data_2P73 # _model_server_result.job_id cB-sNJ_utu4e-DUol3ajhA _model_server_result.datetime_utc '2025-02-27 17:15:25' _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 2p73 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":411}' # _entry.id 2P73 # _exptl.entry_id 2P73 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 114.03 _cell.angle_gamma 90 _cell.entry_id 2P73 _cell.length_a 43.375 _cell.length_b 63.535 _cell.length_c 44.76 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P73 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 A OD2 ASP 80 A ASP 78 1_555 B MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc2 A OD2 ASP 82 A ASP 80 1_555 B MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc3 A OD1 ASP 82 A ASP 80 1_555 B MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc4 A NE2 HIS 195 A HIS 193 1_555 B MN MN . A MN 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc5 B MN MN . A MN 214 1_555 C O1A UDP . A UDP 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc6 B MN MN . A MN 214 1_555 C O1B UDP . A UDP 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? # _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 2P73 _atom_sites.fract_transf_matrix[1][1] 0.023055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.010279 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015739 _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] 0.024461 _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 1 214 214 MN MN . C 3 UDP A 1 411 411 UDP UDP . D 4 HOH A 1 412 412 HOH HOH . D 4 HOH A 2 413 413 HOH HOH . D 4 HOH A 3 414 414 HOH HOH . D 4 HOH A 4 415 415 HOH HOH . D 4 HOH A 5 416 416 HOH HOH . D 4 HOH A 6 417 417 HOH HOH . D 4 HOH A 7 418 418 HOH HOH . D 4 HOH A 8 419 419 HOH HOH . D 4 HOH A 9 420 420 HOH HOH . D 4 HOH A 10 421 421 HOH HOH . D 4 HOH A 11 422 422 HOH HOH . D 4 HOH A 12 423 423 HOH HOH . D 4 HOH A 13 424 424 HOH HOH . D 4 HOH A 14 425 425 HOH HOH . D 4 HOH A 15 426 426 HOH HOH . D 4 HOH A 16 427 427 HOH HOH . D 4 HOH A 17 428 428 HOH HOH . D 4 HOH A 18 429 429 HOH HOH . D 4 HOH A 19 430 430 HOH HOH . D 4 HOH A 20 431 431 HOH HOH . D 4 HOH A 21 432 432 HOH HOH . D 4 HOH A 22 433 433 HOH HOH . D 4 HOH A 23 434 434 HOH HOH . D 4 HOH A 24 435 435 HOH HOH . D 4 HOH A 25 436 436 HOH HOH . D 4 HOH A 26 437 437 HOH HOH . D 4 HOH A 27 438 438 HOH HOH . D 4 HOH A 28 439 439 HOH HOH . D 4 HOH A 29 440 440 HOH HOH . D 4 HOH A 30 441 441 HOH HOH . D 4 HOH A 31 442 442 HOH HOH . D 4 HOH A 32 443 443 HOH HOH . D 4 HOH A 33 444 444 HOH HOH . D 4 HOH A 34 445 445 HOH HOH . D 4 HOH A 35 446 446 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 . . . C 3 24.963 9.374 -1.897 1 46.26 ? N1 UDP 411 A 1 HETATM 2 C C2 UDP . . . C 3 23.582 9.529 -1.965 1 45.33 ? C2 UDP 411 A 1 HETATM 3 N N3 UDP . . . C 3 22.805 8.558 -2.526 1 46.84 ? N3 UDP 411 A 1 HETATM 4 C C4 UDP . . . C 3 23.379 7.405 -3.005 1 47.16 ? C4 UDP 411 A 1 HETATM 5 C C5 UDP . . . C 3 24.772 7.243 -2.93 1 47.5 ? C5 UDP 411 A 1 HETATM 6 C C6 UDP . . . C 3 25.551 8.364 -2.622 1 45.3 ? C6 UDP 411 A 1 HETATM 7 O O2 UDP . . . C 3 23.012 10.531 -1.571 1 47.26 ? O2 UDP 411 A 1 HETATM 8 O O4 UDP . . . C 3 22.634 6.552 -3.492 1 47.65 ? O4 UDP 411 A 1 HETATM 9 C C1' UDP . . . C 3 25.77 10.448 -1.285 1 45.29 ? C1' UDP 411 A 1 HETATM 10 C C2' UDP . . . C 3 25.544 10.365 0.214 1 44.22 ? C2' UDP 411 A 1 HETATM 11 O O2' UDP . . . C 3 25.385 11.677 0.706 1 42.39 ? O2' UDP 411 A 1 HETATM 12 C C3' UDP . . . C 3 26.793 9.683 0.742 1 42.54 ? C3' UDP 411 A 1 HETATM 13 C C4' UDP . . . C 3 27.855 9.97 -0.321 1 41.94 ? C4' UDP 411 A 1 HETATM 14 O O4' UDP . . . C 3 27.163 10.297 -1.517 1 43.67 ? O4' UDP 411 A 1 HETATM 15 O O3' UDP . . . C 3 27.123 10.192 2.015 1 41.44 ? O3' UDP 411 A 1 HETATM 16 C C5' UDP . . . C 3 28.787 8.805 -0.606 1 39.95 ? C5' UDP 411 A 1 HETATM 17 O O5' UDP . . . C 3 28.017 7.663 -0.906 1 37.56 ? O5' UDP 411 A 1 HETATM 18 P PA UDP . . . C 3 28.503 6.224 -0.41 1 37.01 ? PA UDP 411 A 1 HETATM 19 O O1A UDP . . . C 3 28.763 6.243 1.051 1 37.92 ? O1A UDP 411 A 1 HETATM 20 O O2A UDP . . . C 3 27.589 5.137 -0.775 1 37.8 ? O2A UDP 411 A 1 HETATM 21 O O3A UDP . . . C 3 29.954 6.028 -1.111 1 37.51 ? O3A UDP 411 A 1 HETATM 22 P PB UDP . . . C 3 31.04 4.937 -0.639 1 38.59 ? PB UDP 411 A 1 HETATM 23 O O1B UDP . . . C 3 31.63 5.215 0.701 1 39.67 ? O1B UDP 411 A 1 HETATM 24 O O2B UDP . . . C 3 30.398 3.605 -0.53 1 39.01 ? O2B UDP 411 A 1 HETATM 25 O O3B UDP . . . C 3 32.17 4.928 -1.62 1 39.47 ? O3B UDP 411 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 1134 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #