data_6U8F # _model_server_result.job_id Ik5d9nV0zPHK5axD9ep7Vg _model_server_result.datetime_utc '2024-12-01 06:57:16' _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 6u8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 6U8F # _exptl.entry_id 6U8F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 332.187 _entity.id 3 _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 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 120 _cell.entry_id 6U8F _cell.length_a 69.631 _cell.length_b 69.631 _cell.length_c 70.514 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6U8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 _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 # _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 hydrog WATSON-CRICK hydrog1 A N3 C 1 A C 1 1_555 B N1 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 C 1 A C 1 1_555 B O6 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 C 1 A C 1 1_555 B N2 G 12 B G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog4 A N3 U 2 A U 2 1_555 B O2 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_16_PAIR hydrog5 A O4 U 2 A U 2 1_555 B N3 U 11 B U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 G 3 A G 3 1_555 B N3 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N2 G 3 A G 3 1_555 B O2 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O6 G 3 A G 3 1_555 B N4 C 10 B C 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 C 4 A C 4 1_555 B N1 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 C 4 A C 4 1_555 B O6 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 C 4 A C 4 1_555 B N2 G 9 B G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-U MISPAIR' hydrog12 A O4 U 5 A U 5 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 G 6 A G 6 1_555 B N3 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N2 G 6 A G 6 1_555 B O2 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O6 G 6 A G 6 1_555 B N4 C 7 B C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 G 7 A G 7 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 G 7 A G 7 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 G 7 A G 7 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 C 8 A C 8 1_555 B N1 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N4 C 8 A C 8 1_555 B O6 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O2 C 8 A C 8 1_555 B N2 G 5 B G 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog22 A N3 U 9 A U 9 1_555 B N7 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog23 A O2 U 9 A U 9 1_555 B N6 A 3 B A 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 A 11 A A 11 1_555 B N3 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N6 A 11 A A 11 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog26 A N1 G 12 A G 12 1_555 B O2 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog27 A O6 G 12 A G 12 1_555 B N3 U 2 B U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-U MISPAIR' hydrog28 A N2 G 12 A G 12 1_555 B O4 U 4 B U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N1 G 13 A G 13 1_555 B N3 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N2 G 13 A G 13 1_555 B O2 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O6 G 13 A G 13 1_555 B N4 C 1 B C 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N1 A 15 A A 15 1_555 A N3 U 22 A U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N6 A 15 A A 15 1_555 A O4 U 22 A U 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog34 A N3 U 16 A U 16 1_555 A O6 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog35 A O2 U 16 A U 16 1_555 A N1 G 21 A G 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog36 A N2 G 17 A G 17 1_555 A N7 A 20 A A 20 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 116 n n N1 C2 TG sing 117 n n N1 C6 TG sing 118 n n O6 C6 TG doub 119 n n C2 N3 TG doub 120 n n C6 C5 TG sing 121 n n N3 C4 TG sing 122 n n C5 C4 TG doub 123 n y C5 N7 TG sing 124 n y C4 N9 TG sing 125 n y N7 C8 TG doub 126 n y N9 C8 TG sing 127 n y N9 C1' TG sing 128 n n C1' O4' TG sing 129 n n C1' C2' TG sing 130 n n O4' C4' TG sing 131 n n C2' O2' TG sing 132 n n C2' C3' TG sing 133 n n C4' C3' TG sing 134 n n C3' O3' TG sing 135 n n O3' P TG sing 136 n n P O1P TG doub 137 n n P O2P TG doub 138 n n C1' H1 TG sing 139 n n C2' H2 TG sing 140 n n C3' H3 TG sing 141 n n C4' H4 TG sing 142 n n C4' H5 TG sing 143 n n C8 H6 TG sing 144 n n N1 H7 TG sing 145 n n N2 H8 TG sing 146 n n N2 H9 TG sing 147 n n O2' H11 TG sing 148 n n P O3P TG sing 149 n n O3P H10 TG sing 150 n n # _atom_sites.entry_id 6U8F _atom_sites.fract_transf_matrix[1][1] 0.014361 _atom_sites.fract_transf_matrix[1][2] 0.008292 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016583 _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] 0.014182 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id TG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id TG _pdbx_nonpoly_scheme.auth_mon_id TFG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 3 4.928 32.927 -10.351 1 109.6 ? C1' TG 101 A 1 HETATM 2 C C2 TG . . . C 3 1.565 30.62 -11.837 1 88.73 ? C2 TG 101 A 1 HETATM 3 C C2' TG . . . C 3 4.778 33.479 -9.032 1 119.58 ? C2' TG 101 A 1 HETATM 4 C C3' TG . . . C 3 6.228 33.684 -8.61 1 125.8 ? C3' TG 101 A 1 HETATM 5 C C4 TG . . . C 3 3.788 30.853 -11.036 1 82.18 ? C4 TG 101 A 1 HETATM 6 C C4' TG . . . C 3 6.813 34.368 -9.788 1 130.34 ? C4' TG 101 A 1 HETATM 7 C C5 TG . . . C 3 4.03 29.514 -11.198 1 80.64 ? C5 TG 101 A 1 HETATM 8 C C6 TG . . . C 3 3.055 28.721 -11.682 1 75.68 ? C6 TG 101 A 1 HETATM 9 C C8 TG . . . C 3 5.87 30.399 -10.43 1 92.89 ? C8 TG 101 A 1 HETATM 10 N N1 TG . . . C 3 1.786 29.233 -12.003 1 73.98 ? N1 TG 101 A 1 HETATM 11 N N2 TG . . . C 3 0.342 31.102 -12.15 1 87.49 ? N2 TG 101 A 1 HETATM 12 N N3 TG . . . C 3 2.585 31.413 -11.359 1 74.09 ? N3 TG 101 A 1 HETATM 13 N N7 TG . . . C 3 5.319 29.225 -10.826 1 82.26 ? N7 TG 101 A 1 HETATM 14 N N9 TG . . . C 3 4.923 31.396 -10.532 1 100.64 ? N9 TG 101 A 1 HETATM 15 O O1P TG . . . C 3 6.812 31.573 -6.421 1 154.49 ? O1P TG 101 A 1 HETATM 16 O O2' TG . . . C 3 4.105 34.725 -9.309 1 117.27 ? O2' TG 101 A 1 HETATM 17 O O2P TG . . . C 3 8.545 30.833 -8.049 1 161.86 ? O2P TG 101 A 1 HETATM 18 O O3' TG . . . C 3 6.855 32.421 -8.556 1 135.93 ? O3' TG 101 A 1 HETATM 19 O O4' TG . . . C 3 6.204 33.574 -10.852 1 144.82 ? O4' TG 101 A 1 HETATM 20 O O6 TG . . . C 3 3.271 27.523 -11.855 1 75.44 ? O6 TG 101 A 1 HETATM 21 P P TG . . . C 3 7.833 31.966 -7.443 1 173.35 ? P TG 101 A 1 HETATM 22 O O3P TG . . . C 3 8.658 33.177 -7.171 1 133.44 ? O3P TG 101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 22 #