data_6U89 # _model_server_result.job_id 6y3e-lH88qH5pPlRkgrA4A _model_server_result.datetime_utc '2024-11-20 11:35:53' _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 6u89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":102}' # _entry.id 6U89 # _exptl.entry_id 6U89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.187 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one _entity.pdbx_number_of_molecules 2 _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 6U89 _cell.length_a 51.892 _cell.length_b 51.892 _cell.length_c 37.891 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6U89 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,F _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 ? 2 C N N ? 2 D 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 covale ? covale1 A O3' LCC 1 A LCC 1 1_555 A P TLN 2 A TLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale2 A O3' TLN 2 A TLN 2 1_555 A P LCG 3 A LCG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.632 ? covale ? covale3 A O3' LCG 3 A LCG 3 1_555 A P U 4 A U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? covale ? covale4 B O3' LCC 1 B LCC 1 1_555 B P TLN 2 B TLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.624 ? covale ? covale5 B O3' TLN 2 B TLN 2 1_555 B P LCG 3 B LCG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.628 ? covale ? covale6 B O3' LCG 3 B LCG 3 1_555 B P U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? hydrog WATSON-CRICK hydrog1 A N3 TLN 2 A TLN 2 1_555 B N1 A 7 B A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 TLN 2 A TLN 2 1_555 B N6 A 7 B A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 LCG 3 A LCG 3 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 LCG 3 A LCG 3 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 LCG 3 A LCG 3 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 U 4 A U 4 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 U 4 A U 4 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 A 5 A A 5 1_555 B N3 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 A 5 A A 5 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N3 C 6 A C 6 1_555 B N1 LCG 3 B LCG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N4 C 6 A C 6 1_555 B O6 LCG 3 B LCG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O2 C 6 A C 6 1_555 B N2 LCG 3 B LCG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 A 7 A A 7 1_555 B N3 TLN 2 B TLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 A 7 A A 7 1_555 B O4 TLN 2 B TLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H11 N5 O7 P' _chem_comp.formula_weight 332.187 _chem_comp.id TG _chem_comp.mon_nstd_flag n _chem_comp.name 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one _chem_comp.type 'rna linking' _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 N2 C2 TG sing 161 n n N1 C2 TG sing 162 n n N1 C6 TG sing 163 n n O6 C6 TG doub 164 n n C2 N3 TG doub 165 n n C6 C5 TG sing 166 n n N3 C4 TG sing 167 n n C5 C4 TG doub 168 n y C5 N7 TG sing 169 n y C4 N9 TG sing 170 n y N7 C8 TG doub 171 n y N9 C8 TG sing 172 n y N9 C1' TG sing 173 n n C1' O4' TG sing 174 n n C1' C2' TG sing 175 n n O4' C4' TG sing 176 n n C2' O2' TG sing 177 n n C2' C3' TG sing 178 n n C4' C3' TG sing 179 n n C3' O3' TG sing 180 n n O3' P TG sing 181 n n P O1P TG doub 182 n n P O2P TG doub 183 n n C1' H1 TG sing 184 n n C2' H2 TG sing 185 n n C3' H3 TG sing 186 n n C4' H4 TG sing 187 n n C4' H5 TG sing 188 n n C8 H6 TG sing 189 n n N1 H7 TG sing 190 n n N2 H8 TG sing 191 n n N2 H9 TG sing 192 n n O2' H11 TG sing 193 n n P O3P TG sing 194 n n O3P H10 TG sing 195 n n # _atom_sites.entry_id 6U89 _atom_sites.fract_transf_matrix[1][1] 0.019271 _atom_sites.fract_transf_matrix[1][2] 0.011126 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022252 _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] 0.026391 _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 C 2 TG A 1 101 1 TG TFG . D 2 TG A 1 102 2 TG TFG . E 3 HOH A 1 201 4 HOH HOH . E 3 HOH A 2 202 2 HOH HOH . E 3 HOH A 3 203 1 HOH HOH . F 3 HOH B 1 101 3 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 C C1' TG . . . D 2 28.032 19.624 18.638 1 37.42 ? C1' TG 102 A 1 HETATM 2 C C2 TG . . . D 2 32.114 18.699 17.435 1 35.04 ? C2 TG 102 A 1 HETATM 3 C C2' TG . . . D 2 27.916 18.703 19.795 1 43.8 ? C2' TG 102 A 1 HETATM 4 C C3' TG . . . D 2 27.176 19.546 20.827 1 44.02 ? C3' TG 102 A 1 HETATM 5 C C4 TG . . . D 2 30.41 20.12 18.219 1 35.55 ? C4 TG 102 A 1 HETATM 6 C C4' TG . . . D 2 26.177 20.262 20.004 1 40.98 ? C4' TG 102 A 1 HETATM 7 C C5 TG . . . D 2 31.237 21.206 18.287 1 36.55 ? C5 TG 102 A 1 HETATM 8 C C6 TG . . . D 2 32.559 21.044 17.925 1 38.21 ? C6 TG 102 A 1 HETATM 9 C C8 TG . . . D 2 29.309 21.85 18.885 1 33.53 ? C8 TG 102 A 1 HETATM 10 N N1 TG . . . D 2 33.014 19.751 17.5 1 35.93 ? N1 TG 102 A 1 HETATM 11 N N2 TG . . . D 2 32.57 17.525 17.052 1 40.34 ? N2 TG 102 A 1 HETATM 12 N N3 TG . . . D 2 30.82 18.875 17.791 1 34.67 ? N3 TG 102 A 1 HETATM 13 N N7 TG . . . D 2 30.526 22.299 18.704 1 32.52 ? N7 TG 102 A 1 HETATM 14 N N9 TG . . . D 2 29.228 20.532 18.617 1 33.62 ? N9 TG 102 A 1 HETATM 15 O O1P TG . . . D 2 28.473 19.465 23.503 1 50.31 ? O1P TG 102 A 1 HETATM 16 O O2' TG . . . D 2 27.036 17.648 19.4 1 47.66 ? O2' TG 102 A 1 HETATM 17 O O2P TG . . . D 2 28.738 22.001 23.149 1 52.67 ? O2P TG 102 A 1 HETATM 18 O O3' TG . . . D 2 28.006 20.521 21.432 1 45.76 ? O3' TG 102 A 1 HETATM 19 O O4' TG . . . D 2 26.826 20.432 18.74 1 42.45 ? O4' TG 102 A 1 HETATM 20 O O6 TG . . . D 2 33.388 21.982 17.971 1 35.67 ? O6 TG 102 A 1 HETATM 21 P P TG . . . D 2 27.931 20.766 22.97 1 48.58 ? P TG 102 A 1 HETATM 22 O O3P TG . . . D 2 26.489 20.979 23.159 1 57.75 ? O3P TG 102 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 22 #