data_3BHR # _model_server_result.job_id bgS-70bKlSXkHh1TuhXKPA _model_server_result.datetime_utc '2024-10-11 09:30:00' _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 3bhr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":265}' # _entry.id 3BHR # _exptl.entry_id 3BHR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 355.195 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE" _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 3BHR _cell.length_a 71.95 _cell.length_b 71.95 _cell.length_c 115.47 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BHR _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # 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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 76.98 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 E C6 NDU . A NDU 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? # _chem_comp.formula 'C9 H14 N3 O10 P' _chem_comp.formula_weight 355.195 _chem_comp.id NDU _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3BHR _atom_sites.fract_transf_matrix[1][1] 0.013899 _atom_sites.fract_transf_matrix[1][2] 0.008024 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016049 _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] 0.00866 _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 PO4 A 1 267 267 PO4 PO4 . C 3 THG A 1 266 266 THG THG . D 2 PO4 A 1 268 268 PO4 PO4 . E 4 NDU A 1 265 265 NDU NDU . F 5 HOH A 1 269 1 HOH HOH . F 5 HOH A 2 270 2 HOH HOH . F 5 HOH A 3 271 3 HOH HOH . F 5 HOH A 4 272 4 HOH HOH . F 5 HOH A 5 273 5 HOH HOH . F 5 HOH A 6 274 6 HOH HOH . F 5 HOH A 7 275 7 HOH HOH . F 5 HOH A 8 276 8 HOH HOH . F 5 HOH A 9 277 9 HOH HOH . F 5 HOH A 10 278 10 HOH HOH . F 5 HOH A 11 279 11 HOH HOH . F 5 HOH A 12 280 12 HOH HOH . F 5 HOH A 13 281 13 HOH HOH . F 5 HOH A 14 282 14 HOH HOH . F 5 HOH A 15 283 15 HOH HOH . F 5 HOH A 16 284 16 HOH HOH . F 5 HOH A 17 285 17 HOH HOH . F 5 HOH A 18 286 18 HOH HOH . F 5 HOH A 19 287 19 HOH HOH . F 5 HOH A 20 288 20 HOH HOH . F 5 HOH A 21 289 21 HOH HOH . F 5 HOH A 22 290 22 HOH HOH . F 5 HOH A 23 291 23 HOH HOH . F 5 HOH A 24 292 24 HOH HOH . F 5 HOH A 25 293 25 HOH HOH . F 5 HOH A 26 294 26 HOH HOH . F 5 HOH A 27 295 27 HOH HOH . F 5 HOH A 28 296 28 HOH HOH . F 5 HOH A 29 297 29 HOH HOH . F 5 HOH A 30 298 30 HOH HOH . F 5 HOH A 31 299 31 HOH HOH . F 5 HOH A 32 300 32 HOH HOH . F 5 HOH A 33 301 33 HOH HOH . F 5 HOH A 34 302 34 HOH HOH . F 5 HOH A 35 303 35 HOH HOH . F 5 HOH A 36 304 36 HOH HOH . F 5 HOH A 37 305 37 HOH HOH . F 5 HOH A 38 306 38 HOH HOH . F 5 HOH A 39 307 39 HOH HOH . F 5 HOH A 40 308 40 HOH HOH . F 5 HOH A 41 309 41 HOH HOH . F 5 HOH A 42 310 42 HOH HOH . F 5 HOH A 43 311 43 HOH HOH . F 5 HOH A 44 312 44 HOH HOH . F 5 HOH A 45 313 45 HOH HOH . F 5 HOH A 46 314 46 HOH HOH . F 5 HOH A 47 315 47 HOH HOH . F 5 HOH A 48 316 48 HOH HOH . F 5 HOH A 49 317 49 HOH HOH . F 5 HOH A 50 318 50 HOH HOH . F 5 HOH A 51 319 51 HOH HOH . F 5 HOH A 52 320 52 HOH HOH . F 5 HOH A 53 321 53 HOH HOH . F 5 HOH A 54 322 54 HOH HOH . F 5 HOH A 55 323 55 HOH HOH . F 5 HOH A 56 324 56 HOH HOH . F 5 HOH A 57 325 57 HOH HOH . F 5 HOH A 58 326 58 HOH HOH . F 5 HOH A 59 327 59 HOH HOH . F 5 HOH A 60 328 60 HOH HOH . F 5 HOH A 61 329 61 HOH HOH . F 5 HOH A 62 330 62 HOH HOH . F 5 HOH A 63 331 63 HOH HOH . F 5 HOH A 64 332 64 HOH HOH . F 5 HOH A 65 333 65 HOH HOH . F 5 HOH A 66 334 66 HOH HOH . F 5 HOH A 67 335 67 HOH HOH . F 5 HOH A 68 336 68 HOH HOH . F 5 HOH A 69 337 69 HOH HOH . F 5 HOH A 70 338 70 HOH HOH . F 5 HOH A 71 339 72 HOH HOH . F 5 HOH A 72 340 73 HOH HOH . F 5 HOH A 73 341 74 HOH HOH . F 5 HOH A 74 342 75 HOH HOH . F 5 HOH A 75 343 76 HOH HOH . F 5 HOH A 76 344 77 HOH HOH . F 5 HOH A 77 345 78 HOH HOH . F 5 HOH A 78 346 79 HOH HOH . F 5 HOH A 79 347 80 HOH HOH . F 5 HOH A 80 348 81 HOH HOH . F 5 HOH A 81 349 82 HOH HOH . F 5 HOH A 82 350 83 HOH HOH . F 5 HOH A 83 351 84 HOH HOH . F 5 HOH A 84 352 85 HOH HOH . F 5 HOH A 85 353 86 HOH HOH . F 5 HOH A 86 354 87 HOH HOH . F 5 HOH A 87 355 88 HOH HOH . F 5 HOH A 88 356 89 HOH HOH . F 5 HOH A 89 357 90 HOH HOH . F 5 HOH A 90 358 91 HOH HOH . F 5 HOH A 91 359 92 HOH HOH . F 5 HOH A 92 360 93 HOH HOH . F 5 HOH A 93 361 94 HOH HOH . F 5 HOH A 94 362 95 HOH HOH . F 5 HOH A 95 363 96 HOH HOH . F 5 HOH A 96 364 97 HOH HOH . F 5 HOH A 97 365 98 HOH HOH . F 5 HOH A 98 366 99 HOH HOH . F 5 HOH A 99 367 100 HOH HOH . F 5 HOH A 100 368 101 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 P NDU . . . E 4 40.675 -13.947 45.756 1 20 ? P NDU 265 A 1 HETATM 2 O OP1 NDU . . . E 4 41.796 -13.016 45.426 1 20.44 ? OP1 NDU 265 A 1 HETATM 3 O OP2 NDU . . . E 4 40.668 -14.387 47.218 1 20.29 ? OP2 NDU 265 A 1 HETATM 4 O OP3 NDU . . . E 4 39.379 -13.481 45.163 1 17.37 ? OP3 NDU 265 A 1 HETATM 5 O O5' NDU . . . E 4 41.071 -15.324 44.995 1 22.51 ? O5' NDU 265 A 1 HETATM 6 C C5' NDU . . . E 4 41.292 -15.433 43.571 1 19.64 ? C5' NDU 265 A 1 HETATM 7 C C4' NDU . . . E 4 42.589 -16.186 43.303 1 18.53 ? C4' NDU 265 A 1 HETATM 8 C C3' NDU . . . E 4 43.848 -15.413 43.669 1 17.05 ? C3' NDU 265 A 1 HETATM 9 O O3' NDU . . . E 4 44.913 -16.336 43.934 1 20.75 ? O3' NDU 265 A 1 HETATM 10 C C2' NDU . . . E 4 44.064 -14.545 42.424 1 18.45 ? C2' NDU 265 A 1 HETATM 11 C C1' NDU . . . E 4 43.752 -15.586 41.371 1 18.47 ? C1' NDU 265 A 1 HETATM 12 O O4' NDU . . . E 4 42.686 -16.453 41.896 1 18.12 ? O4' NDU 265 A 1 HETATM 13 N N1 NDU . . . E 4 43.35 -15.177 40.034 1 18.35 ? N1 NDU 265 A 1 HETATM 14 C C2 NDU . . . E 4 44.264 -14.85 39.044 1 18.12 ? C2 NDU 265 A 1 HETATM 15 O O2 NDU . . . E 4 45.479 -14.732 39.321 1 19.9 ? O2 NDU 265 A 1 HETATM 16 N N3 NDU . . . E 4 43.806 -14.585 37.798 1 18.28 ? N3 NDU 265 A 1 HETATM 17 C C4 NDU . . . E 4 42.552 -14.747 37.408 1 20.91 ? C4 NDU 265 A 1 HETATM 18 O O4 NDU . . . E 4 42.214 -14.596 36.18 1 20.13 ? O4 NDU 265 A 1 HETATM 19 C C5 NDU . . . E 4 41.608 -15.143 38.467 1 22.31 ? C5 NDU 265 A 1 HETATM 20 C C6 NDU . . . E 4 42.05 -14.845 39.784 1 20.94 ? C6 NDU 265 A 1 HETATM 21 N N5 NDU . . . E 4 40.272 -15.377 38.168 1 25.57 ? N5 NDU 265 A 1 HETATM 22 O O51 NDU . . . E 4 39.458 -15.751 39.002 1 27.76 ? O51 NDU 265 A 1 HETATM 23 O O52 NDU . . . E 4 39.838 -15.208 36.889 1 26.72 ? O52 NDU 265 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #