data_2YAY # _model_server_result.job_id io1_jyleto10yq-m_A355A _model_server_result.datetime_utc '2024-11-08 04:33:18' _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 2yay # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1265}' # _entry.id 2YAY # _exptl.entry_id 2YAY _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 1 _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 2YAY _cell.length_a 86.83 _cell.length_b 86.83 _cell.length_c 145.28 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YAY _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -43.415 75.196986 -24.213333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A OE1 GLU 51 A GLU 48 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? metalc ? metalc2 A OE2 GLU 51 A GLU 48 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 A OE1 GLU 51 A GLU 48 1_555 D CA CA . A CA 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc4 A OE1 GLU 54 A GLU 51 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc5 A OE2 GLU 54 A GLU 51 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc6 A OE1 GLU 54 A GLU 51 1_555 D CA CA . A CA 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc7 A OE1 GLU 79 A GLU 76 1_555 D CA CA . A CA 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc8 A OD2 ASP 82 A ASP 79 1_555 D CA CA . A CA 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc9 B O2A DUP . A DUP 1265 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc10 B O1B DUP . A DUP 1265 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc11 B O1G DUP . A DUP 1265 1_555 C CA CA . A CA 1266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc12 B O1B DUP . A DUP 1265 1_555 D CA CA . A CA 1267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc13 C CA CA . A CA 1266 1_555 E O HOH . A HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc14 D CA CA . A CA 1267 1_555 E O HOH . A HOH 2026 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? # _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 2YAY _atom_sites.fract_transf_matrix[1][1] 0.011517 _atom_sites.fract_transf_matrix[1][2] 0.006649 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013298 _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] 0.006883 _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 B 2 DUP A 1 1265 1265 DUP DUP . C 3 CA A 1 1266 1266 CA CA . D 3 CA A 1 1267 1267 CA CA . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . E 4 HOH A 14 2014 2014 HOH HOH . E 4 HOH A 15 2015 2015 HOH HOH . E 4 HOH A 16 2016 2016 HOH HOH . E 4 HOH A 17 2017 2017 HOH HOH . E 4 HOH A 18 2018 2018 HOH HOH . E 4 HOH A 19 2019 2019 HOH HOH . E 4 HOH A 20 2020 2020 HOH HOH . E 4 HOH A 21 2021 2021 HOH HOH . E 4 HOH A 22 2022 2022 HOH HOH . E 4 HOH A 23 2023 2023 HOH HOH . E 4 HOH A 24 2024 2024 HOH HOH . E 4 HOH A 25 2025 2025 HOH HOH . E 4 HOH A 26 2026 2026 HOH HOH . E 4 HOH A 27 2027 2027 HOH HOH . E 4 HOH A 28 2028 2028 HOH HOH . E 4 HOH A 29 2029 2029 HOH HOH . E 4 HOH A 30 2030 2030 HOH HOH . E 4 HOH A 31 2031 2031 HOH HOH . E 4 HOH A 32 2032 2032 HOH HOH . E 4 HOH A 33 2033 2033 HOH HOH . E 4 HOH A 34 2034 2034 HOH HOH . E 4 HOH A 35 2035 2035 HOH HOH . E 4 HOH A 36 2036 2036 HOH HOH . E 4 HOH A 37 2037 2037 HOH HOH . E 4 HOH A 38 2038 2038 HOH HOH . E 4 HOH A 39 2039 2039 HOH HOH . E 4 HOH A 40 2040 2040 HOH HOH . E 4 HOH A 41 2041 2041 HOH HOH . E 4 HOH A 42 2042 2042 HOH HOH . E 4 HOH A 43 2043 2043 HOH HOH . E 4 HOH A 44 2044 2044 HOH HOH . E 4 HOH A 45 2045 2045 HOH HOH . E 4 HOH A 46 2046 2046 HOH HOH . E 4 HOH A 47 2047 2047 HOH HOH . E 4 HOH A 48 2048 2048 HOH HOH . E 4 HOH A 49 2049 2049 HOH HOH . E 4 HOH A 50 2050 2050 HOH HOH . E 4 HOH A 51 2051 2051 HOH HOH . E 4 HOH A 52 2052 2052 HOH HOH . E 4 HOH A 53 2053 2053 HOH HOH . E 4 HOH A 54 2054 2054 HOH HOH . E 4 HOH A 55 2055 2055 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 . . . B 2 -5.879 28.163 -4.083 1 22.35 ? O4 DUP 1265 A 1 HETATM 2 C C4 DUP . . . B 2 -6.937 28.796 -3.59 1 19.03 ? C4 DUP 1265 A 1 HETATM 3 C C5 DUP . . . B 2 -7.988 29.028 -4.501 1 23.11 ? C5 DUP 1265 A 1 HETATM 4 C C6 DUP . . . B 2 -9.134 29.6 -4.012 1 23.06 ? C6 DUP 1265 A 1 HETATM 5 N N3 DUP . . . B 2 -7.056 29.128 -2.286 1 21.95 ? N3 DUP 1265 A 1 HETATM 6 C C2 DUP . . . B 2 -8.176 29.701 -1.849 1 23.81 ? C2 DUP 1265 A 1 HETATM 7 O O2 DUP . . . B 2 -8.268 30.076 -0.666 1 24.9 ? O2 DUP 1265 A 1 HETATM 8 N N1 DUP . . . B 2 -9.2 29.976 -2.715 1 24.56 ? N1 DUP 1265 A 1 HETATM 9 C C1' DUP . . . B 2 -10.417 30.604 -2.205 1 19.91 ? C1' DUP 1265 A 1 HETATM 10 C C2' DUP . . . B 2 -10.272 31.976 -1.637 1 25.7 ? C2' DUP 1265 A 1 HETATM 11 C C3' DUP . . . B 2 -11.601 32.662 -1.804 1 33.57 ? C3' DUP 1265 A 1 HETATM 12 O O3' DUP . . . B 2 -12.298 32.854 -0.544 1 26.91 ? O3' DUP 1265 A 1 HETATM 13 O O4' DUP . . . B 2 -11.438 30.78 -3.221 1 20.5 ? O4' DUP 1265 A 1 HETATM 14 C C4' DUP . . . B 2 -12.34 31.72 -2.707 1 16.96 ? C4' DUP 1265 A 1 HETATM 15 C C5' DUP . . . B 2 -12.991 32.364 -3.913 1 21.29 ? C5' DUP 1265 A 1 HETATM 16 O O5' DUP . . . B 2 -13.565 31.34 -4.738 1 22.5 ? O5' DUP 1265 A 1 HETATM 17 P PA DUP . . . B 2 -14.453 31.758 -6.061 1 24.99 ? PA DUP 1265 A 1 HETATM 18 O O1A DUP . . . B 2 -14.452 30.553 -6.915 1 23.58 ? O1A DUP 1265 A 1 HETATM 19 O O2A DUP . . . B 2 -13.883 33.063 -6.569 1 23.69 ? O2A DUP 1265 A 1 HETATM 20 N N3A DUP . . . B 2 -16.044 32.098 -5.657 1 22.51 ? N3A DUP 1265 A 1 HETATM 21 P PB DUP . . . B 2 -16.587 33.343 -4.694 1 28.24 ? PB DUP 1265 A 1 HETATM 22 O O1B DUP . . . B 2 -15.836 34.727 -4.821 1 22.03 ? O1B DUP 1265 A 1 HETATM 23 O O2B DUP . . . B 2 -16.684 32.867 -3.247 1 32.06 ? O2B DUP 1265 A 1 HETATM 24 O O3B DUP . . . B 2 -18.024 33.569 -5.418 1 53.15 ? O3B DUP 1265 A 1 HETATM 25 P PG DUP . . . B 2 -18.047 33.893 -7.042 1 80.34 ? PG DUP 1265 A 1 HETATM 26 O O2G DUP . . . B 2 -18.111 32.577 -7.826 1 36.99 ? O2G DUP 1265 A 1 HETATM 27 O O1G DUP . . . B 2 -16.759 34.608 -7.535 1 38.28 ? O1G DUP 1265 A 1 HETATM 28 O O3G DUP . . . B 2 -19.27 34.767 -7.064 1 74.43 ? O3G DUP 1265 A 1 # _model_server_stats.io_time_ms 101 _model_server_stats.parse_time_ms 128 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #