data_3MJA # _model_server_result.job_id 3sUnl8uhRHAypKfrlYQqGQ _model_server_result.datetime_utc '2024-11-25 04:13:43' _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 3mja # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":103}' # _entry.id 3MJA # _exptl.entry_id 3MJA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 142.958 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SELENATE ION' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation U6198U _entity.pdbx_fragment 'Domain 3 RNA' _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3MJA _cell.length_a 59.25 _cell.length_b 59.25 _cell.length_c 99.775 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MJA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F 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 hydrog WATSON-CRICK hydrog1 A N1 G 1 B G 6174 1_555 A N3 C 29 B C 6202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 B G 6174 1_555 A O2 C 29 B C 6202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 B G 6174 1_555 A N4 C 29 B C 6202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 B G 6175 1_555 A N3 C 28 B C 6201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 B G 6175 1_555 A O2 C 28 B C 6201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 B G 6175 1_555 A N4 C 28 B C 6201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 3 B U 6176 1_555 A N1 A 27 B A 6200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 3 B U 6176 1_555 A N6 A 27 B A 6200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog9 A O2 U 4 B U 6177 1_555 A N2 G 26 B G 6199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 A 5 B A 6178 1_555 A N3 U 25 B U 6198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 A 5 B A 6178 1_555 A O4 U 25 B U 6198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 U 6 B U 6179 1_555 A N1 A 24 B A 6197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A O4 U 6 B U 6179 1_555 A N6 A 24 B A 6197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N3 U 7 B U 6180 1_555 A N1 A 23 B A 6196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O4 U 7 B U 6180 1_555 A N6 A 23 B A 6196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 C 8 B C 6181 1_555 A N1 G 22 B G 6195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 C 8 B C 6181 1_555 A O6 G 22 B G 6195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 C 8 B C 6181 1_555 A N2 G 22 B G 6195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N1 G 10 B G 6183 1_555 A N3 C 21 B C 6194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N2 G 10 B G 6183 1_555 A O2 C 21 B C 6194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O6 G 10 B G 6183 1_555 A N4 C 21 B C 6194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N1 A 11 B A 6184 1_555 A N3 U 20 B U 6193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N6 A 11 B A 6184 1_555 A O4 U 20 B U 6193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N1 A 14 B A 6187 1_555 B N3 U 14 C U 6216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N6 A 14 B A 6187 1_555 B O4 U 14 C U 6216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N1 G 15 B G 6188 1_555 B N3 C 13 C C 6215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N2 G 15 B G 6188 1_555 B O2 C 13 C C 6215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O6 G 15 B G 6188 1_555 B N4 C 13 C C 6215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N1 G 16 B G 6189 1_555 B N3 C 12 C C 6214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A N2 G 16 B G 6189 1_555 B O2 C 12 C C 6214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A O6 G 16 B G 6189 1_555 B N4 C 12 C C 6214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N3 U 17 B U 6190 1_555 B N1 A 11 C A 6213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O4 U 17 B U 6190 1_555 B N6 A 11 C A 6213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 A 18 B A 6191 1_555 B N3 U 10 C U 6212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N6 A 18 B A 6191 1_555 B O4 U 10 C U 6212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog36 A N2 G 19 B G 6192 1_555 B N3 A 7 C A 6209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'O4 Se -2' _chem_comp.formula_weight 142.958 _chem_comp.id SE4 _chem_comp.mon_nstd_flag . _chem_comp.name 'SELENATE ION' _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 SE O1 SE4 doub 116 n n SE O2 SE4 doub 117 n n SE O3 SE4 sing 118 n n SE O4 SE4 sing 119 n n # _atom_sites.entry_id 3MJA _atom_sites.fract_transf_matrix[1][1] 0.016878 _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] 0.016878 _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] 0.010023 _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 3 SE4 B 1 100 100 SE4 SE4 . D 3 SE4 B 1 103 103 SE4 SE4 . E 3 SE4 C 1 101 101 SE4 SE4 . F 3 SE4 C 1 102 102 SE4 SE4 . # 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 SE SE SE4 . . . D 3 18.865 -32.125 25.316 1 98.9 ? SE SE4 103 B 1 HETATM 2 O O1 SE4 . . . D 3 17.76 -32.669 24.481 1 98.15 ? O1 SE4 103 B 1 HETATM 3 O O2 SE4 . . . D 3 20.139 -32.746 24.866 1 99.37 ? O2 SE4 103 B 1 HETATM 4 O O3 SE4 . . . D 3 18.951 -30.648 25.142 1 97.91 ? O3 SE4 103 B 1 HETATM 5 O O4 SE4 . . . D 3 18.619 -32.444 26.751 1 96.96 ? O4 SE4 103 B 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 5 #