data_4DE7 # _model_server_result.job_id oliNVIxjpfOEDamquLXJKQ _model_server_result.datetime_utc '2025-01-09 15:34:51' _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 4de7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4DE7 # _exptl.entry_id 4DE7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _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 4DE7 _cell.length_a 98.85 _cell.length_b 98.85 _cell.length_c 127.64 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DE7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _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' 6_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 371 n n N1 C6 UDP sing 372 n n N1 C1' UDP sing 373 n n C2 N3 UDP sing 374 n n C2 O2 UDP doub 375 n n N3 C4 UDP sing 376 n n N3 HN3 UDP sing 377 n n C4 C5 UDP sing 378 n n C4 O4 UDP doub 379 n n C5 C6 UDP doub 380 n n C5 H5 UDP sing 381 n n C6 H6 UDP sing 382 n n C1' C2' UDP sing 383 n n C1' O4' UDP sing 384 n n C1' H1' UDP sing 385 n n C2' O2' UDP sing 386 n n C2' C3' UDP sing 387 n n C2' H2' UDP sing 388 n n O2' HO2' UDP sing 389 n n C3' C4' UDP sing 390 n n C3' O3' UDP sing 391 n n C3' H3' UDP sing 392 n n C4' O4' UDP sing 393 n n C4' C5' UDP sing 394 n n C4' H4' UDP sing 395 n n O3' HO3' UDP sing 396 n n C5' O5' UDP sing 397 n n C5' "H5'1" UDP sing 398 n n C5' "H5'2" UDP sing 399 n n O5' PA UDP sing 400 n n PA O1A UDP doub 401 n n PA O2A UDP sing 402 n n PA O3A UDP sing 403 n n O2A HOA2 UDP sing 404 n n O3A PB UDP sing 405 n n PB O1B UDP doub 406 n n PB O2B UDP sing 407 n n PB O3B UDP sing 408 n n O2B HOB2 UDP sing 409 n n O3B HOB3 UDP sing 410 n n # _atom_sites.entry_id 4DE7 _atom_sites.fract_transf_matrix[1][1] 0.010116 _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] 0.010116 _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] 0.007835 _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 UDP A 1 401 1 UDP UDP . C 3 GOL A 1 402 2 GOL GOL . D 3 GOL A 1 403 5 GOL GOL . E 4 HOH A 1 501 1 HOH HOH . E 4 HOH A 2 502 2 HOH HOH . E 4 HOH A 3 503 3 HOH HOH . E 4 HOH A 4 504 4 HOH HOH . E 4 HOH A 5 505 5 HOH HOH . E 4 HOH A 6 506 6 HOH HOH . E 4 HOH A 7 507 7 HOH HOH . E 4 HOH A 8 508 8 HOH HOH . E 4 HOH A 9 509 9 HOH HOH . E 4 HOH A 10 510 11 HOH HOH . E 4 HOH A 11 511 12 HOH HOH . E 4 HOH A 12 512 13 HOH HOH . E 4 HOH A 13 513 14 HOH HOH . E 4 HOH A 14 514 16 HOH HOH . E 4 HOH A 15 515 17 HOH HOH . E 4 HOH A 16 516 18 HOH HOH . E 4 HOH A 17 517 19 HOH HOH . E 4 HOH A 18 518 22 HOH HOH . E 4 HOH A 19 519 25 HOH HOH . E 4 HOH A 20 520 26 HOH HOH . E 4 HOH A 21 521 27 HOH HOH . E 4 HOH A 22 522 28 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 . . . B 2 14.964 -13.429 23.553 0.59 78.46 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 15.62 -14.467 24.19 0.59 79.02 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 14.895 -15.477 24.791 0.59 78.86 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 13.517 -15.447 24.76 0.59 79.72 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 12.868 -14.396 24.122 0.59 79.4 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 13.612 -13.301 23.697 0.59 78.92 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 16.849 -14.497 24.221 0.59 79.38 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 12.871 -16.347 25.294 0.59 80.84 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 15.741 -12.344 22.922 0.59 78.39 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 15.795 -12.481 21.408 0.59 77.12 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 17.133 -12.433 20.981 0.59 79.7 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 15.071 -11.272 20.859 0.59 78.38 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 14.82 -10.369 22.054 0.59 80.82 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 15.129 -11.104 23.221 0.59 82.29 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 15.922 -10.599 19.961 0.59 79.05 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 13.378 -9.877 22.107 0.59 78.55 ? C5' UDP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 16 #