data_6U89 # _model_server_result.job_id t6OXYN2jt4Sy-HrAmJwbsA _model_server_result.datetime_utc '2024-11-20 11:32:35' _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":"C","auth_seq_id":101}' # _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 . . . C 2 35.078 32.528 -0.448 1 42.33 ? C1' TG 101 A 1 HETATM 2 C C2 TG . . . C 2 38.305 30 0.692 1 38.33 ? C2 TG 101 A 1 HETATM 3 C C2' TG . . . C 2 36.03 33.3 -1.314 1 52.54 ? C2' TG 101 A 1 HETATM 4 C C3' TG . . . C 2 35.124 33.613 -2.496 1 51.8 ? C3' TG 101 A 1 HETATM 5 C C4 TG . . . C 2 36.179 30.407 -0.097 1 38.61 ? C4 TG 101 A 1 HETATM 6 C C4' TG . . . C 2 33.847 33.926 -1.791 1 49.88 ? C4' TG 101 A 1 HETATM 7 C C5 TG . . . C 2 35.885 29.081 -0.188 1 37.09 ? C5 TG 101 A 1 HETATM 8 C C6 TG . . . C 2 36.814 28.188 0.166 1 36.5 ? C6 TG 101 A 1 HETATM 9 C C8 TG . . . C 2 34.16 30.164 -0.867 1 37.01 ? C8 TG 101 A 1 HETATM 10 N N1 TG . . . C 2 38.036 28.67 0.566 1 37.51 ? N1 TG 101 A 1 HETATM 11 N N2 TG . . . C 2 39.52 30.312 1.123 1 35.84 ? N2 TG 101 A 1 HETATM 12 N N3 TG . . . C 2 37.357 30.887 0.36 1 35.96 ? N3 TG 101 A 1 HETATM 13 N N7 TG . . . C 2 34.635 28.934 -0.692 1 37.58 ? N7 TG 101 A 1 HETATM 14 N N9 TG . . . C 2 35.109 31.065 -0.528 1 39.53 ? N9 TG 101 A 1 HETATM 15 O O1P TG . . . C 2 35.979 32.793 -5.155 1 52.27 ? O1P TG 101 A 1 HETATM 16 O O2' TG . . . C 2 36.447 34.481 -0.565 1 55.33 ? O2' TG 101 A 1 HETATM 17 O O2P TG . . . C 2 34.048 31.068 -5.152 1 54.67 ? O2P TG 101 A 1 HETATM 18 O O3' TG . . . C 2 34.847 32.408 -3.244 1 55.67 ? O3' TG 101 A 1 HETATM 19 O O4' TG . . . C 2 33.756 32.799 -0.939 1 45.62 ? O4' TG 101 A 1 HETATM 20 O O6 TG . . . C 2 36.676 26.941 0.102 1 33.66 ? O6 TG 101 A 1 HETATM 21 P P TG . . . C 2 34.578 32.438 -4.802 1 64.77 ? P TG 101 A 1 HETATM 22 O O3P TG . . . C 2 33.635 33.531 -5.066 1 75.37 ? O3P TG 101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #