data_1E2J # _model_server_result.job_id thidnMvqoR5kP1tE3OqQyw _model_server_result.datetime_utc '2024-11-13 18:41:38' _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 1e2j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1E2J # _exptl.entry_id 1E2J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 90 _cell.angle_gamma 90 _cell.entry_id 1E2J _cell.length_a 113.4 _cell.length_b 117.5 _cell.length_c 108.6 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1E2J _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _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 _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 ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 294 n n O5' HO5' THM sing 295 n n C5' C4' THM sing 296 n n C5' "H5'1" THM sing 297 n n C5' "H5'2" THM sing 298 n n C4' O4' THM sing 299 n n C4' C3' THM sing 300 n n C4' H4' THM sing 301 n n O4' C1' THM sing 302 n n C3' O3' THM sing 303 n n C3' C2' THM sing 304 n n C3' H3' THM sing 305 n n O3' HO3' THM sing 306 n n C2' C1' THM sing 307 n n C2' "H2'1" THM sing 308 n n C2' "H2'2" THM sing 309 n n C1' N1 THM sing 310 n n C1' H1' THM sing 311 n n N1 C2 THM sing 312 n n N1 C6 THM sing 313 n n C2 O2 THM doub 314 n n C2 N3 THM sing 315 n n N3 C4 THM sing 316 n n N3 HN3 THM sing 317 n n C4 O4 THM doub 318 n n C4 C5 THM sing 319 n n C5 C5M THM sing 320 n n C5 C6 THM doub 321 n n C5M HM51 THM sing 322 n n C5M HM52 THM sing 323 n n C5M HM53 THM sing 324 n n C6 H6 THM sing 325 n n # _atom_sites.entry_id 1E2J _atom_sites.fract_transf_matrix[1][1] 0.008818 _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] 0.008511 _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] 0.009208 _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 SO4 A 1 400 400 SO4 SO4 . D 3 THM A 1 500 500 THM THM . E 2 SO4 B 1 400 400 SO4 SO4 . F 3 THM B 1 500 500 THM THM . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . G 4 HOH A 46 2046 2046 HOH HOH . G 4 HOH A 47 2047 2047 HOH HOH . G 4 HOH A 48 2048 2048 HOH HOH . G 4 HOH A 49 2049 2049 HOH HOH . G 4 HOH A 50 2050 2050 HOH HOH . G 4 HOH A 51 2051 2051 HOH HOH . G 4 HOH A 52 2052 2052 HOH HOH . G 4 HOH A 53 2053 2053 HOH HOH . G 4 HOH A 54 2054 2054 HOH HOH . G 4 HOH A 55 2055 2055 HOH HOH . G 4 HOH A 56 2056 2056 HOH HOH . G 4 HOH A 57 2057 2057 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 HOH HOH . H 4 HOH B 35 2035 2035 HOH HOH . H 4 HOH B 36 2036 2036 HOH HOH . H 4 HOH B 37 2037 2037 HOH HOH . H 4 HOH B 38 2038 2038 HOH HOH . H 4 HOH B 39 2039 2039 HOH HOH . H 4 HOH B 40 2040 2040 HOH HOH . H 4 HOH B 41 2041 2041 HOH HOH . H 4 HOH B 42 2042 2042 HOH HOH . H 4 HOH B 43 2043 2043 HOH HOH . H 4 HOH B 44 2044 2044 HOH HOH . H 4 HOH B 45 2045 2045 HOH HOH . H 4 HOH B 46 2046 2046 HOH HOH . H 4 HOH B 47 2047 2047 HOH HOH . H 4 HOH B 48 2048 2048 HOH HOH . H 4 HOH B 49 2049 2049 HOH HOH . H 4 HOH B 50 2050 2050 HOH HOH . H 4 HOH B 51 2051 2051 HOH HOH . H 4 HOH B 52 2052 2052 HOH HOH . H 4 HOH B 53 2053 2053 HOH HOH . H 4 HOH B 54 2054 2054 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 O O5' THM . . . D 3 51.177 35.242 1.355 1 37.77 ? O5' THM 500 A 1 HETATM 2 C C5' THM . . . D 3 49.955 34.912 0.626 1 31.72 ? C5' THM 500 A 1 HETATM 3 C C4' THM . . . D 3 49.906 33.472 0.167 1 33.03 ? C4' THM 500 A 1 HETATM 4 O O4' THM . . . D 3 48.704 32.78 0.528 1 33.55 ? O4' THM 500 A 1 HETATM 5 C C3' THM . . . D 3 49.698 33.392 -1.329 1 33.43 ? C3' THM 500 A 1 HETATM 6 O O3' THM . . . D 3 49.902 32.047 -1.623 1 35.32 ? O3' THM 500 A 1 HETATM 7 C C2' THM . . . D 3 48.199 33.624 -1.455 1 34.04 ? C2' THM 500 A 1 HETATM 8 C C1' THM . . . D 3 47.583 32.756 -0.415 1 33.31 ? C1' THM 500 A 1 HETATM 9 N N1 THM . . . D 3 46.294 33.111 0.217 1 31.82 ? N1 THM 500 A 1 HETATM 10 C C2 THM . . . D 3 45.164 32.496 -0.189 1 33.02 ? C2 THM 500 A 1 HETATM 11 O O2 THM . . . D 3 45.135 31.585 -1.038 1 32.99 ? O2 THM 500 A 1 HETATM 12 N N3 THM . . . D 3 43.954 32.92 0.4 1 36.15 ? N3 THM 500 A 1 HETATM 13 C C4 THM . . . D 3 43.837 33.945 1.366 1 35.92 ? C4 THM 500 A 1 HETATM 14 O O4 THM . . . D 3 42.701 34.258 1.832 1 37.78 ? O4 THM 500 A 1 HETATM 15 C C5 THM . . . D 3 45.065 34.504 1.699 1 36.59 ? C5 THM 500 A 1 HETATM 16 C C5M THM . . . D 3 45.143 35.622 2.734 1 35.24 ? C5M THM 500 A 1 HETATM 17 C C6 THM . . . D 3 46.219 34.112 1.155 1 35.37 ? C6 THM 500 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 17 #