data_3ZF0 # _model_server_result.job_id EflNS7yHUG4MfTW5pQZ8-w _model_server_result.datetime_utc '2024-11-05 01:22:07' _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 3zf0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":777}' # _entry.id 3ZF0 # _exptl.entry_id 3ZF0 _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 90 _cell.entry_id 3ZF0 _cell.length_a 87.12 _cell.length_b 87.12 _cell.length_c 87.12 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZF0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 3 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 # _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 OD1 ASP 129 A ASP 95 9_555 D NI NI . A NI 1157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc2 A OD1 ASP 129 A ASP 95 1_555 D NI NI . A NI 1157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc3 A OD1 ASP 129 A ASP 95 5_555 D NI NI . A NI 1157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? # _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 70 n n C4 C5 DUP sing 71 n y C4 N3 DUP sing 72 n y C5 C6 DUP doub 73 n y C5 H5 DUP sing 74 n n C6 N1 DUP sing 75 n y C6 H6 DUP sing 76 n n N3 C2 DUP sing 77 n y N3 HN3 DUP sing 78 n n C2 O2 DUP doub 79 n n C2 N1 DUP sing 80 n y N1 C1' DUP sing 81 n n C1' C2' DUP sing 82 n n C1' O4' DUP sing 83 n n C1' H1' DUP sing 84 n n C2' C3' DUP sing 85 n n C2' "H2'1" DUP sing 86 n n C2' "H2'2" DUP sing 87 n n C3' O3' DUP sing 88 n n C3' C4' DUP sing 89 n n C3' H1 DUP sing 90 n n O3' H3' DUP sing 91 n n O4' C4' DUP sing 92 n n C4' C5' DUP sing 93 n n C4' H4' DUP sing 94 n n C5' O5' DUP sing 95 n n C5' "H5'1" DUP sing 96 n n C5' "H5'2" DUP sing 97 n n O5' PA DUP sing 98 n n PA O1A DUP doub 99 n n PA O2A DUP sing 100 n n PA N3A DUP sing 101 n n O2A H2A DUP sing 102 n n N3A PB DUP sing 103 n n N3A H3A DUP sing 104 n n PB O1B DUP doub 105 n n PB O2B DUP sing 106 n n PB O3B DUP sing 107 n n O2B H2B DUP sing 108 n n O3B PG DUP sing 109 n n PG O2G DUP doub 110 n n PG O1G DUP sing 111 n n PG O3G DUP sing 112 n n O1G H1G DUP sing 113 n n O3G H3G DUP sing 114 n n # _atom_sites.entry_id 3ZF0 _atom_sites.fract_transf_matrix[1][1] 0.011478 _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] 0.011478 _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] 0.011478 _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 1 777 777 DUP DUP . C 3 NI A 1 1156 1156 NI NI . D 3 NI A 1 1157 1157 NI NI . E 4 HOH A 1 2002 2002 HOH HOH . E 4 HOH A 2 2003 2003 HOH HOH . E 4 HOH A 3 2004 2004 HOH HOH . E 4 HOH A 4 2005 2005 HOH HOH . E 4 HOH A 5 2006 2006 HOH HOH . E 4 HOH A 6 2007 2007 HOH HOH . E 4 HOH A 7 2008 2008 HOH HOH . E 4 HOH A 8 2009 2009 HOH HOH . E 4 HOH A 9 2010 2010 HOH HOH . E 4 HOH A 10 2011 2011 HOH HOH . E 4 HOH A 11 2012 2012 HOH HOH . E 4 HOH A 12 2013 2013 HOH HOH . E 4 HOH A 13 2014 2014 HOH HOH . E 4 HOH A 14 2015 2015 HOH HOH . E 4 HOH A 15 2016 2016 HOH HOH . E 4 HOH A 16 2017 2017 HOH HOH . E 4 HOH A 17 2018 2018 HOH HOH . E 4 HOH A 18 2019 2019 HOH HOH . E 4 HOH A 19 2020 2020 HOH HOH . E 4 HOH A 20 2021 2021 HOH HOH . E 4 HOH A 21 2022 2022 HOH HOH . E 4 HOH A 22 2024 2024 HOH HOH . E 4 HOH A 23 2025 2025 HOH HOH . E 4 HOH A 24 2026 2026 HOH HOH . E 4 HOH A 25 2027 2027 HOH HOH . E 4 HOH A 26 2028 2028 HOH HOH . E 4 HOH A 27 2029 2029 HOH HOH . E 4 HOH A 28 2030 2030 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 6.627 5.91 -6.823 1 162.97 ? O4 DUP 777 A 1 HETATM 2 C C4 DUP . . . B 2 6.199 6.085 -7.985 1 170.11 ? C4 DUP 777 A 1 HETATM 3 C C5 DUP . . . B 2 4.963 6.7 -8.181 1 173.48 ? C5 DUP 777 A 1 HETATM 4 C C6 DUP . . . B 2 4.491 6.888 -9.48 1 182.21 ? C6 DUP 777 A 1 HETATM 5 N N3 DUP . . . B 2 6.923 5.681 -9.044 1 173.32 ? N3 DUP 777 A 1 HETATM 6 C C2 DUP . . . B 2 6.479 5.859 -10.303 1 176.83 ? C2 DUP 777 A 1 HETATM 7 O O2 DUP . . . B 2 7.193 5.466 -11.255 1 175.43 ? O2 DUP 777 A 1 HETATM 8 N N1 DUP . . . B 2 5.218 6.483 -10.542 1 180.75 ? N1 DUP 777 A 1 HETATM 9 C C1' DUP . . . B 2 4.714 6.692 -11.922 1 179.93 ? C1' DUP 777 A 1 HETATM 10 C C2' DUP . . . B 2 3.599 5.716 -12.29 1 179.72 ? C2' DUP 777 A 1 HETATM 11 C C3' DUP . . . B 2 2.375 6.56 -12.605 1 176.81 ? C3' DUP 777 A 1 HETATM 12 O O3' DUP . . . B 2 1.889 6.279 -13.921 1 173.29 ? O3' DUP 777 A 1 HETATM 13 O O4' DUP . . . B 2 4.19 8.016 -12.107 1 179.96 ? O4' DUP 777 A 1 HETATM 14 C C4' DUP . . . B 2 2.815 8.014 -12.51 1 179.27 ? C4' DUP 777 A 1 HETATM 15 C C5' DUP . . . B 2 1.994 8.826 -11.506 1 187 ? C5' DUP 777 A 1 HETATM 16 O O5' DUP . . . B 2 0.74 8.206 -11.219 1 198.21 ? O5' DUP 777 A 1 HETATM 17 P PA DUP . . . B 2 0.054 8.331 -9.765 1 205.38 ? PA DUP 777 A 1 HETATM 18 O O1A DUP . . . B 2 0.799 7.52 -8.773 1 202.9 ? O1A DUP 777 A 1 HETATM 19 O O2A DUP . . . B 2 -1.459 7.792 -9.874 1 209.21 ? O2A DUP 777 A 1 HETATM 20 N N3A DUP . . . B 2 0.042 10.004 -9.257 1 217.57 ? N3A DUP 777 A 1 HETATM 21 P PB DUP . . . B 2 -0.601 11.237 -10.32 1 236.17 ? PB DUP 777 A 1 HETATM 22 O O1B DUP . . . B 2 0.378 12.348 -10.416 1 232.7 ? O1B DUP 777 A 1 HETATM 23 O O2B DUP . . . B 2 -1.98 11.786 -9.694 1 243.65 ? O2B DUP 777 A 1 HETATM 24 O O3B DUP . . . B 2 -0.866 10.614 -11.79 1 251.21 ? O3B DUP 777 A 1 HETATM 25 P PG DUP . . . B 2 -2.197 10.937 -12.645 1 261.5 ? PG DUP 777 A 1 HETATM 26 O O2G DUP . . . B 2 -3.296 10.184 -11.925 1 267.97 ? O2G DUP 777 A 1 HETATM 27 O O1G DUP . . . B 2 -1.887 10.404 -14.026 1 260.91 ? O1G DUP 777 A 1 HETATM 28 O O3G DUP . . . B 2 -2.323 12.442 -12.578 1 264.32 ? O3G DUP 777 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #