data_3I93 # _model_server_result.job_id Ap1x9RJqoIR1vE3eJ0QdIg _model_server_result.datetime_utc '2024-11-17 01:26:41' _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 3i93 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 3I93 # _exptl.entry_id 3I93 _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 3I93 _cell.length_a 54.591 _cell.length_b 54.591 _cell.length_c 83.051 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I93 _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 _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,F _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 54.591 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 27.2955 47.277193 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 covale ? covale1 D C TRS . A TRS 202 1_555 D C1 TRS . A TRS 202 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale2 E C TRS . A TRS 203 1_555 E C1 TRS . A TRS 203 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.084 ? # _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 3I93 _atom_sites.fract_transf_matrix[1][1] 0.018318 _atom_sites.fract_transf_matrix[1][2] 0.010576 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021152 _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] 0.012041 _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 1 200 2778 MG MG . C 3 DUP A 1 201 2777 DUP DUP . D 4 TRS A 1 202 2203 TRS TRS . E 4 TRS A 1 203 2204 TRS TRS . F 5 HOH A 1 301 1 HOH HOH . F 5 HOH A 2 302 2 HOH HOH . F 5 HOH A 3 303 3 HOH HOH . F 5 HOH A 4 304 4 HOH HOH . F 5 HOH A 5 305 6 HOH HOH . F 5 HOH A 6 306 7 HOH HOH . F 5 HOH A 7 307 8 HOH HOH . F 5 HOH A 8 308 10 HOH HOH . F 5 HOH A 9 309 13 HOH HOH . F 5 HOH A 10 310 15 HOH HOH . F 5 HOH A 11 311 17 HOH HOH . F 5 HOH A 12 312 18 HOH HOH . F 5 HOH A 13 313 19 HOH HOH . F 5 HOH A 14 314 20 HOH HOH . F 5 HOH A 15 315 21 HOH HOH . F 5 HOH A 16 316 22 HOH HOH . F 5 HOH A 17 317 23 HOH HOH . F 5 HOH A 18 318 25 HOH HOH . F 5 HOH A 19 319 26 HOH HOH . F 5 HOH A 20 320 28 HOH HOH . F 5 HOH A 21 321 29 HOH HOH . F 5 HOH A 22 322 30 HOH HOH . F 5 HOH A 23 323 31 HOH HOH . F 5 HOH A 24 324 33 HOH HOH . F 5 HOH A 25 325 35 HOH HOH . F 5 HOH A 26 326 37 HOH HOH . F 5 HOH A 27 327 40 HOH HOH . F 5 HOH A 28 328 41 HOH HOH . F 5 HOH A 29 329 42 HOH HOH . F 5 HOH A 30 330 43 HOH HOH . F 5 HOH A 31 331 44 HOH HOH . F 5 HOH A 32 332 46 HOH HOH . F 5 HOH A 33 333 48 HOH HOH . F 5 HOH A 34 334 50 HOH HOH . F 5 HOH A 35 335 51 HOH HOH . F 5 HOH A 36 336 52 HOH HOH . F 5 HOH A 37 337 54 HOH HOH . F 5 HOH A 38 338 55 HOH HOH . F 5 HOH A 39 339 56 HOH HOH . F 5 HOH A 40 340 57 HOH HOH . F 5 HOH A 41 341 58 HOH HOH . F 5 HOH A 42 342 59 HOH HOH . F 5 HOH A 43 343 60 HOH HOH . F 5 HOH A 44 344 62 HOH HOH . F 5 HOH A 45 345 66 HOH HOH . F 5 HOH A 46 346 67 HOH HOH . F 5 HOH A 47 347 68 HOH HOH . F 5 HOH A 48 348 69 HOH HOH . F 5 HOH A 49 349 70 HOH HOH . F 5 HOH A 50 350 71 HOH HOH . F 5 HOH A 51 351 75 HOH HOH . F 5 HOH A 52 352 76 HOH HOH . F 5 HOH A 53 353 78 HOH HOH . F 5 HOH A 54 354 79 HOH HOH . F 5 HOH A 55 355 80 HOH HOH . F 5 HOH A 56 356 81 HOH HOH . F 5 HOH A 57 357 83 HOH HOH . F 5 HOH A 58 358 84 HOH HOH . F 5 HOH A 59 359 86 HOH HOH . F 5 HOH A 60 360 87 HOH HOH . F 5 HOH A 61 361 88 HOH HOH . F 5 HOH A 62 362 89 HOH HOH . F 5 HOH A 63 363 90 HOH HOH . F 5 HOH A 64 364 91 HOH HOH . F 5 HOH A 65 365 92 HOH HOH . F 5 HOH A 66 366 93 HOH HOH . F 5 HOH A 67 367 95 HOH HOH . F 5 HOH A 68 368 96 HOH HOH . F 5 HOH A 69 369 97 HOH HOH . F 5 HOH A 70 370 98 HOH HOH . F 5 HOH A 71 371 99 HOH HOH . F 5 HOH A 72 372 100 HOH HOH . F 5 HOH A 73 373 101 HOH HOH . F 5 HOH A 74 374 102 HOH HOH . F 5 HOH A 75 375 103 HOH HOH . F 5 HOH A 76 376 104 HOH HOH . F 5 HOH A 77 377 105 HOH HOH . F 5 HOH A 78 378 106 HOH HOH . F 5 HOH A 79 379 107 HOH HOH . F 5 HOH A 80 380 113 HOH HOH . F 5 HOH A 81 381 114 HOH HOH . F 5 HOH A 82 382 115 HOH HOH . F 5 HOH A 83 383 116 HOH HOH . F 5 HOH A 84 384 117 HOH HOH . F 5 HOH A 85 385 118 HOH HOH . F 5 HOH A 86 386 120 HOH HOH . F 5 HOH A 87 387 121 HOH HOH . F 5 HOH A 88 388 122 HOH HOH . F 5 HOH A 89 389 123 HOH HOH . F 5 HOH A 90 390 124 HOH HOH . F 5 HOH A 91 391 125 HOH HOH . F 5 HOH A 92 392 126 HOH HOH . F 5 HOH A 93 393 127 HOH HOH . F 5 HOH A 94 394 128 HOH HOH . F 5 HOH A 95 395 130 HOH HOH . F 5 HOH A 96 396 131 HOH HOH . F 5 HOH A 97 397 132 HOH HOH . F 5 HOH A 98 398 133 HOH HOH . F 5 HOH A 99 399 134 HOH HOH . F 5 HOH A 100 400 136 HOH HOH . F 5 HOH A 101 401 137 HOH HOH . F 5 HOH A 102 402 138 HOH HOH . F 5 HOH A 103 403 139 HOH HOH . F 5 HOH A 104 404 140 HOH HOH . F 5 HOH A 105 405 141 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 16.771 14.894 41.479 1 17.34 ? O4 DUP 201 A 1 HETATM 2 C C4 DUP . . . C 3 15.887 14.09 40.922 1 15.74 ? C4 DUP 201 A 1 HETATM 3 C C5 DUP . . . C 3 16.26 12.879 40.362 1 19.83 ? C5 DUP 201 A 1 HETATM 4 C C6 DUP . . . C 3 15.277 12.087 39.781 1 15.92 ? C6 DUP 201 A 1 HETATM 5 N N3 DUP . . . C 3 14.619 14.493 40.881 1 17.27 ? N3 DUP 201 A 1 HETATM 6 C C2 DUP . . . C 3 13.666 13.715 40.307 1 18.23 ? C2 DUP 201 A 1 HETATM 7 O O2 DUP . . . C 3 12.38 14.167 40.309 1 14.57 ? O2 DUP 201 A 1 HETATM 8 N N1 DUP . . . C 3 14 12.519 39.769 1 19.09 ? N1 DUP 201 A 1 HETATM 9 C C1' DUP . . . C 3 12.977 11.684 39.151 1 18.91 ? C1' DUP 201 A 1 HETATM 10 C C2' DUP . . . C 3 13.162 11.766 37.643 1 17.4 ? C2' DUP 201 A 1 HETATM 11 C C3' DUP . . . C 3 13.902 10.476 37.328 1 12.66 ? C3' DUP 201 A 1 HETATM 12 O O3' DUP . . . C 3 13.641 10.017 36.006 1 12.37 ? O3' DUP 201 A 1 HETATM 13 O O4' DUP . . . C 3 13.18 10.318 39.56 1 16.35 ? O4' DUP 201 A 1 HETATM 14 C C4' DUP . . . C 3 13.346 9.541 38.377 1 16.76 ? C4' DUP 201 A 1 HETATM 15 C C5' DUP . . . C 3 14.276 8.381 38.662 1 19.6 ? C5' DUP 201 A 1 HETATM 16 O O5' DUP . . . C 3 15.545 8.91 39.072 1 17.91 ? O5' DUP 201 A 1 HETATM 17 P PA DUP . . . C 3 16.595 7.843 39.69 1 21.84 ? PA DUP 201 A 1 HETATM 18 O O1A DUP . . . C 3 17.849 8.618 40.077 1 19.69 ? O1A DUP 201 A 1 HETATM 19 O O2A DUP . . . C 3 16.692 6.725 38.676 1 21.19 ? O2A DUP 201 A 1 HETATM 20 N N3A DUP . . . C 3 15.84 7.274 41.096 1 19.84 ? N3A DUP 201 A 1 HETATM 21 P PB DUP . . . C 3 15.679 5.649 41.51 1 19.64 ? PB DUP 201 A 1 HETATM 22 O O1B DUP . . . C 3 16.644 4.728 40.776 1 18.29 ? O1B DUP 201 A 1 HETATM 23 O O2B DUP . . . C 3 15.776 5.557 43.022 1 16.16 ? O2B DUP 201 A 1 HETATM 24 O O3B DUP . . . C 3 14.161 5.182 41.135 1 22.2 ? O3B DUP 201 A 1 HETATM 25 P PG DUP . . . C 3 13.759 4.323 39.812 1 28.91 ? PG DUP 201 A 1 HETATM 26 O O2G DUP . . . C 3 13.76 2.886 40.268 1 27.94 ? O2G DUP 201 A 1 HETATM 27 O O1G DUP . . . C 3 12.385 4.898 39.479 1 28.09 ? O1G DUP 201 A 1 HETATM 28 O O3G DUP . . . C 3 14.804 4.646 38.748 1 26.65 ? O3G DUP 201 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #