data_2X0E # _model_server_result.job_id wocpgSrT7j4YclnHUXpOUw _model_server_result.datetime_utc '2024-11-05 00:34:37' _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 2x0e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":414}' # _entry.id 2X0E # _exptl.entry_id 2X0E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 103.05 _cell.angle_gamma 90 _cell.entry_id 2X0E _cell.length_a 75.82 _cell.length_b 75.56 _cell.length_c 77.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2X0E _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 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,F,G,H,I _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 F N N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 347 n n PA O2A TYD sing 348 n n PA O3A TYD sing 349 n n PA O5' TYD sing 350 n n O2A HOA2 TYD sing 351 n n O3A PB TYD sing 352 n n PB O1B TYD doub 353 n n PB O2B TYD sing 354 n n PB O3B TYD sing 355 n n O2B HOB2 TYD sing 356 n n O3B HOB3 TYD sing 357 n n O5' C5' TYD sing 358 n n C5' C4' TYD sing 359 n n C5' "H5'1" TYD sing 360 n n C5' "H5'2" TYD sing 361 n n C4' O4' TYD sing 362 n n C4' C3' TYD sing 363 n n C4' H4' TYD sing 364 n n O4' C1' TYD sing 365 n n C3' O3' TYD sing 366 n n C3' C2' TYD sing 367 n n C3' H3' TYD sing 368 n n O3' HO3' TYD sing 369 n n C2' C1' TYD sing 370 n n C2' "H2'1" TYD sing 371 n n C2' "H2'2" TYD sing 372 n n C1' N1 TYD sing 373 n n C1' H1' TYD sing 374 n n N1 C2 TYD sing 375 n y N1 C6 TYD sing 376 n y C2 O2 TYD doub 377 n n C2 N3 TYD sing 378 n y N3 C4 TYD sing 379 n y N3 HN3 TYD sing 380 n n C4 O4 TYD doub 381 n n C4 C5 TYD sing 382 n y C5 C5M TYD sing 383 n n C5 C6 TYD doub 384 n y C5M H51 TYD sing 385 n n C5M H52 TYD sing 386 n n C5M H53 TYD sing 387 n n C6 H6 TYD sing 388 n n # _atom_sites.entry_id 2X0E _atom_sites.fract_transf_matrix[1][1] 0.013189 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003057 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013235 _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] 0.01321 _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 TYD A 1 414 414 TYD TYD . D 3 GOL A 1 415 415 GOL GOL . E 3 GOL A 1 416 416 GOL GOL . F 2 TYD B 1 414 414 TYD TYD . G 3 GOL B 1 415 415 GOL GOL . H 4 HOH A 1 2001 2001 HOH HOH . H 4 HOH A 2 2002 2002 HOH HOH . H 4 HOH A 3 2003 2003 HOH HOH . H 4 HOH A 4 2004 2004 HOH HOH . H 4 HOH A 5 2005 2005 HOH HOH . H 4 HOH A 6 2006 2006 HOH HOH . H 4 HOH A 7 2007 2007 HOH HOH . H 4 HOH A 8 2008 2008 HOH HOH . H 4 HOH A 9 2009 2009 HOH HOH . H 4 HOH A 10 2011 2011 HOH HOH . H 4 HOH A 11 2012 2012 HOH HOH . H 4 HOH A 12 2013 2013 HOH HOH . H 4 HOH A 13 2014 2014 HOH HOH . H 4 HOH A 14 2015 2015 HOH HOH . H 4 HOH A 15 2016 2016 HOH HOH . H 4 HOH A 16 2017 2017 HOH HOH . H 4 HOH A 17 2018 2018 HOH HOH . H 4 HOH A 18 2019 2019 HOH HOH . H 4 HOH A 19 2020 2020 HOH HOH . H 4 HOH A 20 2021 2021 HOH HOH . H 4 HOH A 21 2022 2022 HOH HOH . H 4 HOH A 22 2023 2023 HOH HOH . H 4 HOH A 23 2024 2024 HOH HOH . H 4 HOH A 24 2025 2025 HOH HOH . H 4 HOH A 25 2026 2026 HOH HOH . H 4 HOH A 26 2027 2027 HOH HOH . H 4 HOH A 27 2028 2028 HOH HOH . H 4 HOH A 28 2029 2029 HOH HOH . H 4 HOH A 29 2030 2030 HOH HOH . H 4 HOH A 30 2031 2031 HOH HOH . H 4 HOH A 31 2032 2032 HOH HOH . H 4 HOH A 32 2033 2033 HOH HOH . H 4 HOH A 33 2034 2034 HOH HOH . H 4 HOH A 34 2035 2035 HOH HOH . H 4 HOH A 35 2036 2036 HOH HOH . H 4 HOH A 36 2037 2037 HOH HOH . H 4 HOH A 37 2038 2038 HOH HOH . H 4 HOH A 38 2040 2040 HOH HOH . H 4 HOH A 39 2041 2041 HOH HOH . H 4 HOH A 40 2042 2042 HOH HOH . H 4 HOH A 41 2043 2043 HOH HOH . H 4 HOH A 42 2044 2044 HOH HOH . H 4 HOH A 43 2045 2045 HOH HOH . H 4 HOH A 44 2046 2046 HOH HOH . H 4 HOH A 45 2047 2047 HOH HOH . H 4 HOH A 46 2048 2048 HOH HOH . H 4 HOH A 47 2049 2049 HOH HOH . H 4 HOH A 48 2050 2050 HOH HOH . H 4 HOH A 49 2051 2051 HOH HOH . H 4 HOH A 50 2052 2052 HOH HOH . H 4 HOH A 51 2053 2053 HOH HOH . H 4 HOH A 52 2054 2054 HOH HOH . H 4 HOH A 53 2055 2055 HOH HOH . H 4 HOH A 54 2056 2056 HOH HOH . H 4 HOH A 55 2057 2057 HOH HOH . H 4 HOH A 56 2058 2058 HOH HOH . H 4 HOH A 57 2059 2059 HOH HOH . H 4 HOH A 58 2060 2060 HOH HOH . H 4 HOH A 59 2061 2061 HOH HOH . H 4 HOH A 60 2062 2062 HOH HOH . H 4 HOH A 61 2063 2063 HOH HOH . H 4 HOH A 62 2064 2064 HOH HOH . I 4 HOH B 1 2001 2001 HOH HOH . I 4 HOH B 2 2002 2002 HOH HOH . I 4 HOH B 3 2003 2003 HOH HOH . I 4 HOH B 4 2004 2004 HOH HOH . I 4 HOH B 5 2005 2005 HOH HOH . I 4 HOH B 6 2006 2006 HOH HOH . I 4 HOH B 7 2007 2007 HOH HOH . I 4 HOH B 8 2008 2008 HOH HOH . I 4 HOH B 9 2009 2009 HOH HOH . I 4 HOH B 10 2010 2010 HOH HOH . I 4 HOH B 11 2011 2011 HOH HOH . I 4 HOH B 12 2012 2012 HOH HOH . I 4 HOH B 13 2013 2013 HOH HOH . I 4 HOH B 14 2014 2014 HOH HOH . I 4 HOH B 15 2015 2015 HOH HOH . I 4 HOH B 16 2016 2016 HOH HOH . I 4 HOH B 17 2017 2017 HOH HOH . I 4 HOH B 18 2018 2018 HOH HOH . I 4 HOH B 19 2019 2019 HOH HOH . I 4 HOH B 20 2020 2020 HOH HOH . I 4 HOH B 21 2021 2021 HOH HOH . I 4 HOH B 22 2022 2022 HOH HOH . I 4 HOH B 23 2023 2023 HOH HOH . I 4 HOH B 24 2024 2024 HOH HOH . I 4 HOH B 25 2025 2025 HOH HOH . I 4 HOH B 26 2026 2026 HOH HOH . I 4 HOH B 27 2027 2027 HOH HOH . I 4 HOH B 28 2028 2028 HOH HOH . I 4 HOH B 29 2029 2029 HOH HOH . I 4 HOH B 30 2030 2030 HOH HOH . I 4 HOH B 31 2031 2031 HOH HOH . I 4 HOH B 32 2032 2032 HOH HOH . I 4 HOH B 33 2033 2033 HOH HOH . I 4 HOH B 34 2034 2034 HOH HOH . I 4 HOH B 35 2035 2035 HOH HOH . I 4 HOH B 36 2036 2036 HOH HOH . I 4 HOH B 37 2037 2037 HOH HOH . I 4 HOH B 38 2038 2038 HOH HOH . I 4 HOH B 39 2039 2039 HOH HOH . I 4 HOH B 40 2040 2040 HOH HOH . I 4 HOH B 41 2041 2041 HOH HOH . I 4 HOH B 42 2042 2042 HOH HOH . I 4 HOH B 43 2043 2043 HOH HOH . I 4 HOH B 44 2044 2044 HOH HOH . I 4 HOH B 45 2045 2045 HOH HOH . I 4 HOH B 46 2046 2046 HOH HOH . I 4 HOH B 47 2047 2047 HOH HOH . I 4 HOH B 48 2048 2048 HOH HOH . I 4 HOH B 49 2049 2049 HOH HOH . I 4 HOH B 50 2050 2050 HOH HOH . I 4 HOH B 51 2051 2051 HOH HOH . I 4 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 P PA TYD . . . C 2 -11.26 9.031 -9.915 1 98.02 ? PA TYD 414 A 1 HETATM 2 O O1A TYD . . . C 2 -11.499 10.504 -10.148 1 94.06 ? O1A TYD 414 A 1 HETATM 3 O O2A TYD . . . C 2 -12.09 8.014 -10.654 1 99.77 ? O2A TYD 414 A 1 HETATM 4 O O3A TYD . . . C 2 -11.393 8.732 -8.344 1 284.1 ? O3A TYD 414 A 1 HETATM 5 P PB TYD . . . C 2 -12.851 8.781 -7.676 1 86.24 ? PB TYD 414 A 1 HETATM 6 O O1B TYD . . . C 2 -13.206 10.247 -7.785 1 84.02 ? O1B TYD 414 A 1 HETATM 7 O O2B TYD . . . C 2 -13.682 7.873 -8.559 1 91.73 ? O2B TYD 414 A 1 HETATM 8 O O3B TYD . . . C 2 -12.657 8.248 -6.271 1 76.04 ? O3B TYD 414 A 1 HETATM 9 O O5' TYD . . . C 2 -9.702 8.737 -10.197 1 67.9 ? O5' TYD 414 A 1 HETATM 10 C C5' TYD . . . C 2 -9.273 7.462 -10.648 1 57.72 ? C5' TYD 414 A 1 HETATM 11 C C4' TYD . . . C 2 -9.375 7.291 -12.166 1 48.49 ? C4' TYD 414 A 1 HETATM 12 O O4' TYD . . . C 2 -9.276 8.529 -12.886 1 38.87 ? O4' TYD 414 A 1 HETATM 13 C C3' TYD . . . C 2 -8.233 6.419 -12.65 1 43.28 ? C3' TYD 414 A 1 HETATM 14 O O3' TYD . . . C 2 -8.683 5.082 -12.794 1 46.32 ? O3' TYD 414 A 1 HETATM 15 C C2' TYD . . . C 2 -7.844 6.992 -14 1 37.28 ? C2' TYD 414 A 1 HETATM 16 C C1' TYD . . . C 2 -8.336 8.42 -13.961 1 35.45 ? C1' TYD 414 A 1 HETATM 17 N N1 TYD . . . C 2 -7.213 9.349 -13.762 1 41.91 ? N1 TYD 414 A 1 HETATM 18 C C2 TYD . . . C 2 -6.969 10.374 -14.697 1 41.86 ? C2 TYD 414 A 1 HETATM 19 O O2 TYD . . . C 2 -7.71 10.486 -15.691 1 53.01 ? O2 TYD 414 A 1 HETATM 20 N N3 TYD . . . C 2 -5.951 11.236 -14.544 1 29.46 ? N3 TYD 414 A 1 HETATM 21 C C4 TYD . . . C 2 -5.13 11.158 -13.5 1 24.23 ? C4 TYD 414 A 1 HETATM 22 O O4 TYD . . . C 2 -4.191 11.961 -13.369 1 27.19 ? O4 TYD 414 A 1 HETATM 23 C C5 TYD . . . C 2 -5.352 10.09 -12.502 1 30.08 ? C5 TYD 414 A 1 HETATM 24 C C5M TYD . . . C 2 -4.448 9.966 -11.31 1 31.32 ? C5M TYD 414 A 1 HETATM 25 C C6 TYD . . . C 2 -6.416 9.22 -12.687 1 41.38 ? C6 TYD 414 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #