data_5U6R # _model_server_result.job_id H17zhzmRtjGgRilbNyN_4w _model_server_result.datetime_utc '2024-11-22 13:14:52' _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 5u6r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 5U6R # _exptl.entry_id 5U6R _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 483.156 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 28-meric 28 'representative helical assembly' 1 ? tetrameric 4 'helical asymmetric unit' 2 ? tetrameric 4 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L 1 (1-7) A,B,C,D,E,F,G,H,I,J,K,L 2 4 A,B,C,D,E,F,G,H,I,J,K,L 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'helical symmetry operation' ? ? -0.82599 0.563685 0 -0.563685 -0.82599 0 0 0 1 0 0 -244.773 2 'helical symmetry operation' ? ? -0.124052 0.992276 0 -0.992276 -0.124052 0 0 0 1 0 0 -163.182 3 'helical symmetry operation' ? ? 0.661796 0.749684 0 -0.749684 0.661796 0 0 0 1 0 0 -81.591 4 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 5 'helical symmetry operation' ? ? 0.661796 -0.749684 0 0.749684 0.661796 0 0 0 1 0 0 81.591 6 'helical symmetry operation' ? ? -0.124052 -0.992276 0 0.992276 -0.124052 0 0 0 1 0 0 163.182 7 'helical symmetry operation' ? ? -0.82599 -0.563685 0 0.563685 -0.82599 0 0 0 1 0 0 244.773 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 disulf ? disulf1 A SG CYS 261 A CYS 261 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 B SG CYS 261 B CYS 261 1_555 B SG CYS 268 B CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 C SG CYS 261 C CYS 261 1_555 C SG CYS 268 C CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf4 D SG CYS 261 D CYS 261 1_555 D SG CYS 268 D CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id CTP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-TRIPHOSPHATE" _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 CTP sing 114 n n N1 C6 CTP sing 115 n n N1 C1' CTP sing 116 n n C2 N3 CTP sing 117 n n C2 O2 CTP doub 118 n n N3 C4 CTP doub 119 n n C4 C5 CTP sing 120 n n C4 N4 CTP sing 121 n n C5 C6 CTP doub 122 n n C5 H5 CTP sing 123 n n C6 H6 CTP sing 124 n n N4 HN41 CTP sing 125 n n N4 HN42 CTP sing 126 n n C1' C2' CTP sing 127 n n C1' O4' CTP sing 128 n n C1' H1' CTP sing 129 n n C2' O2' CTP sing 130 n n C2' C3' CTP sing 131 n n C2' H2' CTP sing 132 n n O2' HO2' CTP sing 133 n n C3' C4' CTP sing 134 n n C3' O3' CTP sing 135 n n C3' H3' CTP sing 136 n n C4' O4' CTP sing 137 n n C4' C5' CTP sing 138 n n C4' H4' CTP sing 139 n n O3' HO3' CTP sing 140 n n C5' O5' CTP sing 141 n n C5' "H5'1" CTP sing 142 n n C5' "H5'2" CTP sing 143 n n O5' PA CTP sing 144 n n PA O1A CTP doub 145 n n PA O2A CTP sing 146 n n PA O3A CTP sing 147 n n O2A HOA2 CTP sing 148 n n O3A PB CTP sing 149 n n PB O1B CTP doub 150 n n PB O2B CTP sing 151 n n PB O3B CTP sing 152 n n O2B HOB2 CTP sing 153 n n O3B PG CTP sing 154 n n PG O1G CTP doub 155 n n PG O2G CTP sing 156 n n PG O3G CTP sing 157 n n O2G HOG2 CTP sing 158 n n O3G HOG3 CTP sing 159 n n # _atom_sites.entry_id 5U6R _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 CTP A 1 601 602 CTP CTP . F 3 ADP A 1 602 601 ADP ADP . G 2 CTP B 1 601 602 CTP CTP . H 3 ADP B 1 602 601 ADP ADP . I 2 CTP C 1 601 602 CTP CTP . J 3 ADP C 1 602 601 ADP ADP . K 2 CTP D 1 601 602 CTP CTP . L 3 ADP D 1 602 601 ADP ADP . # 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 CTP . . . G 2 -0.499 -13.438 -12.003 1 38.6 ? N1 CTP 601 B 1 HETATM 2 C C2 CTP . . . G 2 0.089 -13.325 -10.703 1 41.36 ? C2 CTP 601 B 1 HETATM 3 N N3 CTP . . . G 2 -0.361 -12.34 -9.874 1 40.2 ? N3 CTP 601 B 1 HETATM 4 C C4 CTP . . . G 2 -1.58 -11.733 -10.161 1 38.26 ? C4 CTP 601 B 1 HETATM 5 C C5 CTP . . . G 2 -2.3 -12.106 -11.306 1 35.37 ? C5 CTP 601 B 1 HETATM 6 C C6 CTP . . . G 2 -1.727 -12.896 -12.274 1 36.32 ? C6 CTP 601 B 1 HETATM 7 O O2 CTP . . . G 2 1.146 -13.885 -10.449 1 42.93 ? O2 CTP 601 B 1 HETATM 8 N N4 CTP . . . G 2 -1.909 -10.613 -9.514 1 43.37 ? N4 CTP 601 B 1 HETATM 9 C C1' CTP . . . G 2 0.286 -14.029 -13.091 1 38.7 ? C1' CTP 601 B 1 HETATM 10 C C2' CTP . . . G 2 0.098 -15.481 -13.343 1 41.49 ? C2' CTP 601 B 1 HETATM 11 O O2' CTP . . . G 2 1.152 -16.215 -12.713 1 42.81 ? O2' CTP 601 B 1 HETATM 12 C C3' CTP . . . G 2 0.227 -15.595 -14.871 1 43.09 ? C3' CTP 601 B 1 HETATM 13 C C4' CTP . . . G 2 0.217 -14.159 -15.37 1 36.38 ? C4' CTP 601 B 1 HETATM 14 O O4' CTP . . . G 2 -0.319 -13.423 -14.267 1 38.44 ? O4' CTP 601 B 1 HETATM 15 O O3' CTP . . . G 2 1.472 -16.197 -15.198 1 48.47 ? O3' CTP 601 B 1 HETATM 16 C C5' CTP . . . G 2 -0.687 -14.023 -16.612 1 42.49 ? C5' CTP 601 B 1 HETATM 17 O O5' CTP . . . G 2 -0.257 -12.929 -17.373 1 43.36 ? O5' CTP 601 B 1 HETATM 18 P PA CTP . . . G 2 0.838 -13.105 -18.529 1 40.11 ? PA CTP 601 B 1 HETATM 19 O O1A CTP . . . G 2 1.237 -11.777 -19.038 1 41.92 ? O1A CTP 601 B 1 HETATM 20 O O2A CTP . . . G 2 1.909 -14.063 -18.152 1 29.56 ? O2A CTP 601 B 1 HETATM 21 O O3A CTP . . . G 2 -0.007 -13.909 -19.643 1 44.15 ? O3A CTP 601 B 1 HETATM 22 P PB CTP . . . G 2 -1.626 -14.249 -19.631 1 37.55 ? PB CTP 601 B 1 HETATM 23 O O1B CTP . . . G 2 -2.059 -14.871 -20.892 1 38.41 ? O1B CTP 601 B 1 HETATM 24 O O2B CTP . . . G 2 -2.055 -14.905 -18.372 1 44.65 ? O2B CTP 601 B 1 HETATM 25 O O3B CTP . . . G 2 -2.216 -12.747 -19.558 1 39.65 ? O3B CTP 601 B 1 HETATM 26 P PG CTP . . . G 2 -1.341 -11.368 -19.884 1 43.25 ? PG CTP 601 B 1 HETATM 27 O O1G CTP . . . G 2 -0.287 -11.525 -20.912 1 52.65 ? O1G CTP 601 B 1 HETATM 28 O O2G CTP . . . G 2 -0.786 -10.864 -18.462 1 42.39 ? O2G CTP 601 B 1 HETATM 29 O O3G CTP . . . G 2 -2.44 -10.283 -20.33 1 48.69 ? O3G CTP 601 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #