data_2XY3 # _model_server_result.job_id 6gbXAK9L5JVh6ZmLyucxHA _model_server_result.datetime_utc '2025-07-27 10:29:35' _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 2xy3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1130}' # _entry.id 2XY3 # _exptl.entry_id 2XY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 2XY3 _cell.length_a 98.474 _cell.length_b 98.4 _cell.length_c 97.993 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,G,H,I,J,P,Q,R 1 1 D,E,F,K,L,M,N,O,S,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 G N N ? 2 H N N ? 2 I N N ? 2 K N N ? 2 L N N ? 2 N N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 I O1A DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 I O1B DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc3 I O2G DUP . C DUP 1129 1_555 J MG MG . C MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc4 L O1A DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 L O1B DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc6 L O2G DUP . E DUP 1130 1_555 M MG MG . E MG 1131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc7 N O1B DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 N O2G DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc9 N O1A DUP . F DUP 1129 1_555 O MG MG . F MG 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 O4 C4 DUP doub 83 n n C4 C5 DUP sing 84 n y C4 N3 DUP sing 85 n y C5 C6 DUP doub 86 n y C5 H5 DUP sing 87 n n C6 N1 DUP sing 88 n y C6 H6 DUP sing 89 n n N3 C2 DUP sing 90 n y N3 HN3 DUP sing 91 n n C2 O2 DUP doub 92 n n C2 N1 DUP sing 93 n y N1 C1' DUP sing 94 n n C1' C2' DUP sing 95 n n C1' O4' DUP sing 96 n n C1' H1' DUP sing 97 n n C2' C3' DUP sing 98 n n C2' "H2'1" DUP sing 99 n n C2' "H2'2" DUP sing 100 n n C3' O3' DUP sing 101 n n C3' C4' DUP sing 102 n n C3' H1 DUP sing 103 n n O3' H3' DUP sing 104 n n O4' C4' DUP sing 105 n n C4' C5' DUP sing 106 n n C4' H4' DUP sing 107 n n C5' O5' DUP sing 108 n n C5' "H5'1" DUP sing 109 n n C5' "H5'2" DUP sing 110 n n O5' PA DUP sing 111 n n PA O1A DUP doub 112 n n PA O2A DUP sing 113 n n PA N3A DUP sing 114 n n O2A H2A DUP sing 115 n n N3A PB DUP sing 116 n n N3A H3A DUP sing 117 n n PB O1B DUP doub 118 n n PB O2B DUP sing 119 n n PB O3B DUP sing 120 n n O2B H2B DUP sing 121 n n O3B PG DUP sing 122 n n PG O2G DUP doub 123 n n PG O1G DUP sing 124 n n PG O3G DUP sing 125 n n O1G H1G DUP sing 126 n n O3G H3G DUP sing 127 n n # _atom_sites.entry_id 2XY3 _atom_sites.fract_transf_matrix[1][1] 0.010155 _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] 0.010163 _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] 0.010205 _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 G 2 DUP A 1 1130 1130 DUP DUP . H 2 DUP B 1 1129 1129 DUP DUP . I 2 DUP C 1 1129 1129 DUP DUP . J 3 MG C 1 1130 1130 MG MG . K 2 DUP D 1 1130 1130 DUP DUP . L 2 DUP E 1 1130 1130 DUP DUP . M 3 MG E 1 1131 1131 MG MG . N 2 DUP F 1 1129 1129 DUP DUP . O 3 MG F 1 1130 1130 MG MG . P 4 HOH A 1 2001 2001 HOH HOH . P 4 HOH A 2 2002 2002 HOH HOH . P 4 HOH A 3 2003 2003 HOH HOH . P 4 HOH A 4 2004 2004 HOH HOH . P 4 HOH A 5 2005 2005 HOH HOH . P 4 HOH A 6 2006 2006 HOH HOH . P 4 HOH A 7 2007 2007 HOH HOH . P 4 HOH A 8 2008 2008 HOH HOH . P 4 HOH A 9 2009 2009 HOH HOH . P 4 HOH A 10 2010 2010 HOH HOH . P 4 HOH A 11 2011 2011 HOH HOH . P 4 HOH A 12 2012 2012 HOH HOH . P 4 HOH A 13 2013 2013 HOH HOH . P 4 HOH A 14 2014 2014 HOH HOH . P 4 HOH A 15 2015 2015 HOH HOH . P 4 HOH A 16 2016 2016 HOH HOH . P 4 HOH A 17 2017 2017 HOH HOH . P 4 HOH A 18 2018 2018 HOH HOH . P 4 HOH A 19 2019 2019 HOH HOH . P 4 HOH A 20 2020 2020 HOH HOH . P 4 HOH A 21 2021 2021 HOH HOH . P 4 HOH A 22 2022 2022 HOH HOH . Q 4 HOH B 1 2001 2001 HOH HOH . Q 4 HOH B 2 2002 2002 HOH HOH . Q 4 HOH B 3 2003 2003 HOH HOH . Q 4 HOH B 4 2004 2004 HOH HOH . Q 4 HOH B 5 2005 2005 HOH HOH . Q 4 HOH B 6 2006 2006 HOH HOH . Q 4 HOH B 7 2007 2007 HOH HOH . Q 4 HOH B 8 2008 2008 HOH HOH . Q 4 HOH B 9 2009 2009 HOH HOH . Q 4 HOH B 10 2010 2010 HOH HOH . Q 4 HOH B 11 2011 2011 HOH HOH . Q 4 HOH B 12 2012 2012 HOH HOH . R 4 HOH C 1 2001 2001 HOH HOH . R 4 HOH C 2 2002 2002 HOH HOH . R 4 HOH C 3 2003 2003 HOH HOH . R 4 HOH C 4 2004 2004 HOH HOH . R 4 HOH C 5 2005 2005 HOH HOH . R 4 HOH C 6 2006 2006 HOH HOH . R 4 HOH C 7 2007 2007 HOH HOH . R 4 HOH C 8 2008 2008 HOH HOH . R 4 HOH C 9 2009 2009 HOH HOH . R 4 HOH C 10 2010 2010 HOH HOH . R 4 HOH C 11 2011 2011 HOH HOH . R 4 HOH C 12 2012 2012 HOH HOH . R 4 HOH C 13 2013 2013 HOH HOH . R 4 HOH C 14 2014 2014 HOH HOH . R 4 HOH C 15 2015 2015 HOH HOH . R 4 HOH C 16 2016 2016 HOH HOH . R 4 HOH C 17 2017 2017 HOH HOH . R 4 HOH C 18 2018 2018 HOH HOH . R 4 HOH C 19 2019 2019 HOH HOH . R 4 HOH C 20 2020 2020 HOH HOH . S 4 HOH D 1 2001 2001 HOH HOH . S 4 HOH D 2 2002 2002 HOH HOH . S 4 HOH D 3 2003 2003 HOH HOH . S 4 HOH D 4 2004 2004 HOH HOH . S 4 HOH D 5 2005 2005 HOH HOH . S 4 HOH D 6 2006 2006 HOH HOH . S 4 HOH D 7 2007 2007 HOH HOH . S 4 HOH D 8 2008 2008 HOH HOH . S 4 HOH D 9 2009 2009 HOH HOH . S 4 HOH D 10 2010 2010 HOH HOH . S 4 HOH D 11 2011 2011 HOH HOH . S 4 HOH D 12 2012 2012 HOH HOH . S 4 HOH D 13 2013 2013 HOH HOH . S 4 HOH D 14 2014 2014 HOH HOH . S 4 HOH D 15 2015 2015 HOH HOH . S 4 HOH D 16 2016 2016 HOH HOH . S 4 HOH D 17 2017 2017 HOH HOH . S 4 HOH D 18 2018 2018 HOH HOH . S 4 HOH D 19 2019 2019 HOH HOH . S 4 HOH D 20 2020 2020 HOH HOH . S 4 HOH D 21 2021 2021 HOH HOH . S 4 HOH D 22 2022 2022 HOH HOH . T 4 HOH E 1 2001 2001 HOH HOH . T 4 HOH E 2 2002 2002 HOH HOH . T 4 HOH E 3 2003 2003 HOH HOH . T 4 HOH E 4 2004 2004 HOH HOH . T 4 HOH E 5 2005 2005 HOH HOH . T 4 HOH E 6 2006 2006 HOH HOH . T 4 HOH E 7 2007 2007 HOH HOH . T 4 HOH E 8 2008 2008 HOH HOH . T 4 HOH E 9 2009 2009 HOH HOH . T 4 HOH E 10 2010 2010 HOH HOH . T 4 HOH E 11 2011 2011 HOH HOH . T 4 HOH E 12 2012 2012 HOH HOH . T 4 HOH E 13 2013 2013 HOH HOH . T 4 HOH E 14 2014 2014 HOH HOH . T 4 HOH E 15 2015 2015 HOH HOH . T 4 HOH E 16 2016 2016 HOH HOH . T 4 HOH E 17 2017 2017 HOH HOH . T 4 HOH E 18 2018 2018 HOH HOH . T 4 HOH E 19 2019 2019 HOH HOH . T 4 HOH E 20 2020 2020 HOH HOH . U 4 HOH F 1 2001 2001 HOH HOH . U 4 HOH F 2 2002 2002 HOH HOH . U 4 HOH F 3 2003 2003 HOH HOH . U 4 HOH F 4 2004 2004 HOH HOH . U 4 HOH F 5 2005 2005 HOH HOH . U 4 HOH F 6 2006 2006 HOH HOH . U 4 HOH F 7 2007 2007 HOH HOH . U 4 HOH F 8 2008 2008 HOH HOH . U 4 HOH F 9 2009 2009 HOH HOH . U 4 HOH F 10 2010 2010 HOH HOH . U 4 HOH F 11 2011 2011 HOH HOH . U 4 HOH F 12 2012 2012 HOH HOH . U 4 HOH F 13 2013 2013 HOH HOH . U 4 HOH F 14 2014 2014 HOH HOH . U 4 HOH F 15 2015 2015 HOH HOH . U 4 HOH F 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 O O4 DUP . . . K 2 -3.516 38.354 -41.558 1 62.47 ? O4 DUP 1130 D 1 HETATM 2 C C4 DUP . . . K 2 -4.621 37.928 -41.903 1 56.62 ? C4 DUP 1130 D 1 HETATM 3 C C5 DUP . . . K 2 -5.749 37.865 -41.085 1 54.59 ? C5 DUP 1130 D 1 HETATM 4 C C6 DUP . . . K 2 -6.941 37.38 -41.562 1 53.27 ? C6 DUP 1130 D 1 HETATM 5 N N3 DUP . . . K 2 -4.658 37.519 -43.155 1 59.25 ? N3 DUP 1130 D 1 HETATM 6 C C2 DUP . . . K 2 -5.817 37.047 -43.59 1 58.52 ? C2 DUP 1130 D 1 HETATM 7 O O2 DUP . . . K 2 -5.797 36.679 -44.762 1 60.18 ? O2 DUP 1130 D 1 HETATM 8 N N1 DUP . . . K 2 -6.937 36.991 -42.842 1 57.73 ? N1 DUP 1130 D 1 HETATM 9 C C1' DUP . . . K 2 -8.148 36.43 -43.442 1 57.46 ? C1' DUP 1130 D 1 HETATM 10 C C2' DUP . . . K 2 -8.453 36.971 -44.83 1 57.82 ? C2' DUP 1130 D 1 HETATM 11 C C3' DUP . . . K 2 -8.327 35.772 -45.755 1 59.3 ? C3' DUP 1130 D 1 HETATM 12 O O3' DUP . . . K 2 -9.415 35.742 -46.666 1 64.14 ? O3' DUP 1130 D 1 HETATM 13 O O4' DUP . . . K 2 -7.938 35.016 -43.575 1 56.39 ? O4' DUP 1130 D 1 HETATM 14 C C4' DUP . . . K 2 -8.346 34.547 -44.859 1 58.03 ? C4' DUP 1130 D 1 HETATM 15 C C5' DUP . . . K 2 -7.407 33.45 -45.312 1 57.81 ? C5' DUP 1130 D 1 HETATM 16 O O5' DUP . . . K 2 -8.159 32.424 -45.919 1 59.27 ? O5' DUP 1130 D 1 HETATM 17 P PA DUP . . . K 2 -7.874 31.882 -47.417 1 63.72 ? PA DUP 1130 D 1 HETATM 18 O O1A DUP . . . K 2 -6.383 31.807 -47.704 1 59.78 ? O1A DUP 1130 D 1 HETATM 19 O O2A DUP . . . K 2 -8.766 30.67 -47.584 1 62.55 ? O2A DUP 1130 D 1 HETATM 20 N N3A DUP . . . K 2 -8.485 33.023 -48.434 1 62.64 ? N3A DUP 1130 D 1 HETATM 21 P PB DUP . . . K 2 -7.404 33.831 -49.371 1 62.31 ? PB DUP 1130 D 1 HETATM 22 O O1B DUP . . . K 2 -6.077 33.995 -48.693 1 61.03 ? O1B DUP 1130 D 1 HETATM 23 O O2B DUP . . . K 2 -8.235 35.013 -49.79 1 67.39 ? O2B DUP 1130 D 1 HETATM 24 O O3B DUP . . . K 2 -7.075 32.89 -50.625 1 66.71 ? O3B DUP 1130 D 1 HETATM 25 P PG DUP . . . K 2 -7.643 33.092 -52.125 1 63.55 ? PG DUP 1130 D 1 HETATM 26 O O2G DUP . . . K 2 -7.678 31.636 -52.518 1 68.25 ? O2G DUP 1130 D 1 HETATM 27 O O1G DUP . . . K 2 -9.053 33.646 -51.911 1 67.25 ? O1G DUP 1130 D 1 HETATM 28 O O3G DUP . . . K 2 -6.622 33.958 -52.866 1 60.84 ? O3G DUP 1130 D 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #