HETATM 14 O O3' TYD . . . D 3 53.099 11.057 -4.698 1 23.77 ? O3' TYD 201 A 1 HETATM 15 C C2' TYD . . . D 3 55.017 12.422 -5.344 1 18.47 ? C2' TYD 201 A 1 HETATM 16 C C1' TYD . . . D 3 56.257 12.067 -6.147 1 23.49 ? C1' TYD 201 A 1 HETATM 17 N N1 TYD . . . D 3 56.372 13 -7.266 1 21.98 ? N1 TYD 201 A 1 HETATM 18 C C2 TYD . . . D 3 57.248 14.097 -7.158 1 25.91 ? C2 TYD 201 A 1 HETATM 19 O O2 TYD . . . D 3 57.915 14.256 -6.106 1 24.8 ? O2 TYD 201 A 1 HETATM 20 N N3 TYD . . . D 3 57.369 14.972 -8.163 1 23.74 ? N3 TYD 201 A 1 HETATM 21 C C4 TYD . . . D 3 56.675 14.819 -9.292 1 25.08 ? C4 TYD 201 A 1 HETATM 22 O O4 TYD . . . D 3 56.813 15.647 -10.221 1 35.74 ? O4 TYD 201 A 1 HETATM 23 C C5 TYD . . . D 3 55.741 13.672 -9.428 1 26.85 ? C5 TYD 201 A 1 HETATM 24 C C5M TYD . . . D 3 54.934 13.454 -10.683 1 30.95 ? C5M TYD 201 A 1 HETATM 25 C C6 TYD . . . D 3 55.643 12.784 -8.367 1 23.61 ? C6 TYD 201 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #