data_1BDU # _model_server_result.job_id 6Bc9dGOFNXel9_Pdka904Q _model_server_result.datetime_utc '2024-11-24 17:25:26' _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 1bdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1BDU # _exptl.entry_id 1BDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 228.202 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE" _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 1BDU _cell.length_a 133.05 _cell.length_b 133.05 _cell.length_c 133.05 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 16_555 x,-y,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 0 66.525 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 covale ? covale1 A C FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A O2 FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? # _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 ? # _atom_sites.entry_id 1BDU _atom_sites.fract_transf_matrix[1][1] 0.007516 _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] 0.007516 _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] 0.007516 _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 PO4 A 1 603 603 PO4 PO4 . C 3 DUR A 1 301 301 DUR DUR . D 4 HOH A 1 750 750 HOH HOH . D 4 HOH A 2 751 751 HOH HOH . D 4 HOH A 3 752 752 HOH HOH . D 4 HOH A 4 753 753 HOH HOH . D 4 HOH A 5 754 754 HOH HOH . D 4 HOH A 6 755 755 HOH HOH . D 4 HOH A 7 756 756 HOH HOH . D 4 HOH A 8 758 758 HOH HOH . D 4 HOH A 9 759 759 HOH HOH . D 4 HOH A 10 760 760 HOH HOH . D 4 HOH A 11 761 761 HOH HOH . D 4 HOH A 12 762 762 HOH HOH . D 4 HOH A 13 763 763 HOH HOH . D 4 HOH A 14 764 764 HOH HOH . D 4 HOH A 15 765 765 HOH HOH . D 4 HOH A 16 766 766 HOH HOH . D 4 HOH A 17 767 767 HOH HOH . D 4 HOH A 18 768 768 HOH HOH . D 4 HOH A 19 769 769 HOH HOH . D 4 HOH A 20 770 770 HOH HOH . D 4 HOH A 21 771 771 HOH HOH . D 4 HOH A 22 772 772 HOH HOH . D 4 HOH A 23 773 773 HOH HOH . D 4 HOH A 24 774 774 HOH HOH . D 4 HOH A 25 775 775 HOH HOH . D 4 HOH A 26 776 776 HOH HOH . D 4 HOH A 27 777 777 HOH HOH . D 4 HOH A 28 778 778 HOH HOH . D 4 HOH A 29 779 779 HOH HOH . D 4 HOH A 30 780 780 HOH HOH . D 4 HOH A 31 781 781 HOH HOH . D 4 HOH A 32 782 782 HOH HOH . D 4 HOH A 33 783 783 HOH HOH . D 4 HOH A 34 784 784 HOH HOH . D 4 HOH A 35 785 785 HOH HOH . D 4 HOH A 36 786 786 HOH HOH . D 4 HOH A 37 787 787 HOH HOH . D 4 HOH A 38 788 788 HOH HOH . D 4 HOH A 39 789 789 HOH HOH . D 4 HOH A 40 790 790 HOH HOH . D 4 HOH A 41 791 791 HOH HOH . D 4 HOH A 42 792 792 HOH HOH . D 4 HOH A 43 793 793 HOH HOH . D 4 HOH A 44 794 794 HOH HOH . D 4 HOH A 45 795 795 HOH HOH . D 4 HOH A 46 796 796 HOH HOH . D 4 HOH A 47 797 797 HOH HOH . D 4 HOH A 48 798 798 HOH HOH . D 4 HOH A 49 799 799 HOH HOH . D 4 HOH A 50 800 800 HOH HOH . D 4 HOH A 51 801 801 HOH HOH . D 4 HOH A 52 802 802 HOH HOH . D 4 HOH A 53 803 803 HOH HOH . D 4 HOH A 54 804 804 HOH HOH . D 4 HOH A 55 805 805 HOH HOH . D 4 HOH A 56 806 806 HOH HOH . D 4 HOH A 57 807 807 HOH HOH . D 4 HOH A 58 808 808 HOH HOH . D 4 HOH A 59 809 809 HOH HOH . D 4 HOH A 60 810 810 HOH HOH . D 4 HOH A 61 811 811 HOH HOH . D 4 HOH A 62 812 812 HOH HOH . D 4 HOH A 63 813 813 HOH HOH . D 4 HOH A 64 816 816 HOH HOH . D 4 HOH A 65 817 817 HOH HOH . D 4 HOH A 66 818 818 HOH HOH . D 4 HOH A 67 819 819 HOH HOH . D 4 HOH A 68 820 820 HOH HOH . D 4 HOH A 69 821 821 HOH HOH . D 4 HOH A 70 822 822 HOH HOH . D 4 HOH A 71 823 823 HOH HOH . D 4 HOH A 72 824 824 HOH HOH . D 4 HOH A 73 825 825 HOH HOH . D 4 HOH A 74 826 826 HOH HOH . D 4 HOH A 75 827 827 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 . . . C 3 -28.487 -8.988 20.192 1 73.23 ? N1 DUR 301 A 1 HETATM 2 C C2 DUR . . . C 3 -27.488 -8.02 20.228 1 70.87 ? C2 DUR 301 A 1 HETATM 3 N N3 DUR . . . C 3 -27.912 -6.723 20.094 1 74.54 ? N3 DUR 301 A 1 HETATM 4 C C4 DUR . . . C 3 -29.228 -6.307 19.916 1 76.87 ? C4 DUR 301 A 1 HETATM 5 C C5 DUR . . . C 3 -30.196 -7.393 19.876 1 78.12 ? C5 DUR 301 A 1 HETATM 6 C C6 DUR . . . C 3 -29.77 -8.715 20.015 1 74.44 ? C6 DUR 301 A 1 HETATM 7 O O2 DUR . . . C 3 -26.292 -8.259 20.326 1 61.5 ? O2 DUR 301 A 1 HETATM 8 O O4 DUR . . . C 3 -29.516 -5.108 19.883 1 72.34 ? O4 DUR 301 A 1 HETATM 9 C C1' DUR . . . C 3 -28.125 -10.401 20.419 1 73.96 ? C1' DUR 301 A 1 HETATM 10 C C2' DUR . . . C 3 -28.252 -10.829 21.873 1 72.83 ? C2' DUR 301 A 1 HETATM 11 C C3' DUR . . . C 3 -28.108 -12.332 21.793 1 70.19 ? C3' DUR 301 A 1 HETATM 12 C C4' DUR . . . C 3 -29.083 -12.569 20.633 1 73.69 ? C4' DUR 301 A 1 HETATM 13 O O3' DUR . . . C 3 -26.773 -12.637 21.378 1 65.5 ? O3' DUR 301 A 1 HETATM 14 O O4' DUR . . . C 3 -28.834 -11.462 19.688 1 74.25 ? O4' DUR 301 A 1 HETATM 15 C C5' DUR . . . C 3 -30.537 -12.526 21.144 1 76.41 ? C5' DUR 301 A 1 HETATM 16 O O5' DUR . . . C 3 -31.496 -12.761 20.106 1 79.08 ? O5' DUR 301 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #