data_1VYQ # _model_server_result.job_id oS_Pkrz-KFxT44wuLDgM4Q _model_server_result.datetime_utc '2024-10-10 16:24:25' _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 1vyq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1160}' # _entry.id 1VYQ # _exptl.entry_id 1VYQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 472.508 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE _entity.pdbx_number_of_molecules 3 _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 1VYQ _cell.length_a 62.83 _cell.length_b 62.83 _cell.length_c 121.527 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VYQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C28 H25 F N2 O4' _chem_comp.formula_weight 472.508 _chem_comp.id DUX _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE # 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 F3' C3' DUX sing 83 n n C3' C2' DUX sing 84 n n C3' C4' DUX sing 85 n n C3' H3' DUX sing 86 n n C2' C1' DUX sing 87 n n C2' "H2'1" DUX sing 88 n n C2' "H2'2" DUX sing 89 n n C1' N1 DUX sing 90 n n C1' O4' DUX sing 91 n n C1' H1' DUX sing 92 n n N1 C2 DUX sing 93 n n N1 C6 DUX sing 94 n n C2 N3 DUX sing 95 n n C2 O2 DUX doub 96 n n N3 C4 DUX sing 97 n n N3 H3 DUX sing 98 n n C4 C5 DUX sing 99 n n C4 O4 DUX doub 100 n n C5 C6 DUX doub 101 n n C5 H5 DUX sing 102 n n C6 H6 DUX sing 103 n n O4' C4' DUX sing 104 n n C4' C5' DUX sing 105 n n C4' H4' DUX sing 106 n n C5' O5' DUX sing 107 n n C5' "H5'1" DUX sing 108 n n C5' "H5'2" DUX sing 109 n n O5' C17 DUX sing 110 n n C17 C30 DUX sing 111 n n C17 C24 DUX sing 112 n n C17 C18 DUX sing 113 n n C30 C31 DUX doub 114 n y C30 C35 DUX sing 115 n y C31 C32 DUX sing 116 n y C31 H31 DUX sing 117 n n C32 C33 DUX doub 118 n y C32 H32 DUX sing 119 n n C33 C34 DUX sing 120 n y C33 H33 DUX sing 121 n n C34 C35 DUX doub 122 n y C34 H34 DUX sing 123 n n C35 H35 DUX sing 124 n n C24 C25 DUX doub 125 n y C24 C29 DUX sing 126 n y C25 C26 DUX sing 127 n y C25 H25 DUX sing 128 n n C26 C27 DUX doub 129 n y C26 H26 DUX sing 130 n n C27 C28 DUX sing 131 n y C27 H27 DUX sing 132 n n C28 C29 DUX doub 133 n y C28 H28 DUX sing 134 n n C29 H29 DUX sing 135 n n C18 C19 DUX doub 136 n y C18 C23 DUX sing 137 n y C19 C20 DUX sing 138 n y C19 H19 DUX sing 139 n n C20 C21 DUX doub 140 n y C20 H20 DUX sing 141 n n C21 C22 DUX sing 142 n y C21 H21 DUX sing 143 n n C22 C23 DUX doub 144 n y C22 H22 DUX sing 145 n n C23 H23 DUX sing 146 n n # _atom_sites.entry_id 1VYQ _atom_sites.fract_transf_matrix[1][1] 0.015916 _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] 0.015916 _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] 0.008229 _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 D 2 DUX A 1 1160 1160 DUX DUX . E 2 DUX B 1 1160 1160 DUX DUX . F 2 DUX C 1 1160 1160 DUX DUX . G 3 HOH A 1 2001 2001 HOH HOH . G 3 HOH A 2 2002 2002 HOH HOH . G 3 HOH A 3 2003 2003 HOH HOH . G 3 HOH A 4 2004 2004 HOH HOH . G 3 HOH A 5 2005 2005 HOH HOH . G 3 HOH A 6 2006 2006 HOH HOH . G 3 HOH A 7 2007 2007 HOH HOH . G 3 HOH A 8 2008 2008 HOH HOH . G 3 HOH A 9 2009 2009 HOH HOH . G 3 HOH A 10 2010 2010 HOH HOH . G 3 HOH A 11 2011 2011 HOH HOH . G 3 HOH A 12 2012 2012 HOH HOH . G 3 HOH A 13 2013 2013 HOH HOH . G 3 HOH A 14 2014 2014 HOH HOH . G 3 HOH A 15 2015 2015 HOH HOH . G 3 HOH A 16 2016 2016 HOH HOH . G 3 HOH A 17 2017 2017 HOH HOH . G 3 HOH A 18 2018 2018 HOH HOH . G 3 HOH A 19 2019 2019 HOH HOH . G 3 HOH A 20 2020 2020 HOH HOH . G 3 HOH A 21 2021 2021 HOH HOH . G 3 HOH A 22 2022 2022 HOH HOH . G 3 HOH A 23 2023 2023 HOH HOH . G 3 HOH A 24 2024 2024 HOH HOH . G 3 HOH A 25 2025 2025 HOH HOH . G 3 HOH A 26 2026 2026 HOH HOH . G 3 HOH A 27 2027 2027 HOH HOH . G 3 HOH A 28 2028 2028 HOH HOH . G 3 HOH A 29 2029 2029 HOH HOH . G 3 HOH A 30 2030 2030 HOH HOH . G 3 HOH A 31 2031 2031 HOH HOH . G 3 HOH A 32 2032 2032 HOH HOH . G 3 HOH A 33 2033 2033 HOH HOH . G 3 HOH A 34 2034 2034 HOH HOH . G 3 HOH A 35 2035 2035 HOH HOH . G 3 HOH A 36 2036 2036 HOH HOH . G 3 HOH A 37 2037 2037 HOH HOH . G 3 HOH A 38 2038 2038 HOH HOH . G 3 HOH A 39 2039 2039 HOH HOH . G 3 HOH A 40 2040 2040 HOH HOH . G 3 HOH A 41 2041 2041 HOH HOH . G 3 HOH A 42 2042 2042 HOH HOH . G 3 HOH A 43 2043 2043 HOH HOH . G 3 HOH A 44 2044 2044 HOH HOH . G 3 HOH A 45 2045 2045 HOH HOH . G 3 HOH A 46 2046 2046 HOH HOH . G 3 HOH A 47 2047 2047 HOH HOH . G 3 HOH A 48 2048 2048 HOH HOH . G 3 HOH A 49 2049 2049 HOH HOH . G 3 HOH A 50 2050 2050 HOH HOH . G 3 HOH A 51 2051 2051 HOH HOH . G 3 HOH A 52 2052 2052 HOH HOH . H 3 HOH B 1 2001 2001 HOH HOH . H 3 HOH B 2 2002 2002 HOH HOH . H 3 HOH B 3 2003 2003 HOH HOH . H 3 HOH B 4 2004 2004 HOH HOH . H 3 HOH B 5 2005 2005 HOH HOH . H 3 HOH B 6 2006 2006 HOH HOH . H 3 HOH B 7 2007 2007 HOH HOH . H 3 HOH B 8 2008 2008 HOH HOH . H 3 HOH B 9 2009 2009 HOH HOH . H 3 HOH B 10 2010 2010 HOH HOH . H 3 HOH B 11 2011 2011 HOH HOH . H 3 HOH B 12 2012 2012 HOH HOH . H 3 HOH B 13 2013 2013 HOH HOH . H 3 HOH B 14 2014 2014 HOH HOH . H 3 HOH B 15 2015 2015 HOH HOH . H 3 HOH B 16 2016 2016 HOH HOH . H 3 HOH B 17 2017 2017 HOH HOH . H 3 HOH B 18 2018 2018 HOH HOH . H 3 HOH B 19 2019 2019 HOH HOH . H 3 HOH B 20 2020 2020 HOH HOH . H 3 HOH B 21 2021 2021 HOH HOH . H 3 HOH B 22 2022 2022 HOH HOH . H 3 HOH B 23 2023 2023 HOH HOH . H 3 HOH B 24 2024 2024 HOH HOH . H 3 HOH B 25 2025 2025 HOH HOH . I 3 HOH C 1 2001 2001 HOH HOH . I 3 HOH C 2 2002 2002 HOH HOH . I 3 HOH C 3 2003 2003 HOH HOH . I 3 HOH C 4 2004 2004 HOH HOH . I 3 HOH C 5 2005 2005 HOH HOH . I 3 HOH C 6 2006 2006 HOH HOH . I 3 HOH C 7 2007 2007 HOH HOH . I 3 HOH C 8 2008 2008 HOH HOH . I 3 HOH C 9 2009 2009 HOH HOH . I 3 HOH C 10 2010 2010 HOH HOH . I 3 HOH C 11 2011 2011 HOH HOH . I 3 HOH C 12 2012 2012 HOH HOH . I 3 HOH C 13 2013 2013 HOH HOH . I 3 HOH C 14 2014 2014 HOH HOH . I 3 HOH C 15 2015 2015 HOH HOH . I 3 HOH C 16 2016 2016 HOH HOH . I 3 HOH C 17 2017 2017 HOH HOH . I 3 HOH C 18 2018 2018 HOH HOH . I 3 HOH C 19 2019 2019 HOH HOH . I 3 HOH C 20 2020 2020 HOH HOH . I 3 HOH C 21 2021 2021 HOH HOH . I 3 HOH C 22 2022 2022 HOH HOH . I 3 HOH C 23 2023 2023 HOH HOH . I 3 HOH C 24 2024 2024 HOH HOH . I 3 HOH C 25 2025 2025 HOH HOH . I 3 HOH C 26 2026 2026 HOH HOH . I 3 HOH C 27 2027 2027 HOH HOH . I 3 HOH C 28 2028 2028 HOH HOH . I 3 HOH C 29 2029 2029 HOH HOH . I 3 HOH C 30 2030 2030 HOH HOH . I 3 HOH C 31 2031 2031 HOH HOH . I 3 HOH C 32 2032 2032 HOH HOH . I 3 HOH C 33 2033 2033 HOH HOH . I 3 HOH C 34 2034 2034 HOH HOH . I 3 HOH C 35 2035 2035 HOH HOH . I 3 HOH C 36 2036 2036 HOH HOH . I 3 HOH C 37 2037 2037 HOH HOH . I 3 HOH C 38 2038 2038 HOH HOH . I 3 HOH C 39 2039 2039 HOH HOH . I 3 HOH C 40 2040 2040 HOH HOH . I 3 HOH C 41 2041 2041 HOH HOH . I 3 HOH C 42 2042 2042 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 F F3' DUX . . . F 2 17.446 -21.655 3.989 1 33.6 ? F3' DUX 1160 C 1 HETATM 2 C C3' DUX . . . F 2 18.019 -20.616 4.667 1 32.13 ? C3' DUX 1160 C 1 HETATM 3 C C2' DUX . . . F 2 17.056 -19.431 4.632 1 30.04 ? C2' DUX 1160 C 1 HETATM 4 C C1' DUX . . . F 2 17.263 -18.796 5.973 1 28.64 ? C1' DUX 1160 C 1 HETATM 5 N N1 DUX . . . F 2 18.217 -17.691 5.91 1 26.63 ? N1 DUX 1160 C 1 HETATM 6 C C2 DUX . . . F 2 18.033 -16.69 6.866 1 24.91 ? C2 DUX 1160 C 1 HETATM 7 N N3 DUX . . . F 2 18.832 -15.625 6.976 1 24.47 ? N3 DUX 1160 C 1 HETATM 8 C C4 DUX . . . F 2 19.865 -15.451 6.12 1 25.97 ? C4 DUX 1160 C 1 HETATM 9 C C5 DUX . . . F 2 20.081 -16.417 5.123 1 27.06 ? C5 DUX 1160 C 1 HETATM 10 C C6 DUX . . . F 2 19.239 -17.554 5.044 1 27.41 ? C6 DUX 1160 C 1 HETATM 11 O O4 DUX . . . F 2 20.624 -14.457 6.222 1 23.64 ? O4 DUX 1160 C 1 HETATM 12 O O2 DUX . . . F 2 17.107 -16.876 7.64 1 25.57 ? O2 DUX 1160 C 1 HETATM 13 O O4' DUX . . . F 2 17.787 -19.805 6.879 1 29.75 ? O4' DUX 1160 C 1 HETATM 14 C C4' DUX . . . F 2 18.246 -20.935 6.143 1 28.54 ? C4' DUX 1160 C 1 HETATM 15 C C5' DUX . . . F 2 19.702 -21.179 6.465 1 26.42 ? C5' DUX 1160 C 1 HETATM 16 O O5' DUX . . . F 2 19.738 -21.481 7.858 1 23.12 ? O5' DUX 1160 C 1 HETATM 17 C C17 DUX . . . F 2 20.864 -21.234 8.663 1 22.9 ? C17 DUX 1160 C 1 HETATM 18 C C30 DUX . . . F 2 21.934 -22.252 8.457 1 23.66 ? C30 DUX 1160 C 1 HETATM 19 C C31 DUX . . . F 2 21.644 -23.486 7.934 1 23.64 ? C31 DUX 1160 C 1 HETATM 20 C C32 DUX . . . F 2 22.657 -24.443 7.796 1 25.42 ? C32 DUX 1160 C 1 HETATM 21 C C33 DUX . . . F 2 23.968 -24.174 8.117 1 22.81 ? C33 DUX 1160 C 1 HETATM 22 C C34 DUX . . . F 2 24.25 -22.951 8.625 1 25.81 ? C34 DUX 1160 C 1 HETATM 23 C C35 DUX . . . F 2 23.248 -22.009 8.81 1 26.08 ? C35 DUX 1160 C 1 HETATM 24 C C24 DUX . . . F 2 21.325 -19.837 8.49 1 26.35 ? C24 DUX 1160 C 1 HETATM 25 C C25 DUX . . . F 2 22.411 -19.536 7.642 1 25.72 ? C25 DUX 1160 C 1 HETATM 26 C C26 DUX . . . F 2 22.822 -18.219 7.503 1 26.4 ? C26 DUX 1160 C 1 HETATM 27 C C27 DUX . . . F 2 22.136 -17.201 8.154 1 25.99 ? C27 DUX 1160 C 1 HETATM 28 C C28 DUX . . . F 2 21.056 -17.489 8.988 1 27.07 ? C28 DUX 1160 C 1 HETATM 29 C C29 DUX . . . F 2 20.624 -18.814 9.151 1 24.96 ? C29 DUX 1160 C 1 HETATM 30 C C18 DUX . . . F 2 20.299 -21.427 10.053 1 24.75 ? C18 DUX 1160 C 1 HETATM 31 C C19 DUX . . . F 2 18.917 -21.503 10.261 1 24.61 ? C19 DUX 1160 C 1 HETATM 32 C C20 DUX . . . F 2 18.388 -21.687 11.529 1 23.9 ? C20 DUX 1160 C 1 HETATM 33 C C21 DUX . . . F 2 19.244 -21.811 12.608 1 24.78 ? C21 DUX 1160 C 1 HETATM 34 C C22 DUX . . . F 2 20.628 -21.749 12.436 1 22.45 ? C22 DUX 1160 C 1 HETATM 35 C C23 DUX . . . F 2 21.148 -21.56 11.169 1 24.47 ? C23 DUX 1160 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #