data_9KT0 # _model_server_result.job_id 2QVnHpYxefPMUuNXsQDouA _model_server_result.datetime_utc '2025-06-27 04:40:21' _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 9kt0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 9KT0 # _exptl.entry_id 9KT0 _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 90 _cell.angle_gamma 120 _cell.entry_id 9KT0 _cell.length_a 75.23 _cell.length_b 75.23 _cell.length_c 161.624 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KT0 _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 ? _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 # _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 412 n n N1 C6 UDP sing 413 n n N1 C1' UDP sing 414 n n C2 N3 UDP sing 415 n n C2 O2 UDP doub 416 n n N3 C4 UDP sing 417 n n N3 HN3 UDP sing 418 n n C4 C5 UDP sing 419 n n C4 O4 UDP doub 420 n n C5 C6 UDP doub 421 n n C5 H5 UDP sing 422 n n C6 H6 UDP sing 423 n n C1' C2' UDP sing 424 n n C1' O4' UDP sing 425 n n C1' H1' UDP sing 426 n n C2' O2' UDP sing 427 n n C2' C3' UDP sing 428 n n C2' H2' UDP sing 429 n n O2' HO2' UDP sing 430 n n C3' C4' UDP sing 431 n n C3' O3' UDP sing 432 n n C3' H3' UDP sing 433 n n C4' O4' UDP sing 434 n n C4' C5' UDP sing 435 n n C4' H4' UDP sing 436 n n O3' HO3' UDP sing 437 n n C5' O5' UDP sing 438 n n C5' "H5'1" UDP sing 439 n n C5' "H5'2" UDP sing 440 n n O5' PA UDP sing 441 n n PA O1A UDP doub 442 n n PA O2A UDP sing 443 n n PA O3A UDP sing 444 n n O2A HOA2 UDP sing 445 n n O3A PB UDP sing 446 n n PB O1B UDP doub 447 n n PB O2B UDP sing 448 n n PB O3B UDP sing 449 n n O2B HOB2 UDP sing 450 n n O3B HOB3 UDP sing 451 n n # _atom_sites.entry_id 9KT0 _atom_sites.fract_transf_matrix[1][1] 0.013293 _atom_sites.fract_transf_matrix[1][2] 0.007674 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015349 _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] 0.006187 _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 A1EGY A 1 501 501 A1EGY G7G . C 3 UDP A 1 502 502 UDP UDP . D 4 HOH A 1 601 10 HOH HOH . D 4 HOH A 2 602 8 HOH HOH . D 4 HOH A 3 603 3 HOH HOH . D 4 HOH A 4 604 11 HOH HOH . D 4 HOH A 5 605 4 HOH HOH . D 4 HOH A 6 606 7 HOH HOH . D 4 HOH A 7 607 15 HOH HOH . D 4 HOH A 8 608 9 HOH HOH . D 4 HOH A 9 609 6 HOH HOH . D 4 HOH A 10 610 5 HOH HOH . D 4 HOH A 11 611 2 HOH HOH . D 4 HOH A 12 612 1 HOH HOH . D 4 HOH A 13 613 12 HOH HOH . D 4 HOH A 14 614 16 HOH HOH . D 4 HOH A 15 615 14 HOH HOH . D 4 HOH A 16 616 13 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 15.458 -18.581 -14.89 1 60.63 ? N1 UDP 502 A 1 HETATM 2 C C2 UDP . . . C 3 14.184 -19.088 -15.036 1 62.99 ? C2 UDP 502 A 1 HETATM 3 N N3 UDP . . . C 3 13.471 -18.539 -16.07 1 63.5 ? N3 UDP 502 A 1 HETATM 4 C C4 UDP . . . C 3 13.902 -17.566 -16.954 1 68.03 ? C4 UDP 502 A 1 HETATM 5 C C5 UDP . . . C 3 15.233 -17.085 -16.724 1 65.33 ? C5 UDP 502 A 1 HETATM 6 C C6 UDP . . . C 3 15.943 -17.592 -15.708 1 59.66 ? C6 UDP 502 A 1 HETATM 7 O O2 UDP . . . C 3 13.73 -19.961 -14.303 1 62.76 ? O2 UDP 502 A 1 HETATM 8 O O4 UDP . . . C 3 13.146 -17.175 -17.841 1 69.73 ? O4 UDP 502 A 1 HETATM 9 C C1' UDP . . . C 3 16.252 -19.088 -13.766 1 55.93 ? C1' UDP 502 A 1 HETATM 10 C C2' UDP . . . C 3 17.353 -20.056 -14.188 1 53.99 ? C2' UDP 502 A 1 HETATM 11 O O2' UDP . . . C 3 16.86 -21.379 -14.126 1 48.05 ? O2' UDP 502 A 1 HETATM 12 C C3' UDP . . . C 3 18.358 -19.852 -13.057 1 55.9 ? C3' UDP 502 A 1 HETATM 13 C C4' UDP . . . C 3 18.214 -18.359 -12.715 1 54.21 ? C4' UDP 502 A 1 HETATM 14 O O4' UDP . . . C 3 16.887 -17.977 -13.172 1 51.41 ? O4' UDP 502 A 1 HETATM 15 O O3' UDP . . . C 3 17.829 -20.686 -12.038 1 51.92 ? O3' UDP 502 A 1 HETATM 16 C C5' UDP . . . C 3 19.244 -17.44 -13.328 1 55.44 ? C5' UDP 502 A 1 HETATM 17 O O5' UDP . . . C 3 20.538 -17.672 -12.7 1 58.79 ? O5' UDP 502 A 1 HETATM 18 P PA UDP . . . C 3 21.853 -17.56 -13.609 1 61.12 ? PA UDP 502 A 1 HETATM 19 O O1A UDP . . . C 3 23.072 -17.463 -12.75 1 58.05 -1 O1A UDP 502 A 1 HETATM 20 O O2A UDP . . . C 3 21.812 -18.625 -14.657 1 57.36 ? O2A UDP 502 A 1 HETATM 21 O O3A UDP . . . C 3 21.593 -16.142 -14.307 1 56.88 ? O3A UDP 502 A 1 HETATM 22 P PB UDP . . . C 3 21.498 -14.607 -13.854 1 63.59 ? PB UDP 502 A 1 HETATM 23 O O1B UDP . . . C 3 20.051 -14.213 -14.027 1 57.86 ? O1B UDP 502 A 1 HETATM 24 O O2B UDP . . . C 3 21.973 -14.548 -12.435 1 63.13 -1 O2B UDP 502 A 1 HETATM 25 O O3B UDP . . . C 3 22.407 -13.853 -14.81 1 62.47 -1 O3B UDP 502 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #