data_3CKN # _model_server_result.job_id 08KhPEbYhz2ntHXMR1tGvQ _model_server_result.datetime_utc '2024-10-19 08:33:53' _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 3ckn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":332}' # _entry.id 3CKN # _exptl.entry_id 3CKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 3CKN _cell.length_a 86.862 _cell.length_b 86.862 _cell.length_c 104.243 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CKN _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _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 metalc ? metalc1 A OD2 ASP 141 A ASP 141 1_555 B MN MN . A MN 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc2 B MN MN . A MN 330 1_555 D O1A UDP . A UDP 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc3 B MN MN . A MN 330 1_555 D O2B UDP . A UDP 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc4 B MN MN . A MN 330 1_555 E O HOH . A HOH 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 B MN MN . A MN 330 1_555 E O HOH . A HOH 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 362 n n N1 C6 UDP sing 363 n n N1 C1' UDP sing 364 n n C2 N3 UDP sing 365 n n C2 O2 UDP doub 366 n n N3 C4 UDP sing 367 n n N3 HN3 UDP sing 368 n n C4 C5 UDP sing 369 n n C4 O4 UDP doub 370 n n C5 C6 UDP doub 371 n n C5 H5 UDP sing 372 n n C6 H6 UDP sing 373 n n C1' C2' UDP sing 374 n n C1' O4' UDP sing 375 n n C1' H1' UDP sing 376 n n C2' O2' UDP sing 377 n n C2' C3' UDP sing 378 n n C2' H2' UDP sing 379 n n O2' HO2' UDP sing 380 n n C3' C4' UDP sing 381 n n C3' O3' UDP sing 382 n n C3' H3' UDP sing 383 n n C4' O4' UDP sing 384 n n C4' C5' UDP sing 385 n n C4' H4' UDP sing 386 n n O3' HO3' UDP sing 387 n n C5' O5' UDP sing 388 n n C5' "H5'1" UDP sing 389 n n C5' "H5'2" UDP sing 390 n n O5' PA UDP sing 391 n n PA O1A UDP doub 392 n n PA O2A UDP sing 393 n n PA O3A UDP sing 394 n n O2A HOA2 UDP sing 395 n n O3A PB UDP sing 396 n n PB O1B UDP doub 397 n n PB O2B UDP sing 398 n n PB O3B UDP sing 399 n n O2B HOB2 UDP sing 400 n n O3B HOB3 UDP sing 401 n n # _atom_sites.entry_id 3CKN _atom_sites.fract_transf_matrix[1][1] 0.011513 _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] 0.011513 _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] 0.009593 _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 MN A 1 330 1 MN MN . C 3 SO4 A 1 331 1 SO4 SO4 . D 4 UDP A 1 332 1 UDP UDP . E 5 HOH A 1 333 1 HOH HOH . E 5 HOH A 2 334 2 HOH HOH . E 5 HOH A 3 335 3 HOH HOH . E 5 HOH A 4 336 4 HOH HOH . E 5 HOH A 5 337 5 HOH HOH . E 5 HOH A 6 338 6 HOH HOH . E 5 HOH A 7 339 7 HOH HOH . E 5 HOH A 8 340 8 HOH HOH . E 5 HOH A 9 341 9 HOH HOH . E 5 HOH A 10 342 10 HOH HOH . E 5 HOH A 11 343 11 HOH HOH . E 5 HOH A 12 344 12 HOH HOH . E 5 HOH A 13 345 13 HOH HOH . E 5 HOH A 14 346 14 HOH HOH . E 5 HOH A 15 347 15 HOH HOH . E 5 HOH A 16 348 16 HOH HOH . E 5 HOH A 17 349 17 HOH HOH . E 5 HOH A 18 350 18 HOH HOH . E 5 HOH A 19 351 19 HOH HOH . E 5 HOH A 20 352 20 HOH HOH . E 5 HOH A 21 353 21 HOH HOH . E 5 HOH A 22 354 22 HOH HOH . E 5 HOH A 23 355 23 HOH HOH . E 5 HOH A 24 356 24 HOH HOH . E 5 HOH A 25 357 25 HOH HOH . E 5 HOH A 26 358 26 HOH HOH . E 5 HOH A 27 359 27 HOH HOH . E 5 HOH A 28 360 28 HOH HOH . E 5 HOH A 29 361 29 HOH HOH . E 5 HOH A 30 362 30 HOH HOH . E 5 HOH A 31 363 31 HOH HOH . E 5 HOH A 32 364 32 HOH HOH . E 5 HOH A 33 365 33 HOH HOH . E 5 HOH A 34 366 34 HOH HOH . E 5 HOH A 35 367 35 HOH HOH . E 5 HOH A 36 368 36 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 UDP . . . D 4 6.763 27.135 15.184 1 53.18 ? N1 UDP 332 A 1 HETATM 2 C C2 UDP . . . D 4 6.626 28.419 15.7 1 52.22 ? C2 UDP 332 A 1 HETATM 3 N N3 UDP . . . D 4 6.545 29.497 14.838 1 51.67 ? N3 UDP 332 A 1 HETATM 4 C C4 UDP . . . D 4 6.602 29.309 13.471 1 52.54 ? C4 UDP 332 A 1 HETATM 5 C C5 UDP . . . D 4 6.74 28.017 12.95 1 51.73 ? C5 UDP 332 A 1 HETATM 6 C C6 UDP . . . D 4 6.951 26.957 13.833 1 51.91 ? C6 UDP 332 A 1 HETATM 7 O O2 UDP . . . D 4 6.574 28.608 16.917 1 51.32 ? O2 UDP 332 A 1 HETATM 8 O O4 UDP . . . D 4 6.52 30.285 12.721 1 52.51 ? O4 UDP 332 A 1 HETATM 9 C C1' UDP . . . D 4 6.862 25.999 16.127 1 53.51 ? C1' UDP 332 A 1 HETATM 10 C C2' UDP . . . D 4 5.935 24.821 15.813 1 54.63 ? C2' UDP 332 A 1 HETATM 11 O O2' UDP . . . D 4 4.69 24.924 16.455 1 54.39 ? O2' UDP 332 A 1 HETATM 12 C C3' UDP . . . D 4 6.732 23.62 16.29 1 54.96 ? C3' UDP 332 A 1 HETATM 13 C C4' UDP . . . D 4 8.176 24.066 16.125 1 55.48 ? C4' UDP 332 A 1 HETATM 14 O O4' UDP . . . D 4 8.177 25.485 16.07 1 54.8 ? O4' UDP 332 A 1 HETATM 15 O O3' UDP . . . D 4 6.511 23.349 17.655 1 55.48 ? O3' UDP 332 A 1 HETATM 16 C C5' UDP . . . D 4 8.787 23.523 14.847 1 57.09 ? C5' UDP 332 A 1 HETATM 17 O O5' UDP . . . D 4 7.936 23.827 13.764 1 60.17 ? O5' UDP 332 A 1 HETATM 18 P PA UDP . . . D 4 7.696 22.719 12.63 1 62.67 ? PA UDP 332 A 1 HETATM 19 O O1A UDP . . . D 4 7.078 21.518 13.239 1 63.46 ? O1A UDP 332 A 1 HETATM 20 O O2A UDP . . . D 4 6.886 23.228 11.498 1 61.47 ? O2A UDP 332 A 1 HETATM 21 O O3A UDP . . . D 4 9.231 22.522 12.166 1 65.9 ? O3A UDP 332 A 1 HETATM 22 P PB UDP . . . D 4 9.961 21.146 11.749 1 69.51 ? PB UDP 332 A 1 HETATM 23 O O1B UDP . . . D 4 9.624 20.867 10.339 1 69.56 ? O1B UDP 332 A 1 HETATM 24 O O2B UDP . . . D 4 9.576 20.01 12.621 1 70.13 ? O2B UDP 332 A 1 HETATM 25 O O3B UDP . . . D 4 11.428 21.35 11.872 1 69.78 ? O3B UDP 332 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #