data_2YB0 # _model_server_result.job_id lgBquqSoNbO1NxAK5DQt3w _model_server_result.datetime_utc '2024-11-05 00:08:52' _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 2yb0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1266}' # _entry.id 2YB0 # _exptl.entry_id 2YB0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE" _entity.pdbx_number_of_molecules 4 _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 2YB0 _cell.length_a 109.186 _cell.length_b 109.186 _cell.length_c 308.882 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YB0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,B,E,F,G,H,I,J,K,R,S 1 1 C,D,L,M,N,O,P,Q,T,U 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 E N N ? 2 I N N ? 2 L N N ? 2 O N N # _chem_comp.formula 'C9 H12 N2 O5' _chem_comp.formula_weight 228.202 _chem_comp.id DUR _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE" _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 N1 C2 DUR sing 83 n n N1 C6 DUR sing 84 n n N1 C1' DUR sing 85 n n C2 N3 DUR sing 86 n n C2 O2 DUR doub 87 n n N3 C4 DUR sing 88 n n N3 HN3 DUR sing 89 n n C4 C5 DUR sing 90 n n C4 O4 DUR doub 91 n n C5 C6 DUR doub 92 n n C5 H5 DUR sing 93 n n C6 H6 DUR sing 94 n n C1' C2' DUR sing 95 n n C1' O4' DUR sing 96 n n C1' H1' DUR sing 97 n n C2' C3' DUR sing 98 n n C2' "H2'1" DUR sing 99 n n C2' "H2'2" DUR sing 100 n n C3' C4' DUR sing 101 n n C3' O3' DUR sing 102 n n C3' H3' DUR sing 103 n n C4' O4' DUR sing 104 n n C4' C5' DUR sing 105 n n C4' H4' DUR sing 106 n n O3' HO3' DUR sing 107 n n C5' O5' DUR sing 108 n n C5' "H5'1" DUR sing 109 n n C5' "H5'2" DUR sing 110 n n O5' HO5' DUR sing 111 n n # _atom_sites.entry_id 2YB0 _atom_sites.fract_transf_matrix[1][1] 0.009159 _atom_sites.fract_transf_matrix[1][2] 0.005288 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010576 _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] 0.003237 _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 E 2 DUR A 1 1266 1266 DUR DUR . F 3 SO4 A 1 1267 1267 SO4 SO4 . G 3 SO4 A 1 1268 1268 SO4 SO4 . H 3 SO4 A 1 1269 1269 SO4 SO4 . I 2 DUR B 1 1266 1266 DUR DUR . J 3 SO4 B 1 1267 1267 SO4 SO4 . K 3 SO4 B 1 1268 1268 SO4 SO4 . L 2 DUR D 1 1266 1266 DUR DUR . M 3 SO4 D 1 1267 1267 SO4 SO4 . N 3 SO4 D 1 1268 1268 SO4 SO4 . O 2 DUR E 1 1266 1266 DUR DUR . P 3 SO4 E 1 1267 1267 SO4 SO4 . Q 3 SO4 E 1 1268 1268 SO4 SO4 . R 4 HOH A 1 2001 2001 HOH HOH . R 4 HOH A 2 2002 2002 HOH HOH . R 4 HOH A 3 2003 2003 HOH HOH . R 4 HOH A 4 2004 2004 HOH HOH . R 4 HOH A 5 2005 2005 HOH HOH . R 4 HOH A 6 2006 2006 HOH HOH . R 4 HOH A 7 2007 2007 HOH HOH . R 4 HOH A 8 2008 2008 HOH HOH . R 4 HOH A 9 2009 2009 HOH HOH . R 4 HOH A 10 2010 2010 HOH HOH . R 4 HOH A 11 2011 2011 HOH HOH . R 4 HOH A 12 2012 2012 HOH HOH . R 4 HOH A 13 2013 2013 HOH HOH . R 4 HOH A 14 2014 2014 HOH HOH . R 4 HOH A 15 2015 2015 HOH HOH . R 4 HOH A 16 2016 2016 HOH HOH . R 4 HOH A 17 2017 2017 HOH HOH . R 4 HOH A 18 2018 2018 HOH HOH . R 4 HOH A 19 2019 2019 HOH HOH . R 4 HOH A 20 2020 2020 HOH HOH . R 4 HOH A 21 2021 2021 HOH HOH . R 4 HOH A 22 2022 2022 HOH HOH . R 4 HOH A 23 2023 2023 HOH HOH . R 4 HOH A 24 2024 2024 HOH HOH . R 4 HOH A 25 2025 2025 HOH HOH . R 4 HOH A 26 2026 2026 HOH HOH . R 4 HOH A 27 2027 2027 HOH HOH . R 4 HOH A 28 2028 2028 HOH HOH . R 4 HOH A 29 2029 2029 HOH HOH . R 4 HOH A 30 2030 2030 HOH HOH . R 4 HOH A 31 2031 2031 HOH HOH . R 4 HOH A 32 2032 2032 HOH HOH . R 4 HOH A 33 2033 2033 HOH HOH . R 4 HOH A 34 2034 2034 HOH HOH . R 4 HOH A 35 2035 2035 HOH HOH . R 4 HOH A 36 2036 2036 HOH HOH . R 4 HOH A 37 2037 2037 HOH HOH . R 4 HOH A 38 2038 2038 HOH HOH . R 4 HOH A 39 2039 2039 HOH HOH . S 4 HOH B 1 2001 2001 HOH HOH . S 4 HOH B 2 2002 2002 HOH HOH . S 4 HOH B 3 2003 2003 HOH HOH . S 4 HOH B 4 2004 2004 HOH HOH . S 4 HOH B 5 2005 2005 HOH HOH . S 4 HOH B 6 2006 2006 HOH HOH . S 4 HOH B 7 2007 2007 HOH HOH . S 4 HOH B 8 2008 2008 HOH HOH . S 4 HOH B 9 2009 2009 HOH HOH . S 4 HOH B 10 2010 2010 HOH HOH . S 4 HOH B 11 2011 2011 HOH HOH . S 4 HOH B 12 2012 2012 HOH HOH . S 4 HOH B 13 2013 2013 HOH HOH . S 4 HOH B 14 2014 2014 HOH HOH . S 4 HOH B 15 2015 2015 HOH HOH . S 4 HOH B 16 2016 2016 HOH HOH . S 4 HOH B 17 2017 2017 HOH HOH . S 4 HOH B 18 2018 2018 HOH HOH . S 4 HOH B 19 2019 2019 HOH HOH . T 4 HOH D 1 2001 2001 HOH HOH . T 4 HOH D 2 2002 2002 HOH HOH . T 4 HOH D 3 2003 2003 HOH HOH . T 4 HOH D 4 2004 2004 HOH HOH . T 4 HOH D 5 2005 2005 HOH HOH . T 4 HOH D 6 2006 2006 HOH HOH . T 4 HOH D 7 2007 2007 HOH HOH . T 4 HOH D 8 2008 2008 HOH HOH . T 4 HOH D 9 2009 2009 HOH HOH . T 4 HOH D 10 2010 2010 HOH HOH . T 4 HOH D 11 2011 2011 HOH HOH . T 4 HOH D 12 2012 2012 HOH HOH . T 4 HOH D 13 2013 2013 HOH HOH . T 4 HOH D 14 2014 2014 HOH HOH . T 4 HOH D 15 2015 2015 HOH HOH . T 4 HOH D 16 2016 2016 HOH HOH . T 4 HOH D 17 2017 2017 HOH HOH . T 4 HOH D 18 2018 2018 HOH HOH . T 4 HOH D 19 2019 2019 HOH HOH . T 4 HOH D 20 2020 2020 HOH HOH . T 4 HOH D 21 2021 2021 HOH HOH . T 4 HOH D 22 2022 2022 HOH HOH . T 4 HOH D 23 2023 2023 HOH HOH . U 4 HOH E 1 2001 2001 HOH HOH . U 4 HOH E 2 2002 2002 HOH HOH . U 4 HOH E 3 2003 2003 HOH HOH . U 4 HOH E 4 2004 2004 HOH HOH . U 4 HOH E 5 2005 2005 HOH HOH . U 4 HOH E 6 2006 2006 HOH HOH . U 4 HOH E 7 2007 2007 HOH HOH . U 4 HOH E 8 2008 2008 HOH HOH . U 4 HOH E 9 2009 2009 HOH HOH . U 4 HOH E 10 2010 2010 HOH HOH . U 4 HOH E 11 2011 2011 HOH HOH . U 4 HOH E 12 2012 2012 HOH HOH . U 4 HOH E 13 2013 2013 HOH HOH . U 4 HOH E 14 2014 2014 HOH HOH . U 4 HOH E 15 2015 2015 HOH HOH . U 4 HOH E 16 2016 2016 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 DUR . . . I 2 -15.832 66.303 -16.974 1 35 ? N1 DUR 1266 B 1 HETATM 2 C C2 DUR . . . I 2 -15.989 67.606 -16.467 1 33.69 ? C2 DUR 1266 B 1 HETATM 3 N N3 DUR . . . I 2 -17.177 68.206 -16.489 1 34.26 ? N3 DUR 1266 B 1 HETATM 4 C C4 DUR . . . I 2 -18.251 67.601 -17.015 1 37.6 ? C4 DUR 1266 B 1 HETATM 5 C C5 DUR . . . I 2 -18.129 66.314 -17.522 1 34.04 ? C5 DUR 1266 B 1 HETATM 6 C C6 DUR . . . I 2 -16.884 65.673 -17.517 1 29.73 ? C6 DUR 1266 B 1 HETATM 7 O O2 DUR . . . I 2 -15.011 68.181 -15.967 1 45.99 ? O2 DUR 1266 B 1 HETATM 8 O O4 DUR . . . I 2 -19.358 68.187 -17.03 1 39.37 ? O4 DUR 1266 B 1 HETATM 9 C C1' DUR . . . I 2 -14.505 65.715 -16.931 1 32.18 ? C1' DUR 1266 B 1 HETATM 10 C C2' DUR . . . I 2 -14.131 65.118 -15.6 1 35.46 ? C2' DUR 1266 B 1 HETATM 11 C C3' DUR . . . I 2 -13.154 64.014 -15.956 1 41.98 ? C3' DUR 1266 B 1 HETATM 12 C C4' DUR . . . I 2 -13.429 63.728 -17.409 1 43.86 ? C4' DUR 1266 B 1 HETATM 13 O O3' DUR . . . I 2 -11.766 64.397 -15.785 1 43.4 ? O3' DUR 1266 B 1 HETATM 14 O O4' DUR . . . I 2 -14.379 64.679 -17.87 1 42.18 ? O4' DUR 1266 B 1 HETATM 15 C C5' DUR . . . I 2 -13.96 62.316 -17.628 1 65.94 ? C5' DUR 1266 B 1 HETATM 16 O O5' DUR . . . I 2 -13.031 61.357 -17.103 1 70.83 ? O5' DUR 1266 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 16 #