data_1SIX # _model_server_result.job_id agFZtrxT6SxC26-9hc0ChA _model_server_result.datetime_utc '2024-11-22 17:07:01' _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 1six # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":170}' # _entry.id 1SIX # _exptl.entry_id 1SIX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 _cell.angle_gamma 120 _cell.entry_id 1SIX _cell.length_a 54.822 _cell.length_b 54.822 _cell.length_c 84.21 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SIX _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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 54.822 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 27.411 47.477245 0 # _struct_asym.details ? _struct_asym.entity_id 3 _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 metalc ? metalc1 C O1G DUP . A DUP 170 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 C O1B DUP . A DUP 170 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc3 C O1A DUP . A DUP 170 1_555 B MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc4 B MG MG . A MG 171 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc5 B MG MG . A MG 171 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc6 B MG MG . A MG 171 1_555 E O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 O4 C4 DUP doub 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 1SIX _atom_sites.fract_transf_matrix[1][1] 0.018241 _atom_sites.fract_transf_matrix[1][2] 0.010531 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021063 _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] 0.011875 _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 MG A 1 171 171 MG MG2 . C 3 DUP A 1 170 170 DUP UPN . D 4 TRS A 1 172 172 TRS TRS . E 5 HOH A 1 301 301 HOH HOH . E 5 HOH A 2 302 302 HOH HOH . E 5 HOH A 3 303 303 HOH HOH . E 5 HOH A 4 304 304 HOH HOH . E 5 HOH A 5 305 305 HOH HOH . E 5 HOH A 6 306 306 HOH HOH . E 5 HOH A 7 307 307 HOH HOH . E 5 HOH A 8 308 308 HOH HOH . E 5 HOH A 9 309 309 HOH HOH . E 5 HOH A 10 310 310 HOH HOH . E 5 HOH A 11 311 311 HOH HOH . E 5 HOH A 12 312 312 HOH HOH . E 5 HOH A 13 313 313 HOH HOH . E 5 HOH A 14 314 314 HOH HOH . E 5 HOH A 15 315 315 HOH HOH . E 5 HOH A 16 316 316 HOH HOH . E 5 HOH A 17 317 317 HOH HOH . E 5 HOH A 18 318 318 HOH HOH . E 5 HOH A 19 319 319 HOH HOH . E 5 HOH A 20 320 320 HOH HOH . E 5 HOH A 21 321 321 HOH HOH . E 5 HOH A 22 322 322 HOH HOH . E 5 HOH A 23 323 323 HOH HOH . E 5 HOH A 24 324 324 HOH HOH . E 5 HOH A 25 325 325 HOH HOH . E 5 HOH A 26 326 326 HOH HOH . E 5 HOH A 27 327 327 HOH HOH . E 5 HOH A 28 328 328 HOH HOH . E 5 HOH A 29 329 329 HOH HOH . E 5 HOH A 30 330 330 HOH HOH . E 5 HOH A 31 331 331 HOH HOH . E 5 HOH A 32 332 332 HOH HOH . E 5 HOH A 33 333 333 HOH HOH . E 5 HOH A 34 334 334 HOH HOH . E 5 HOH A 35 335 335 HOH HOH . E 5 HOH A 36 336 336 HOH HOH . E 5 HOH A 37 337 337 HOH HOH . E 5 HOH A 38 338 338 HOH HOH . E 5 HOH A 39 339 339 HOH HOH . E 5 HOH A 40 340 340 HOH HOH . E 5 HOH A 41 341 341 HOH HOH . E 5 HOH A 42 342 342 HOH HOH . E 5 HOH A 43 343 343 HOH HOH . E 5 HOH A 44 344 344 HOH HOH . E 5 HOH A 45 345 345 HOH HOH . E 5 HOH A 46 346 346 HOH HOH . E 5 HOH A 47 347 347 HOH HOH . E 5 HOH A 48 348 348 HOH HOH . E 5 HOH A 49 349 349 HOH HOH . E 5 HOH A 50 350 350 HOH HOH . E 5 HOH A 51 351 351 HOH HOH . E 5 HOH A 52 352 352 HOH HOH . E 5 HOH A 53 353 353 HOH HOH . E 5 HOH A 54 354 354 HOH HOH . E 5 HOH A 55 355 355 HOH HOH . E 5 HOH A 56 356 356 HOH HOH . E 5 HOH A 57 357 357 HOH HOH . E 5 HOH A 58 358 358 HOH HOH . E 5 HOH A 59 359 359 HOH HOH . E 5 HOH A 60 360 360 HOH HOH . E 5 HOH A 61 361 361 HOH HOH . E 5 HOH A 62 362 362 HOH HOH . E 5 HOH A 63 363 363 HOH HOH . E 5 HOH A 64 364 364 HOH HOH . E 5 HOH A 65 365 365 HOH HOH . E 5 HOH A 66 366 366 HOH HOH . E 5 HOH A 67 367 367 HOH HOH . E 5 HOH A 68 368 368 HOH HOH . E 5 HOH A 69 369 369 HOH HOH . E 5 HOH A 70 370 370 HOH HOH . E 5 HOH A 71 371 371 HOH HOH . E 5 HOH A 72 372 372 HOH HOH . E 5 HOH A 73 373 373 HOH HOH . E 5 HOH A 74 374 374 HOH HOH . E 5 HOH A 75 375 375 HOH HOH . E 5 HOH A 76 376 376 HOH HOH . E 5 HOH A 77 377 377 HOH HOH . E 5 HOH A 78 378 378 HOH HOH . E 5 HOH A 79 379 379 HOH HOH . E 5 HOH A 80 380 380 HOH HOH . E 5 HOH A 81 381 381 HOH HOH . E 5 HOH A 82 382 382 HOH HOH . E 5 HOH A 83 383 383 HOH HOH . E 5 HOH A 84 384 384 HOH HOH . E 5 HOH A 85 385 385 HOH HOH . E 5 HOH A 86 386 386 HOH HOH . E 5 HOH A 87 387 387 HOH HOH . E 5 HOH A 88 388 388 HOH HOH . E 5 HOH A 89 389 389 HOH HOH . E 5 HOH A 90 390 390 HOH HOH . E 5 HOH A 91 391 391 HOH HOH . E 5 HOH A 92 392 392 HOH HOH . E 5 HOH A 93 393 393 HOH HOH . E 5 HOH A 94 394 394 HOH HOH . E 5 HOH A 95 395 395 HOH HOH . E 5 HOH A 96 396 396 HOH HOH . E 5 HOH A 97 397 397 HOH HOH . E 5 HOH A 98 398 398 HOH HOH . E 5 HOH A 99 399 399 HOH HOH . E 5 HOH A 100 400 400 HOH HOH . E 5 HOH A 101 401 401 HOH HOH . E 5 HOH A 102 402 402 HOH HOH . E 5 HOH A 103 403 403 HOH HOH . E 5 HOH A 104 404 404 HOH HOH . E 5 HOH A 105 405 405 HOH HOH . E 5 HOH A 106 406 406 HOH HOH . E 5 HOH A 107 407 407 HOH HOH . E 5 HOH A 108 408 408 HOH HOH . E 5 HOH A 109 409 409 HOH HOH . E 5 HOH A 110 410 410 HOH HOH . E 5 HOH A 111 411 411 HOH HOH . E 5 HOH A 112 412 412 HOH HOH . E 5 HOH A 113 413 413 HOH HOH . E 5 HOH A 114 414 414 HOH HOH . E 5 HOH A 115 415 415 HOH HOH . E 5 HOH A 116 416 416 HOH HOH . E 5 HOH A 117 417 417 HOH HOH . E 5 HOH A 118 418 418 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 O O4 DUP . . . C 3 37.996 15.049 15.512 1 13.22 ? O4 DUP 170 A 1 HETATM 2 C C4 DUP . . . C 3 38.792 14.285 15.997 1 11.59 ? C4 DUP 170 A 1 HETATM 3 C C5 DUP . . . C 3 38.504 12.976 16.504 1 12.06 ? C5 DUP 170 A 1 HETATM 4 C C6 DUP . . . C 3 39.491 12.22 16.972 1 12.31 ? C6 DUP 170 A 1 HETATM 5 N N3 DUP . . . C 3 40.174 14.664 16.064 1 12.02 ? N3 DUP 170 A 1 HETATM 6 C C2 DUP . . . C 3 41.209 13.92 16.643 1 12.29 ? C2 DUP 170 A 1 HETATM 7 O O2 DUP . . . C 3 42.365 14.339 16.639 1 13.75 ? O2 DUP 170 A 1 HETATM 8 N N1 DUP . . . C 3 40.822 12.638 17.092 1 12.59 ? N1 DUP 170 A 1 HETATM 9 C C1' DUP . . . C 3 41.84 11.826 17.77 1 13.42 ? C1' DUP 170 A 1 HETATM 10 C C2' DUP . . . C 3 41.604 11.825 19.3 1 13.37 ? C2' DUP 170 A 1 HETATM 11 C C3' DUP . . . C 3 40.86 10.534 19.563 1 12.79 ? C3' DUP 170 A 1 HETATM 12 O O3' DUP . . . C 3 41.114 10.103 20.9 1 14.52 ? O3' DUP 170 A 1 HETATM 13 O O4' DUP . . . C 3 41.654 10.461 17.372 1 13.33 ? O4' DUP 170 A 1 HETATM 14 C C4' DUP . . . C 3 41.462 9.634 18.545 1 13.04 ? C4' DUP 170 A 1 HETATM 15 C C5' DUP . . . C 3 40.583 8.494 18.177 1 13.21 ? C5' DUP 170 A 1 HETATM 16 O O5' DUP . . . C 3 39.295 8.933 17.675 1 12.37 ? O5' DUP 170 A 1 HETATM 17 P PA DUP . . . C 3 38.265 7.862 17.08 1 13.12 ? PA DUP 170 A 1 HETATM 18 O O1A DUP . . . C 3 38.026 6.797 18.086 1 13.52 ? O1A DUP 170 A 1 HETATM 19 O O2A DUP . . . C 3 37.08 8.656 16.616 1 13.97 ? O2A DUP 170 A 1 HETATM 20 N N3A DUP . . . C 3 39.033 7.267 15.796 1 14.08 ? N3A DUP 170 A 1 HETATM 21 P PB DUP . . . C 3 39.282 5.627 15.342 1 14.17 ? PB DUP 170 A 1 HETATM 22 O O1B DUP . . . C 3 38.302 4.799 16.057 1 14.12 ? O1B DUP 170 A 1 HETATM 23 O O2B DUP . . . C 3 39.296 5.568 13.868 1 15.2 ? O2B DUP 170 A 1 HETATM 24 O O3B DUP . . . C 3 40.692 5.248 15.795 1 16.11 ? O3B DUP 170 A 1 HETATM 25 P PG DUP . . . C 3 41.271 4.563 17.181 1 15.88 ? PG DUP 170 A 1 HETATM 26 O O2G DUP . . . C 3 42.492 5.326 17.538 1 18.84 ? O2G DUP 170 A 1 HETATM 27 O O1G DUP . . . C 3 40.175 4.681 18.172 1 14.6 ? O1G DUP 170 A 1 HETATM 28 O O3G DUP . . . C 3 41.627 3.183 16.807 1 19.75 ? O3G DUP 170 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #