data_1EXC # _model_server_result.job_id Pdkb0B5qEyjmVj4GkPwXuA _model_server_result.datetime_utc '2024-11-05 15:27:34' _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 1exc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 1EXC # _exptl.entry_id 1EXC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 1EXC _cell.length_a 62.1 _cell.length_b 86.58 _cell.length_c 93.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1EXC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_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,I 1 1 A,C,D,E,H 2 1 B,F,G,I 2 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' 2_455 -x-1/2,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 -31.05 0 46.865 # 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 E N N ? 3 F N N ? 3 G 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 disulf ? disulf1 A SG CYS 74 A CYS 74 1_555 A SG CYS 79 A CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 74 B CYS 74 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OE1 GLU 116 A GLU 116 1_555 C NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc2 A OE2 GLU 116 A GLU 116 1_555 C NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? metalc ? metalc3 C NA NA . A NA 205 1_555 B OE1 GLU 116 B GLU 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? metalc ? metalc4 C NA NA . A NA 205 1_555 B OE2 GLU 116 B GLU 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-5'-TRIPHOSPHATE" _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 N1 C2 DUT sing 83 n n N1 C6 DUT sing 84 n n N1 C1' DUT sing 85 n n C2 N3 DUT sing 86 n n C2 O2 DUT doub 87 n n N3 C4 DUT sing 88 n n N3 HN3 DUT sing 89 n n C4 C5 DUT sing 90 n n C4 O4 DUT doub 91 n n C5 C6 DUT doub 92 n n C5 H5 DUT sing 93 n n C6 H6 DUT sing 94 n n C1' C2' DUT sing 95 n n C1' O4' DUT sing 96 n n C1' H1' DUT sing 97 n n C2' C3' DUT sing 98 n n C2' "H2'1" DUT sing 99 n n C2' "H2'2" DUT sing 100 n n C3' C4' DUT sing 101 n n C3' O3' DUT sing 102 n n C3' H3' DUT sing 103 n n C4' O4' DUT sing 104 n n C4' C5' DUT sing 105 n n C4' H4' DUT sing 106 n n O3' HO3' DUT sing 107 n n C5' O5' DUT sing 108 n n C5' "H5'1" DUT sing 109 n n C5' "H5'2" DUT sing 110 n n O5' PA DUT sing 111 n n PA O1A DUT doub 112 n n PA O2A DUT sing 113 n n PA O3A DUT sing 114 n n O2A HOA2 DUT sing 115 n n O3A PB DUT sing 116 n n PB O1B DUT doub 117 n n PB O2B DUT sing 118 n n PB O3B DUT sing 119 n n O2B HOB2 DUT sing 120 n n O3B PG DUT sing 121 n n PG O1G DUT doub 122 n n PG O2G DUT sing 123 n n PG O3G DUT sing 124 n n O2G HOG2 DUT sing 125 n n O3G HOG3 DUT sing 126 n n # _atom_sites.entry_id 1EXC _atom_sites.fract_transf_matrix[1][1] 0.016103 _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] 0.01155 _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] 0.010669 _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 NA A 1 205 205 NA NA . D 3 DUT A 1 201 201 DUT DUT . E 3 DUT A 1 204 204 DUT DUT . F 3 DUT B 1 202 202 DUT DUT . G 3 DUT B 1 203 203 DUT DUT . H 4 HOH A 1 206 206 HOH HOH . H 4 HOH A 2 208 208 HOH HOH . H 4 HOH A 3 209 209 HOH HOH . H 4 HOH A 4 210 210 HOH HOH . H 4 HOH A 5 211 211 HOH HOH . H 4 HOH A 6 213 213 HOH HOH . H 4 HOH A 7 215 215 HOH HOH . H 4 HOH A 8 217 217 HOH HOH . H 4 HOH A 9 218 218 HOH HOH . H 4 HOH A 10 219 219 HOH HOH . H 4 HOH A 11 220 220 HOH HOH . H 4 HOH A 12 221 221 HOH HOH . H 4 HOH A 13 222 222 HOH HOH . H 4 HOH A 14 223 223 HOH HOH . H 4 HOH A 15 225 225 HOH HOH . H 4 HOH A 16 226 226 HOH HOH . H 4 HOH A 17 229 229 HOH HOH . H 4 HOH A 18 231 231 HOH HOH . H 4 HOH A 19 232 232 HOH HOH . H 4 HOH A 20 233 233 HOH HOH . H 4 HOH A 21 234 234 HOH HOH . H 4 HOH A 22 235 235 HOH HOH . H 4 HOH A 23 238 238 HOH HOH . H 4 HOH A 24 240 240 HOH HOH . H 4 HOH A 25 245 245 HOH HOH . H 4 HOH A 26 246 246 HOH HOH . H 4 HOH A 27 251 251 HOH HOH . H 4 HOH A 28 252 252 HOH HOH . H 4 HOH A 29 253 253 HOH HOH . H 4 HOH A 30 254 254 HOH HOH . H 4 HOH A 31 255 255 HOH HOH . H 4 HOH A 32 256 256 HOH HOH . H 4 HOH A 33 257 257 HOH HOH . H 4 HOH A 34 259 259 HOH HOH . H 4 HOH A 35 260 260 HOH HOH . H 4 HOH A 36 261 261 HOH HOH . H 4 HOH A 37 262 262 HOH HOH . H 4 HOH A 38 263 263 HOH HOH . H 4 HOH A 39 264 264 HOH HOH . H 4 HOH A 40 265 265 HOH HOH . H 4 HOH A 41 266 266 HOH HOH . H 4 HOH A 42 271 271 HOH HOH . H 4 HOH A 43 273 273 HOH HOH . H 4 HOH A 44 275 275 HOH HOH . H 4 HOH A 45 276 276 HOH HOH . H 4 HOH A 46 277 277 HOH HOH . H 4 HOH A 47 278 278 HOH HOH . H 4 HOH A 48 284 284 HOH HOH . H 4 HOH A 49 287 287 HOH HOH . H 4 HOH A 50 288 288 HOH HOH . H 4 HOH A 51 289 289 HOH HOH . H 4 HOH A 52 290 290 HOH HOH . H 4 HOH A 53 291 291 HOH HOH . H 4 HOH A 54 292 292 HOH HOH . H 4 HOH A 55 293 293 HOH HOH . H 4 HOH A 56 294 294 HOH HOH . H 4 HOH A 57 296 296 HOH HOH . H 4 HOH A 58 299 299 HOH HOH . H 4 HOH A 59 300 300 HOH HOH . H 4 HOH A 60 301 301 HOH HOH . H 4 HOH A 61 302 302 HOH HOH . H 4 HOH A 62 303 303 HOH HOH . H 4 HOH A 63 305 305 HOH HOH . H 4 HOH A 64 307 307 HOH HOH . H 4 HOH A 65 308 308 HOH HOH . H 4 HOH A 66 315 315 HOH HOH . H 4 HOH A 67 316 316 HOH HOH . H 4 HOH A 68 317 317 HOH HOH . H 4 HOH A 69 318 318 HOH HOH . H 4 HOH A 70 319 319 HOH HOH . H 4 HOH A 71 320 320 HOH HOH . H 4 HOH A 72 321 321 HOH HOH . H 4 HOH A 73 323 323 HOH HOH . H 4 HOH A 74 324 324 HOH HOH . H 4 HOH A 75 325 325 HOH HOH . H 4 HOH A 76 326 326 HOH HOH . H 4 HOH A 77 328 328 HOH HOH . H 4 HOH A 78 329 329 HOH HOH . H 4 HOH A 79 330 330 HOH HOH . H 4 HOH A 80 331 331 HOH HOH . H 4 HOH A 81 334 334 HOH HOH . H 4 HOH A 82 335 335 HOH HOH . H 4 HOH A 83 336 336 HOH HOH . H 4 HOH A 84 337 337 HOH HOH . H 4 HOH A 85 340 340 HOH HOH . H 4 HOH A 86 343 343 HOH HOH . I 4 HOH B 1 207 207 HOH HOH . I 4 HOH B 2 212 212 HOH HOH . I 4 HOH B 3 214 214 HOH HOH . I 4 HOH B 4 216 216 HOH HOH . I 4 HOH B 5 224 224 HOH HOH . I 4 HOH B 6 227 227 HOH HOH . I 4 HOH B 7 228 228 HOH HOH . I 4 HOH B 8 230 230 HOH HOH . I 4 HOH B 9 236 236 HOH HOH . I 4 HOH B 10 237 237 HOH HOH . I 4 HOH B 11 239 239 HOH HOH . I 4 HOH B 12 241 241 HOH HOH . I 4 HOH B 13 242 242 HOH HOH . I 4 HOH B 14 243 243 HOH HOH . I 4 HOH B 15 244 244 HOH HOH . I 4 HOH B 16 247 247 HOH HOH . I 4 HOH B 17 248 248 HOH HOH . I 4 HOH B 18 249 249 HOH HOH . I 4 HOH B 19 250 250 HOH HOH . I 4 HOH B 20 258 258 HOH HOH . I 4 HOH B 21 267 267 HOH HOH . I 4 HOH B 22 268 268 HOH HOH . I 4 HOH B 23 269 269 HOH HOH . I 4 HOH B 24 270 270 HOH HOH . I 4 HOH B 25 272 272 HOH HOH . I 4 HOH B 26 274 274 HOH HOH . I 4 HOH B 27 279 279 HOH HOH . I 4 HOH B 28 280 280 HOH HOH . I 4 HOH B 29 281 281 HOH HOH . I 4 HOH B 30 282 282 HOH HOH . I 4 HOH B 31 283 283 HOH HOH . I 4 HOH B 32 285 285 HOH HOH . I 4 HOH B 33 286 286 HOH HOH . I 4 HOH B 34 295 295 HOH HOH . I 4 HOH B 35 297 297 HOH HOH . I 4 HOH B 36 298 298 HOH HOH . I 4 HOH B 37 304 304 HOH HOH . I 4 HOH B 38 306 306 HOH HOH . I 4 HOH B 39 309 309 HOH HOH . I 4 HOH B 40 310 310 HOH HOH . I 4 HOH B 41 311 311 HOH HOH . I 4 HOH B 42 312 312 HOH HOH . I 4 HOH B 43 313 313 HOH HOH . I 4 HOH B 44 314 314 HOH HOH . I 4 HOH B 45 322 322 HOH HOH . I 4 HOH B 46 327 327 HOH HOH . I 4 HOH B 47 332 332 HOH HOH . I 4 HOH B 48 333 333 HOH HOH . I 4 HOH B 49 338 338 HOH HOH . I 4 HOH B 50 339 339 HOH HOH . I 4 HOH B 51 341 341 HOH HOH . I 4 HOH B 52 342 342 HOH HOH . I 4 HOH B 53 344 344 HOH HOH . I 4 HOH B 54 345 345 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 N N1 DUT . . . D 3 4.666 -15.848 37.967 0.8 59.67 ? N1 DUT 201 A 1 HETATM 2 C C2 DUT . . . D 3 5.221 -14.655 38.408 0.8 61.35 ? C2 DUT 201 A 1 HETATM 3 N N3 DUT . . . D 3 6.015 -14.764 39.523 0.8 62.06 ? N3 DUT 201 A 1 HETATM 4 C C4 DUT . . . D 3 6.305 -15.919 40.229 0.8 61.96 ? C4 DUT 201 A 1 HETATM 5 C C5 DUT . . . D 3 5.699 -17.11 39.706 0.8 61.26 ? C5 DUT 201 A 1 HETATM 6 C C6 DUT . . . D 3 4.921 -17.034 38.619 0.8 59.57 ? C6 DUT 201 A 1 HETATM 7 O O2 DUT . . . D 3 5.02 -13.583 37.853 0.8 60.73 ? O2 DUT 201 A 1 HETATM 8 O O4 DUT . . . D 3 7.009 -15.852 41.242 0.8 62.22 ? O4 DUT 201 A 1 HETATM 9 C C1' DUT . . . D 3 3.793 -15.803 36.785 0.8 57.82 ? C1' DUT 201 A 1 HETATM 10 C C2' DUT . . . D 3 4.254 -16.697 35.644 0.8 56.46 ? C2' DUT 201 A 1 HETATM 11 C C3' DUT . . . D 3 2.952 -17.1 34.975 0.8 54.38 ? C3' DUT 201 A 1 HETATM 12 C C4' DUT . . . D 3 1.939 -17.094 36.121 0.8 53.51 ? C4' DUT 201 A 1 HETATM 13 O O4' DUT . . . D 3 2.518 -16.285 37.176 0.8 55.39 ? O4' DUT 201 A 1 HETATM 14 O O3' DUT . . . D 3 2.61 -16.077 34.051 0.8 55.14 ? O3' DUT 201 A 1 HETATM 15 C C5' DUT . . . D 3 1.557 -18.45 36.679 0.8 49.3 ? C5' DUT 201 A 1 HETATM 16 O O5' DUT . . . D 3 0.577 -18.297 37.739 0.8 42.15 ? O5' DUT 201 A 1 HETATM 17 P PA DUT . . . D 3 1.016 -17.802 39.228 0.8 36.4 ? PA DUT 201 A 1 HETATM 18 O O1A DUT . . . D 3 0.002 -18.341 40.164 0.8 34.03 ? O1A DUT 201 A 1 HETATM 19 O O2A DUT . . . D 3 2.44 -18.165 39.37 0.8 36.73 ? O2A DUT 201 A 1 HETATM 20 O O3A DUT . . . D 3 0.958 -16.162 39.316 0.8 39.44 ? O3A DUT 201 A 1 HETATM 21 P PB DUT . . . D 3 -0.214 -15.086 39.723 0.8 37.86 ? PB DUT 201 A 1 HETATM 22 O O1B DUT . . . D 3 0.282 -13.719 39.478 0.8 35.53 ? O1B DUT 201 A 1 HETATM 23 O O2B DUT . . . D 3 -0.725 -15.472 41.064 0.8 38.74 ? O2B DUT 201 A 1 HETATM 24 O O3B DUT . . . D 3 -1.403 -15.326 38.636 0.8 34.53 ? O3B DUT 201 A 1 HETATM 25 P PG DUT . . . D 3 -1.322 -15.516 37.023 0.8 28.73 ? PG DUT 201 A 1 HETATM 26 O O1G DUT . . . D 3 0.135 -15.248 36.713 0.8 26.97 ? O1G DUT 201 A 1 HETATM 27 O O2G DUT . . . D 3 -1.729 -16.95 36.746 0.8 25.48 ? O2G DUT 201 A 1 HETATM 28 O O3G DUT . . . D 3 -2.271 -14.493 36.434 0.8 27.34 ? O3G DUT 201 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #