data_3T6Y # _model_server_result.job_id Z9Bcu8m_r1n7vIN6rPN92Q _model_server_result.datetime_utc '2024-10-10 16:31:59' _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 3t6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":400}' # _entry.id 3T6Y # _exptl.entry_id 3T6Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 397.428 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine" _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 3T6Y _cell.length_a 76.83 _cell.length_b 76.83 _cell.length_c 106.13 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T6Y _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,J,K,L,M,N,O,P _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 ? 3 E N N ? 3 G N N ? 3 I N N # _chem_comp.formula 'C20 H23 N5 O4' _chem_comp.formula_weight 397.428 _chem_comp.id DU2 _chem_comp.mon_nstd_flag . _chem_comp.name "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine" _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 N1 C2 DU2 sing 83 n n N1 C6 DU2 sing 84 n n N1 C1' DU2 sing 85 n n C2 O2 DU2 doub 86 n n C2 N3 DU2 sing 87 n n N3 C4 DU2 sing 88 n n C4 O4 DU2 doub 89 n n C4 C5 DU2 sing 90 n n C5 C6 DU2 doub 91 n n C1' C2' DU2 sing 92 n n C1' O4' DU2 sing 93 n n C17 C18 DU2 sing 94 n n C17 C24 DU2 sing 95 n n C17 N5' DU2 sing 96 n n C18 C19 DU2 doub 97 n y C18 C23 DU2 sing 98 n y C19 C20 DU2 sing 99 n y C2' C3' DU2 sing 100 n n C20 C21 DU2 doub 101 n y C21 C22 DU2 sing 102 n y C22 C23 DU2 doub 103 n y C24 N25 DU2 doub 104 n y C24 N28 DU2 sing 105 n y N25 C26 DU2 sing 106 n y C26 C27 DU2 doub 107 n y C27 N28 DU2 sing 108 n y N28 C29 DU2 sing 109 n n C3' C4' DU2 sing 110 n n C3' O41 DU2 sing 111 n n C4' O4' DU2 sing 112 n n C4' C5' DU2 sing 113 n n C5' N5' DU2 sing 114 n n N3 HN3 DU2 sing 115 n n C5 H5 DU2 sing 116 n n C6 H6 DU2 sing 117 n n C1' H1' DU2 sing 118 n n C17 H17 DU2 sing 119 n n C19 H19 DU2 sing 120 n n C2' H2' DU2 sing 121 n n C2' "H2'A" DU2 sing 122 n n C20 H20 DU2 sing 123 n n C21 H21 DU2 sing 124 n n C22 H22 DU2 sing 125 n n C23 H23 DU2 sing 126 n n C26 H26 DU2 sing 127 n n C27 H27 DU2 sing 128 n n C29 H29 DU2 sing 129 n n C29 H29A DU2 sing 130 n n C29 H29B DU2 sing 131 n n C3' H3' DU2 sing 132 n n C4' H4' DU2 sing 133 n n O41 HO41 DU2 sing 134 n n C5' H5' DU2 sing 135 n n C5' "H5'A" DU2 sing 136 n n N5' HN5' DU2 sing 137 n n # _atom_sites.entry_id 3T6Y _atom_sites.fract_transf_matrix[1][1] 0.013016 _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] 0.013016 _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] 0.009422 _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 E 3 DU2 A 1 400 400 DU2 DU2 . F 4 SO4 A 1 182 182 SO4 SO4 . G 3 DU2 B 1 400 400 DU2 DU2 . H 4 SO4 B 1 182 182 SO4 SO4 . I 3 DU2 C 1 400 400 DU2 DU2 . J 4 SO4 C 1 182 182 SO4 SO4 . K 4 SO4 C 1 183 183 SO4 SO4 . L 4 SO4 C 1 184 184 SO4 SO4 . M 5 HOH A 1 183 183 HOH HOH . M 5 HOH A 2 184 184 HOH HOH . M 5 HOH A 3 185 185 HOH HOH . M 5 HOH A 4 186 186 HOH HOH . M 5 HOH A 5 187 187 HOH HOH . M 5 HOH A 6 188 188 HOH HOH . M 5 HOH A 7 189 189 HOH HOH . M 5 HOH A 8 190 190 HOH HOH . M 5 HOH A 9 191 191 HOH HOH . M 5 HOH A 10 192 192 HOH HOH . M 5 HOH A 11 193 193 HOH HOH . M 5 HOH A 12 194 194 HOH HOH . M 5 HOH A 13 195 195 HOH HOH . M 5 HOH A 14 196 196 HOH HOH . M 5 HOH A 15 197 197 HOH HOH . M 5 HOH A 16 198 198 HOH HOH . M 5 HOH A 17 199 199 HOH HOH . M 5 HOH A 18 200 200 HOH HOH . M 5 HOH A 19 201 201 HOH HOH . M 5 HOH A 20 202 202 HOH HOH . M 5 HOH A 21 203 203 HOH HOH . M 5 HOH A 22 204 204 HOH HOH . M 5 HOH A 23 205 205 HOH HOH . M 5 HOH A 24 206 206 HOH HOH . M 5 HOH A 25 207 207 HOH HOH . M 5 HOH A 26 208 208 HOH HOH . M 5 HOH A 27 209 209 HOH HOH . M 5 HOH A 28 210 210 HOH HOH . M 5 HOH A 29 211 211 HOH HOH . M 5 HOH A 30 212 212 HOH HOH . M 5 HOH A 31 213 213 HOH HOH . M 5 HOH A 32 214 214 HOH HOH . M 5 HOH A 33 215 215 HOH HOH . M 5 HOH A 34 216 216 HOH HOH . M 5 HOH A 35 217 217 HOH HOH . M 5 HOH A 36 218 218 HOH HOH . M 5 HOH A 37 219 219 HOH HOH . M 5 HOH A 38 220 220 HOH HOH . M 5 HOH A 39 221 221 HOH HOH . M 5 HOH A 40 222 222 HOH HOH . M 5 HOH A 41 223 223 HOH HOH . M 5 HOH A 42 224 224 HOH HOH . M 5 HOH A 43 225 225 HOH HOH . M 5 HOH A 44 226 226 HOH HOH . M 5 HOH A 45 227 227 HOH HOH . M 5 HOH A 46 228 228 HOH HOH . M 5 HOH A 47 229 229 HOH HOH . M 5 HOH A 48 230 230 HOH HOH . M 5 HOH A 49 231 1 HOH HOH . M 5 HOH A 50 232 4 HOH HOH . M 5 HOH A 51 233 5 HOH HOH . N 5 HOH B 1 183 183 HOH HOH . N 5 HOH B 2 184 184 HOH HOH . N 5 HOH B 3 185 185 HOH HOH . N 5 HOH B 4 186 186 HOH HOH . N 5 HOH B 5 187 187 HOH HOH . N 5 HOH B 6 188 188 HOH HOH . N 5 HOH B 7 189 189 HOH HOH . N 5 HOH B 8 190 190 HOH HOH . N 5 HOH B 9 191 191 HOH HOH . N 5 HOH B 10 192 192 HOH HOH . N 5 HOH B 11 193 193 HOH HOH . N 5 HOH B 12 194 194 HOH HOH . N 5 HOH B 13 195 195 HOH HOH . N 5 HOH B 14 196 196 HOH HOH . N 5 HOH B 15 197 197 HOH HOH . N 5 HOH B 16 198 198 HOH HOH . N 5 HOH B 17 199 199 HOH HOH . N 5 HOH B 18 200 200 HOH HOH . N 5 HOH B 19 201 201 HOH HOH . N 5 HOH B 20 202 202 HOH HOH . N 5 HOH B 21 203 203 HOH HOH . N 5 HOH B 22 204 204 HOH HOH . N 5 HOH B 23 205 205 HOH HOH . N 5 HOH B 24 206 206 HOH HOH . N 5 HOH B 25 207 207 HOH HOH . N 5 HOH B 26 208 208 HOH HOH . N 5 HOH B 27 209 209 HOH HOH . N 5 HOH B 28 210 210 HOH HOH . N 5 HOH B 29 211 211 HOH HOH . N 5 HOH B 30 212 212 HOH HOH . N 5 HOH B 31 213 213 HOH HOH . N 5 HOH B 32 214 214 HOH HOH . N 5 HOH B 33 215 207 HOH HOH . N 5 HOH B 34 216 3 HOH HOH . O 5 HOH C 1 185 185 HOH HOH . O 5 HOH C 2 186 186 HOH HOH . O 5 HOH C 3 187 187 HOH HOH . O 5 HOH C 4 188 188 HOH HOH . O 5 HOH C 5 189 189 HOH HOH . O 5 HOH C 6 190 190 HOH HOH . O 5 HOH C 7 191 191 HOH HOH . O 5 HOH C 8 192 192 HOH HOH . O 5 HOH C 9 193 193 HOH HOH . O 5 HOH C 10 194 194 HOH HOH . O 5 HOH C 11 195 195 HOH HOH . O 5 HOH C 12 196 196 HOH HOH . O 5 HOH C 13 197 197 HOH HOH . O 5 HOH C 14 198 198 HOH HOH . O 5 HOH C 15 199 199 HOH HOH . O 5 HOH C 16 200 200 HOH HOH . O 5 HOH C 17 201 201 HOH HOH . O 5 HOH C 18 202 202 HOH HOH . O 5 HOH C 19 203 203 HOH HOH . O 5 HOH C 20 204 204 HOH HOH . O 5 HOH C 21 205 205 HOH HOH . O 5 HOH C 22 206 206 HOH HOH . O 5 HOH C 23 207 2 HOH HOH . O 5 HOH C 24 208 208 HOH HOH . O 5 HOH C 25 209 209 HOH HOH . O 5 HOH C 26 210 210 HOH HOH . O 5 HOH C 27 211 211 HOH HOH . O 5 HOH C 28 212 212 HOH HOH . O 5 HOH C 29 213 213 HOH HOH . O 5 HOH C 30 214 214 HOH HOH . O 5 HOH C 31 215 215 HOH HOH . O 5 HOH C 32 216 216 HOH HOH . O 5 HOH C 33 217 217 HOH HOH . O 5 HOH C 34 218 218 HOH HOH . O 5 HOH C 35 219 219 HOH HOH . O 5 HOH C 36 220 220 HOH HOH . O 5 HOH C 37 221 221 HOH HOH . O 5 HOH C 38 222 222 HOH HOH . O 5 HOH C 39 223 223 HOH HOH . O 5 HOH C 40 224 224 HOH HOH . O 5 HOH C 41 225 225 HOH HOH . P 5 HOH F 1 41 41 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 DU2 . . . I 3 17.709 21.784 -0.311 1 25.23 ? N1 DU2 400 C 1 HETATM 2 C C2 DU2 . . . I 3 18.477 22.746 -0.831 1 24.47 ? C2 DU2 400 C 1 HETATM 3 O O2 DU2 . . . I 3 19.686 22.605 -0.761 1 26.51 ? O2 DU2 400 C 1 HETATM 4 N N3 DU2 . . . I 3 17.946 23.843 -1.436 1 23.06 ? N3 DU2 400 C 1 HETATM 5 C C4 DU2 . . . I 3 16.593 23.921 -1.525 1 25.41 ? C4 DU2 400 C 1 HETATM 6 O O4 DU2 . . . I 3 16.063 24.874 -2.09 1 24.69 ? O4 DU2 400 C 1 HETATM 7 C C5 DU2 . . . I 3 15.795 22.935 -0.976 1 26.17 ? C5 DU2 400 C 1 HETATM 8 C C6 DU2 . . . I 3 16.354 21.863 -0.354 1 25.88 ? C6 DU2 400 C 1 HETATM 9 C C1' DU2 . . . I 3 18.37 20.668 0.333 1 28.22 ? C1' DU2 400 C 1 HETATM 10 C C17 DU2 . . . I 3 18.245 18.512 -4.09 1 51.12 ? C17 DU2 400 C 1 HETATM 11 C C18 DU2 . . . I 3 17.689 19.732 -4.491 1 39.64 ? C18 DU2 400 C 1 HETATM 12 C C19 DU2 . . . I 3 18.091 20.929 -3.887 1 35.99 ? C19 DU2 400 C 1 HETATM 13 C C2' DU2 . . . I 3 17.457 19.987 1.365 1 30.13 ? C2' DU2 400 C 1 HETATM 14 C C20 DU2 . . . I 3 17.533 22.154 -4.309 1 34.83 ? C20 DU2 400 C 1 HETATM 15 C C21 DU2 . . . I 3 16.572 22.201 -5.332 1 31.55 ? C21 DU2 400 C 1 HETATM 16 C C22 DU2 . . . I 3 16.189 20.98 -5.911 1 31.66 ? C22 DU2 400 C 1 HETATM 17 C C23 DU2 . . . I 3 16.722 19.756 -5.51 1 31.96 ? C23 DU2 400 C 1 HETATM 18 C C24 DU2 . . . I 3 19.186 17.833 -4.898 1 69.03 ? C24 DU2 400 C 1 HETATM 19 N N25 DU2 . . . I 3 19.741 16.661 -4.55 1 89.34 ? N25 DU2 400 C 1 HETATM 20 C C26 DU2 . . . I 3 20.733 16.181 -5.542 1 88.41 ? C26 DU2 400 C 1 HETATM 21 C C27 DU2 . . . I 3 20.709 17.255 -6.612 1 74.91 ? C27 DU2 400 C 1 HETATM 22 N N28 DU2 . . . I 3 19.733 18.197 -6.062 1 70.62 ? N28 DU2 400 C 1 HETATM 23 C C29 DU2 . . . I 3 19.409 19.39 -6.761 1 73.16 ? C29 DU2 400 C 1 HETATM 24 C C3' DU2 . . . I 3 16.748 18.965 0.515 1 32.61 ? C3' DU2 400 C 1 HETATM 25 C C4' DU2 . . . I 3 17.754 18.579 -0.555 1 34.01 ? C4' DU2 400 C 1 HETATM 26 O O4' DU2 . . . I 3 18.631 19.737 -0.737 1 32.9 ? O4' DU2 400 C 1 HETATM 27 O O41 DU2 . . . I 3 16.55 17.863 1.328 1 35.65 ? O41 DU2 400 C 1 HETATM 28 C C5' DU2 . . . I 3 16.954 18.411 -1.834 1 36.68 ? C5' DU2 400 C 1 HETATM 29 N N5' DU2 . . . I 3 17.862 17.81 -2.822 1 48.97 ? N5' DU2 400 C 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 29 #