data_8J2U # _model_server_result.job_id MAtQOmSlnusqf1nd_QWzcw _model_server_result.datetime_utc '2025-07-28 14:22:34' _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 8j2u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8J2U # _exptl.entry_id 8J2U _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.25 _cell.angle_gamma 90 _cell.entry_id 8J2U _cell.length_a 100.492 _cell.length_b 112.559 _cell.length_c 103.632 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J2U _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 1 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 356 n n N1 C6 UDP sing 357 n n N1 C1' UDP sing 358 n n C2 N3 UDP sing 359 n n C2 O2 UDP doub 360 n n N3 C4 UDP sing 361 n n N3 HN3 UDP sing 362 n n C4 C5 UDP sing 363 n n C4 O4 UDP doub 364 n n C5 C6 UDP doub 365 n n C5 H5 UDP sing 366 n n C6 H6 UDP sing 367 n n C1' C2' UDP sing 368 n n C1' O4' UDP sing 369 n n C1' H1' UDP sing 370 n n C2' O2' UDP sing 371 n n C2' C3' UDP sing 372 n n C2' H2' UDP sing 373 n n O2' HO2' UDP sing 374 n n C3' C4' UDP sing 375 n n C3' O3' UDP sing 376 n n C3' H3' UDP sing 377 n n C4' O4' UDP sing 378 n n C4' C5' UDP sing 379 n n C4' H4' UDP sing 380 n n O3' HO3' UDP sing 381 n n C5' O5' UDP sing 382 n n C5' "H5'1" UDP sing 383 n n C5' "H5'2" UDP sing 384 n n O5' PA UDP sing 385 n n PA O1A UDP doub 386 n n PA O2A UDP sing 387 n n PA O3A UDP sing 388 n n O2A HOA2 UDP sing 389 n n O3A PB UDP sing 390 n n PB O1B UDP doub 391 n n PB O2B UDP sing 392 n n PB O3B UDP sing 393 n n O2B HOB2 UDP sing 394 n n O3B HOB3 UDP sing 395 n n # _atom_sites.entry_id 8J2U _atom_sites.fract_transf_matrix[1][1] 0.009951 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002161 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008884 _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] 0.009875 _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 C 2 UDP A 1 501 501 UDP UDP . D 2 UDP B 1 501 501 UDP UDP . # 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 2 -27.426 -36.388 15.727 1 105.98 ? N1 UDP 501 B 1 HETATM 2 C C2 UDP . . . D 2 -27.591 -37.264 14.676 1 101.37 ? C2 UDP 501 B 1 HETATM 3 N N3 UDP . . . D 2 -28.69 -37.021 13.899 1 101.47 ? N3 UDP 501 B 1 HETATM 4 C C4 UDP . . . D 2 -29.626 -36.023 14.062 1 101.34 ? C4 UDP 501 B 1 HETATM 5 C C5 UDP . . . D 2 -29.385 -35.155 15.176 1 101.34 ? C5 UDP 501 B 1 HETATM 6 C C6 UDP . . . D 2 -28.314 -35.365 15.954 1 103.95 ? C6 UDP 501 B 1 HETATM 7 O O2 UDP . . . D 2 -26.821 -38.186 14.452 1 97.43 ? O2 UDP 501 B 1 HETATM 8 O O4 UDP . . . D 2 -30.565 -35.947 13.271 1 98 ? O4 UDP 501 B 1 HETATM 9 C C1' UDP . . . D 2 -26.262 -36.604 16.596 1 112.47 ? C1' UDP 501 B 1 HETATM 10 C C2' UDP . . . D 2 -25.073 -35.736 16.2 1 113.41 ? C2' UDP 501 B 1 HETATM 11 O O2' UDP . . . D 2 -24.252 -36.532 15.377 1 112.3 ? O2' UDP 501 B 1 HETATM 12 C C3' UDP . . . D 2 -24.437 -35.462 17.557 1 114.67 ? C3' UDP 501 B 1 HETATM 13 C C4' UDP . . . D 2 -25.66 -35.332 18.47 1 122.46 ? C4' UDP 501 B 1 HETATM 14 O O4' UDP . . . D 2 -26.628 -36.252 17.911 1 119.38 ? O4' UDP 501 B 1 HETATM 15 O O3' UDP . . . D 2 -23.636 -36.568 17.943 1 107.34 ? O3' UDP 501 B 1 HETATM 16 C C5' UDP . . . D 2 -26.275 -33.96 18.577 1 132.85 ? C5' UDP 501 B 1 HETATM 17 O O5' UDP . . . D 2 -26.604 -33.691 19.965 1 149.67 ? O5' UDP 501 B 1 HETATM 18 P PA UDP . . . D 2 -26.28 -32.247 20.581 1 171.17 ? PA UDP 501 B 1 HETATM 19 O O1A UDP . . . D 2 -27.43 -31.334 20.321 1 172.43 ? O1A UDP 501 B 1 HETATM 20 O O2A UDP . . . D 2 -25.811 -32.392 21.988 1 171.59 ? O2A UDP 501 B 1 HETATM 21 O O3A UDP . . . D 2 -25.035 -31.804 19.677 1 181.01 ? O3A UDP 501 B 1 HETATM 22 P PB UDP . . . D 2 -23.516 -32.329 19.586 1 189.42 ? PB UDP 501 B 1 HETATM 23 O O1B UDP . . . D 2 -23.524 -33.702 20.179 1 188.33 ? O1B UDP 501 B 1 HETATM 24 O O2B UDP . . . D 2 -22.676 -31.381 20.389 1 189.24 ? O2B UDP 501 B 1 HETATM 25 O O3B UDP . . . D 2 -23.185 -32.317 18.118 1 188.69 ? O3B UDP 501 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #