data_2XA2 # _model_server_result.job_id ykADYz1utZcMtwxDbzO1Xw _model_server_result.datetime_utc '2024-11-22 11:54:32' _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 2xa2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1415}' # _entry.id 2XA2 # _exptl.entry_id 2XA2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 98.83 _cell.angle_gamma 90 _cell.entry_id 2XA2 _cell.length_a 80.844 _cell.length_b 63.139 _cell.length_c 91.517 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XA2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 UPG sing 358 n n N1 C6 UPG sing 359 n n N1 C1C UPG sing 360 n n C2 N3 UPG sing 361 n n C2 O2 UPG doub 362 n n N3 C4 UPG sing 363 n n N3 HN3 UPG sing 364 n n C4 C5 UPG sing 365 n n C4 O4 UPG doub 366 n n C5 C6 UPG doub 367 n n C5 H5 UPG sing 368 n n C6 H6 UPG sing 369 n n C1C C2C UPG sing 370 n n C1C O4C UPG sing 371 n n C1C H1C UPG sing 372 n n C2C O2C UPG sing 373 n n C2C C3C UPG sing 374 n n C2C H2C UPG sing 375 n n O2C HO2C UPG sing 376 n n C3C C4C UPG sing 377 n n C3C O3C UPG sing 378 n n C3C H3C UPG sing 379 n n C4C O4C UPG sing 380 n n C4C C5C UPG sing 381 n n C4C H4C UPG sing 382 n n O3C HO3C UPG sing 383 n n C5C O5C UPG sing 384 n n C5C H5C1 UPG sing 385 n n C5C H5C2 UPG sing 386 n n O5C PA UPG sing 387 n n PA O1A UPG doub 388 n n PA O2A UPG sing 389 n n PA O3A UPG sing 390 n n O2A HOA2 UPG sing 391 n n O3A PB UPG sing 392 n n PB O1B UPG doub 393 n n PB O2B UPG sing 394 n n PB O3B UPG sing 395 n n O2B HOB2 UPG sing 396 n n O3B C1' UPG sing 397 n n C1' C2' UPG sing 398 n n C1' O5' UPG sing 399 n n C1' H1' UPG sing 400 n n C2' C3' UPG sing 401 n n C2' O2' UPG sing 402 n n C2' H2' UPG sing 403 n n C3' C4' UPG sing 404 n n C3' O3' UPG sing 405 n n C3' H3' UPG sing 406 n n C4' C5' UPG sing 407 n n C4' O4' UPG sing 408 n n C4' H4' UPG sing 409 n n C5' C6' UPG sing 410 n n C5' O5' UPG sing 411 n n C5' H5' UPG sing 412 n n C6' O6' UPG sing 413 n n C6' "H6'1" UPG sing 414 n n C6' "H6'2" UPG sing 415 n n O2' HO2' UPG sing 416 n n O3' HO3' UPG sing 417 n n O4' HO4' UPG sing 418 n n O6' HO6' UPG sing 419 n n # _atom_sites.entry_id 2XA2 _atom_sites.fract_transf_matrix[1][1] 0.01237 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001922 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015838 _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] 0.011058 _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 UPG A 1 1415 1415 UPG UPG . D 2 UPG B 1 1415 1415 UPG UPG . E 3 HOH A 1 2001 2001 HOH HOH . E 3 HOH A 2 2002 2002 HOH HOH . E 3 HOH A 3 2003 2003 HOH HOH . E 3 HOH A 4 2004 2004 HOH HOH . E 3 HOH A 5 2005 2005 HOH HOH . E 3 HOH A 6 2006 2006 HOH HOH . E 3 HOH A 7 2007 2007 HOH HOH . E 3 HOH A 8 2008 2008 HOH HOH . E 3 HOH A 9 2009 2009 HOH HOH . E 3 HOH A 10 2010 2010 HOH HOH . E 3 HOH A 11 2011 2011 HOH HOH . E 3 HOH A 12 2012 2012 HOH HOH . E 3 HOH A 13 2013 2013 HOH HOH . E 3 HOH A 14 2014 2014 HOH HOH . E 3 HOH A 15 2015 2015 HOH HOH . E 3 HOH A 16 2016 2016 HOH HOH . E 3 HOH A 17 2017 2017 HOH HOH . E 3 HOH A 18 2018 2018 HOH HOH . E 3 HOH A 19 2019 2019 HOH HOH . E 3 HOH A 20 2020 2020 HOH HOH . E 3 HOH A 21 2021 2021 HOH HOH . E 3 HOH A 22 2022 2022 HOH HOH . E 3 HOH A 23 2023 2023 HOH HOH . E 3 HOH A 24 2024 2024 HOH HOH . E 3 HOH A 25 2025 2025 HOH HOH . E 3 HOH A 26 2026 2026 HOH HOH . E 3 HOH A 27 2027 2027 HOH HOH . E 3 HOH A 28 2028 2028 HOH HOH . E 3 HOH A 29 2029 2029 HOH HOH . E 3 HOH A 30 2030 2030 HOH HOH . E 3 HOH A 31 2031 2031 HOH HOH . E 3 HOH A 32 2032 2032 HOH HOH . E 3 HOH A 33 2033 2033 HOH HOH . E 3 HOH A 34 2034 2034 HOH HOH . E 3 HOH A 35 2035 2035 HOH HOH . E 3 HOH A 36 2036 2036 HOH HOH . E 3 HOH A 37 2037 2037 HOH HOH . E 3 HOH A 38 2038 2038 HOH HOH . E 3 HOH A 39 2039 2039 HOH HOH . E 3 HOH A 40 2040 2040 HOH HOH . E 3 HOH A 41 2041 2041 HOH HOH . E 3 HOH A 42 2042 2042 HOH HOH . E 3 HOH A 43 2043 2043 HOH HOH . E 3 HOH A 44 2044 2044 HOH HOH . E 3 HOH A 45 2045 2045 HOH HOH . E 3 HOH A 46 2046 2046 HOH HOH . E 3 HOH A 47 2047 2047 HOH HOH . E 3 HOH A 48 2048 2048 HOH HOH . E 3 HOH A 49 2049 2049 HOH HOH . E 3 HOH A 50 2050 2050 HOH HOH . E 3 HOH A 51 2051 2051 HOH HOH . E 3 HOH A 52 2052 2052 HOH HOH . E 3 HOH A 53 2053 2053 HOH HOH . E 3 HOH A 54 2054 2054 HOH HOH . E 3 HOH A 55 2055 2055 HOH HOH . E 3 HOH A 56 2056 2056 HOH HOH . E 3 HOH A 57 2057 2057 HOH HOH . E 3 HOH A 58 2058 2058 HOH HOH . E 3 HOH A 59 2059 2059 HOH HOH . E 3 HOH A 60 2060 2060 HOH HOH . E 3 HOH A 61 2061 2061 HOH HOH . E 3 HOH A 62 2062 2062 HOH HOH . E 3 HOH A 63 2063 2063 HOH HOH . E 3 HOH A 64 2064 2064 HOH HOH . E 3 HOH A 65 2065 2065 HOH HOH . E 3 HOH A 66 2066 2066 HOH HOH . E 3 HOH A 67 2067 2067 HOH HOH . E 3 HOH A 68 2068 2068 HOH HOH . F 3 HOH B 1 2001 2001 HOH HOH . F 3 HOH B 2 2002 2002 HOH HOH . F 3 HOH B 3 2003 2003 HOH HOH . F 3 HOH B 4 2004 2004 HOH HOH . F 3 HOH B 5 2005 2005 HOH HOH . F 3 HOH B 6 2006 2006 HOH HOH . F 3 HOH B 7 2007 2007 HOH HOH . F 3 HOH B 8 2008 2008 HOH HOH . F 3 HOH B 9 2009 2009 HOH HOH . F 3 HOH B 10 2010 2010 HOH HOH . F 3 HOH B 11 2011 2011 HOH HOH . F 3 HOH B 12 2012 2012 HOH HOH . F 3 HOH B 13 2013 2013 HOH HOH . F 3 HOH B 14 2014 2014 HOH HOH . F 3 HOH B 15 2015 2015 HOH HOH . F 3 HOH B 16 2016 2016 HOH HOH . F 3 HOH B 17 2017 2017 HOH HOH . F 3 HOH B 18 2018 2018 HOH HOH . F 3 HOH B 19 2019 2019 HOH HOH . F 3 HOH B 20 2020 2020 HOH HOH . F 3 HOH B 21 2021 2021 HOH HOH . F 3 HOH B 22 2022 2022 HOH HOH . F 3 HOH B 23 2023 2023 HOH HOH . F 3 HOH B 24 2024 2024 HOH HOH . F 3 HOH B 25 2025 2025 HOH HOH . F 3 HOH B 26 2026 2026 HOH HOH . F 3 HOH B 27 2027 2027 HOH HOH . F 3 HOH B 28 2028 2028 HOH HOH . F 3 HOH B 29 2029 2029 HOH HOH . F 3 HOH B 30 2030 2030 HOH HOH . F 3 HOH B 31 2031 2031 HOH HOH . F 3 HOH B 32 2032 2032 HOH HOH . F 3 HOH B 33 2033 2033 HOH HOH . F 3 HOH B 34 2034 2034 HOH HOH . F 3 HOH B 35 2035 2035 HOH HOH . F 3 HOH B 36 2036 2036 HOH HOH . F 3 HOH B 37 2037 2037 HOH HOH . F 3 HOH B 38 2038 2038 HOH HOH . F 3 HOH B 39 2039 2039 HOH HOH . F 3 HOH B 40 2040 2040 HOH HOH . F 3 HOH B 41 2041 2041 HOH HOH . F 3 HOH B 42 2042 2042 HOH HOH . F 3 HOH B 43 2043 2043 HOH HOH . F 3 HOH B 44 2044 2044 HOH HOH . F 3 HOH B 45 2045 2045 HOH HOH . F 3 HOH B 46 2046 2046 HOH HOH . F 3 HOH B 47 2047 2047 HOH HOH . F 3 HOH B 48 2048 2048 HOH HOH . F 3 HOH B 49 2049 2049 HOH HOH . F 3 HOH B 50 2050 2050 HOH HOH . F 3 HOH B 51 2051 2051 HOH HOH . F 3 HOH B 52 2052 2052 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 UPG . . . D 2 57.523 42.742 105.444 1 90.47 ? N1 UPG 1415 B 1 HETATM 2 C C2 UPG . . . D 2 56.224 42.55 104.96 1 89.14 ? C2 UPG 1415 B 1 HETATM 3 N N3 UPG . . . D 2 55.795 43.271 103.88 1 88.2 ? N3 UPG 1415 B 1 HETATM 4 C C4 UPG . . . D 2 56.616 44.18 103.262 1 87.27 ? C4 UPG 1415 B 1 HETATM 5 C C5 UPG . . . D 2 57.944 44.388 103.741 1 87.8 ? C5 UPG 1415 B 1 HETATM 6 C C6 UPG . . . D 2 58.366 43.669 104.816 1 88.9 ? C6 UPG 1415 B 1 HETATM 7 O O2 UPG . . . D 2 55.449 41.748 105.482 1 87.45 ? O2 UPG 1415 B 1 HETATM 8 O O4 UPG . . . D 2 56.217 44.811 102.309 1 86.41 ? O4 UPG 1415 B 1 HETATM 9 C C1C UPG . . . D 2 58.046 41.987 106.628 1 92.83 ? C1C UPG 1415 B 1 HETATM 10 C C2C UPG . . . D 2 57.941 40.441 106.475 1 93.88 ? C2C UPG 1415 B 1 HETATM 11 O O2C UPG . . . D 2 57.14 39.897 107.519 1 94.17 ? O2C UPG 1415 B 1 HETATM 12 C C3C UPG . . . D 2 59.389 39.906 106.504 1 95.27 ? C3C UPG 1415 B 1 HETATM 13 C C4C UPG . . . D 2 60.277 41.116 106.754 1 96.53 ? C4C UPG 1415 B 1 HETATM 14 O O4C UPG . . . D 2 59.456 42.293 106.885 1 94.93 ? O4C UPG 1415 B 1 HETATM 15 O O3C UPG . . . D 2 59.56 38.967 107.575 1 95.22 ? O3C UPG 1415 B 1 HETATM 16 C C5C UPG . . . D 2 61.26 41.267 105.585 1 100.3 ? C5C UPG 1415 B 1 HETATM 17 O O5C UPG . . . D 2 62.118 42.405 105.824 1 105.37 ? O5C UPG 1415 B 1 HETATM 18 P PA UPG . . . D 2 63.231 42.659 104.626 1 108.97 ? PA UPG 1415 B 1 HETATM 19 O O1A UPG . . . D 2 63.768 41.334 104.996 1 108.05 ? O1A UPG 1415 B 1 HETATM 20 O O2A UPG . . . D 2 61.958 42.871 103.651 1 108.42 ? O2A UPG 1415 B 1 HETATM 21 O O3A UPG . . . D 2 63.629 43.877 105.624 1 110.83 ? O3A UPG 1415 B 1 HETATM 22 P PB UPG . . . D 2 64.866 44.725 105.031 1 113.54 ? PB UPG 1415 B 1 HETATM 23 O O1B UPG . . . D 2 64.477 45.371 103.742 1 112.22 ? O1B UPG 1415 B 1 HETATM 24 O O2B UPG . . . D 2 66.134 43.75 104.805 1 113.03 ? O2B UPG 1415 B 1 HETATM 25 O O3B UPG . . . D 2 65.183 45.86 106.144 1 113.53 ? O3B UPG 1415 B 1 HETATM 26 C C1' UPG . . . D 2 66.296 46.695 105.754 1 113.98 ? C1' UPG 1415 B 1 HETATM 27 C C2' UPG . . . D 2 67.547 46.327 106.616 1 113.6 ? C2' UPG 1415 B 1 HETATM 28 C C3' UPG . . . D 2 67.177 46.512 108.101 1 113.37 ? C3' UPG 1415 B 1 HETATM 29 C C4' UPG . . . D 2 66.784 47.983 108.312 1 113.6 ? C4' UPG 1415 B 1 HETATM 30 C C5' UPG . . . D 2 65.573 48.316 107.395 1 113.91 ? C5' UPG 1415 B 1 HETATM 31 C C6' UPG . . . D 2 65.187 49.791 107.597 1 113.37 ? C6' UPG 1415 B 1 HETATM 32 O O2' UPG . . . D 2 67.917 44.959 106.402 1 113.51 ? O2' UPG 1415 B 1 HETATM 33 O O3' UPG . . . D 2 68.303 46.187 108.926 1 113.21 ? O3' UPG 1415 B 1 HETATM 34 O O4' UPG . . . D 2 66.425 48.185 109.686 1 112.58 ? O4' UPG 1415 B 1 HETATM 35 O O5' UPG . . . D 2 65.933 48.097 105.983 1 114.08 ? O5' UPG 1415 B 1 HETATM 36 O O6' UPG . . . D 2 64.075 50.12 106.762 1 113.12 ? O6' UPG 1415 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 36 #