data_3B9H # _model_server_result.job_id wli7QjrpFf0XXGgFz-EZfw _model_server_result.datetime_utc '2024-10-11 09:22:15' _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 3b9h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":265}' # _entry.id 3B9H # _exptl.entry_id 3B9H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 355.195 _entity.id 3 _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 3B9H _cell.length_a 71.6 _cell.length_b 71.6 _cell.length_c 115.32 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B9H _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 _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 76.88 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale2 A SG CYS 146 A CYS 146 1_555 D C6 NDU . A NDU 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? # _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 ? # 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 P OP1 NDU doub 259 n n P OP2 NDU sing 260 n n P OP3 NDU sing 261 n n P O5' NDU sing 262 n n O5' C5' NDU sing 263 n n C5' C4' NDU sing 264 n n C4' C3' NDU sing 265 n n C4' O4' NDU sing 266 n n C3' O3' NDU sing 267 n n C3' C2' NDU sing 268 n n C2' C1' NDU sing 269 n n C1' O4' NDU sing 270 n n C1' N1 NDU sing 271 n n N1 C2 NDU sing 272 n n N1 C6 NDU sing 273 n n C2 O2 NDU doub 274 n n C2 N3 NDU sing 275 n n N3 C4 NDU sing 276 n n C4 O4 NDU doub 277 n n C4 C5 NDU sing 278 n n C5 C6 NDU sing 279 n n C5 N5 NDU sing 280 n n N5 O51 NDU sing 281 n n N5 O52 NDU doub 282 n n OP2 HP2 NDU sing 283 n n OP3 HP3 NDU sing 284 n n C5' H51' NDU sing 285 n n C5' H52' NDU sing 286 n n C4' H4' NDU sing 287 n n C3' H3' NDU sing 288 n n O3' HA NDU sing 289 n n C2' H21' NDU sing 290 n n C2' H22' NDU sing 291 n n C1' H1' NDU sing 292 n n C6 H611 NDU sing 293 n n C6 H612 NDU sing 294 n n N3 H3 NDU sing 295 n n C5 H5 NDU sing 296 n n # _atom_sites.entry_id 3B9H _atom_sites.fract_transf_matrix[1][1] 0.013966 _atom_sites.fract_transf_matrix[1][2] 0.008064 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016127 _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] 0.008672 _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 2 PO4 A 1 268 268 PO4 PO4 . D 3 NDU A 1 265 265 NDU NDU . E 4 HOH A 1 300 300 HOH HOH . E 4 HOH A 2 301 301 HOH HOH . E 4 HOH A 3 302 302 HOH HOH . E 4 HOH A 4 303 303 HOH HOH . E 4 HOH A 5 304 304 HOH HOH . E 4 HOH A 6 305 305 HOH HOH . E 4 HOH A 7 306 306 HOH HOH . E 4 HOH A 8 307 307 HOH HOH . E 4 HOH A 9 308 308 HOH HOH . E 4 HOH A 10 309 309 HOH HOH . E 4 HOH A 11 310 310 HOH HOH . E 4 HOH A 12 311 311 HOH HOH . E 4 HOH A 13 312 312 HOH HOH . E 4 HOH A 14 313 313 HOH HOH . E 4 HOH A 15 314 314 HOH HOH . E 4 HOH A 16 315 315 HOH HOH . E 4 HOH A 17 316 316 HOH HOH . E 4 HOH A 18 317 317 HOH HOH . E 4 HOH A 19 318 318 HOH HOH . E 4 HOH A 20 319 319 HOH HOH . E 4 HOH A 21 320 320 HOH HOH . E 4 HOH A 22 321 321 HOH HOH . E 4 HOH A 23 322 322 HOH HOH . E 4 HOH A 24 323 323 HOH HOH . E 4 HOH A 25 324 324 HOH HOH . E 4 HOH A 26 325 325 HOH HOH . E 4 HOH A 27 326 326 HOH HOH . E 4 HOH A 28 327 327 HOH HOH . E 4 HOH A 29 328 328 HOH HOH . E 4 HOH A 30 329 329 HOH HOH . E 4 HOH A 31 330 330 HOH HOH . E 4 HOH A 32 331 331 HOH HOH . E 4 HOH A 33 332 332 HOH HOH . E 4 HOH A 34 333 333 HOH HOH . E 4 HOH A 35 334 334 HOH HOH . E 4 HOH A 36 335 335 HOH HOH . E 4 HOH A 37 336 336 HOH HOH . E 4 HOH A 38 337 337 HOH HOH . E 4 HOH A 39 338 338 HOH HOH . E 4 HOH A 40 339 339 HOH HOH . E 4 HOH A 41 340 340 HOH HOH . E 4 HOH A 42 341 341 HOH HOH . E 4 HOH A 43 342 342 HOH HOH . E 4 HOH A 44 343 343 HOH HOH . E 4 HOH A 45 344 344 HOH HOH . E 4 HOH A 46 345 345 HOH HOH . E 4 HOH A 47 346 346 HOH HOH . E 4 HOH A 48 347 347 HOH HOH . E 4 HOH A 49 348 348 HOH HOH . E 4 HOH A 50 349 349 HOH HOH . E 4 HOH A 51 350 350 HOH HOH . E 4 HOH A 52 351 351 HOH HOH . E 4 HOH A 53 352 352 HOH HOH . E 4 HOH A 54 353 353 HOH HOH . E 4 HOH A 55 354 354 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 . . . D 3 40.599 -13.857 45.69 1 19.43 ? P NDU 265 A 1 HETATM 2 O OP1 NDU . . . D 3 40.635 -14.266 47.148 1 17.34 ? OP1 NDU 265 A 1 HETATM 3 O OP2 NDU . . . D 3 41.702 -12.893 45.333 1 20.02 ? OP2 NDU 265 A 1 HETATM 4 O OP3 NDU . . . D 3 39.236 -13.493 45.113 1 21.6 ? OP3 NDU 265 A 1 HETATM 5 O O5' NDU . . . D 3 40.974 -15.223 44.933 1 21.14 ? O5' NDU 265 A 1 HETATM 6 C C5' NDU . . . D 3 41.09 -15.384 43.515 1 18.5 ? C5' NDU 265 A 1 HETATM 7 C C4' NDU . . . D 3 42.41 -16.117 43.268 1 18.84 ? C4' NDU 265 A 1 HETATM 8 C C3' NDU . . . D 3 43.656 -15.27 43.599 1 17.97 ? C3' NDU 265 A 1 HETATM 9 O O3' NDU . . . D 3 44.754 -16.092 43.989 1 15.67 ? O3' NDU 265 A 1 HETATM 10 C C2' NDU . . . D 3 44.029 -14.546 42.305 1 17.03 ? C2' NDU 265 A 1 HETATM 11 C C1' NDU . . . D 3 43.596 -15.618 41.3 1 18.71 ? C1' NDU 265 A 1 HETATM 12 O O4' NDU . . . D 3 42.481 -16.339 41.855 1 20.22 ? O4' NDU 265 A 1 HETATM 13 N N1 NDU . . . D 3 43.182 -15.263 39.948 1 18.64 ? N1 NDU 265 A 1 HETATM 14 C C2 NDU . . . D 3 44.129 -14.852 39.001 1 18.05 ? C2 NDU 265 A 1 HETATM 15 O O2 NDU . . . D 3 45.323 -14.684 39.336 1 22.37 ? O2 NDU 265 A 1 HETATM 16 N N3 NDU . . . D 3 43.767 -14.606 37.754 1 17.57 ? N3 NDU 265 A 1 HETATM 17 C C4 NDU . . . D 3 42.522 -14.785 37.339 1 19.8 ? C4 NDU 265 A 1 HETATM 18 O O4 NDU . . . D 3 42.167 -14.605 36.155 1 20.7 ? O4 NDU 265 A 1 HETATM 19 C C5 NDU . . . D 3 41.538 -15.222 38.325 1 22.33 ? C5 NDU 265 A 1 HETATM 20 C C6 NDU . . . D 3 41.872 -15.011 39.701 1 20.68 ? C6 NDU 265 A 1 HETATM 21 N N5 NDU . . . D 3 40.232 -15.441 37.866 1 20.93 ? N5 NDU 265 A 1 HETATM 22 O O51 NDU . . . D 3 40.014 -15.498 36.663 1 23 ? O51 NDU 265 A 1 HETATM 23 O O52 NDU . . . D 3 39.205 -15.672 38.762 1 20.77 ? O52 NDU 265 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #