data_3S8C # _model_server_result.job_id PdujCjQvI7wLOixVx-8PkQ _model_server_result.datetime_utc '2024-12-02 12:03:15' _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 3s8c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":891}' # _entry.id 3S8C # _exptl.entry_id 3S8C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 3S8C _cell.length_a 107.781 _cell.length_b 116.81 _cell.length_c 64.126 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S8C _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 116.81 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 metalc ? metalc1 B O1A ANP . A ANP 889 1_555 C MG MG . A MG 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 B O2B ANP . A ANP 889 1_555 C MG MG . A MG 890 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc3 C MG MG . A MG 890 1_555 E O HOH . A HOH 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _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 O3B PB CDP sing 120 n n PB O1B CDP doub 121 n n PB O2B CDP sing 122 n n PB O3A CDP sing 123 n n O3A PA CDP sing 124 n n PA O1A CDP doub 125 n n PA O2A CDP sing 126 n n PA O5' CDP sing 127 n n O5' C5' CDP sing 128 n n C5' C4' CDP sing 129 n n C5' "H5'1" CDP sing 130 n n C5' "H5'2" CDP sing 131 n n C4' O4' CDP sing 132 n n C4' C3' CDP sing 133 n n C4' H4' CDP sing 134 n n O4' C1' CDP sing 135 n n C3' O3' CDP sing 136 n n C3' C2' CDP sing 137 n n C3' H3' CDP sing 138 n n O3' HA CDP sing 139 n n C2' O2' CDP sing 140 n n C2' C1' CDP sing 141 n n C2' H2' CDP sing 142 n n O2' HB CDP sing 143 n n C1' N1 CDP sing 144 n n C1' H1' CDP sing 145 n n N1 C2 CDP sing 146 n n N1 C6 CDP sing 147 n n C2 O2 CDP doub 148 n n C2 N3 CDP sing 149 n n N3 C4 CDP doub 150 n n C4 N4 CDP sing 151 n n C4 C5 CDP sing 152 n n N4 H4N1 CDP sing 153 n n N4 H4N2 CDP sing 154 n n C5 C6 CDP doub 155 n n C5 H5 CDP sing 156 n n C6 H6 CDP sing 157 n n HO1 O2A CDP sing 158 n n HO2 O2B CDP sing 159 n n HO3 O3B CDP sing 160 n n # _atom_sites.entry_id 3S8C _atom_sites.fract_transf_matrix[1][1] 0.009278 _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] 0.008561 _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] 0.015594 _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 B 2 ANP A 1 889 1 ANP ANP . C 3 MG A 1 890 1 MG MG . D 4 CDP A 1 891 1 CDP CDP . E 5 HOH A 1 892 1 HOH HOH . E 5 HOH A 2 893 2 HOH HOH . E 5 HOH A 3 894 3 HOH HOH . E 5 HOH A 4 895 4 HOH HOH . E 5 HOH A 5 896 5 HOH HOH . E 5 HOH A 6 897 7 HOH HOH . E 5 HOH A 7 898 8 HOH HOH . E 5 HOH A 8 899 9 HOH HOH . E 5 HOH A 9 900 10 HOH HOH . E 5 HOH A 10 901 11 HOH HOH . E 5 HOH A 11 902 14 HOH HOH . E 5 HOH A 12 903 15 HOH HOH . E 5 HOH A 13 904 16 HOH HOH . E 5 HOH A 14 905 18 HOH HOH . E 5 HOH A 15 906 20 HOH HOH . E 5 HOH A 16 907 21 HOH HOH . E 5 HOH A 17 908 23 HOH HOH . E 5 HOH A 18 909 24 HOH HOH . E 5 HOH A 19 910 28 HOH HOH . E 5 HOH A 20 911 29 HOH HOH . E 5 HOH A 21 912 30 HOH HOH . E 5 HOH A 22 913 32 HOH HOH . E 5 HOH A 23 914 34 HOH HOH . E 5 HOH A 24 915 35 HOH HOH . E 5 HOH A 25 916 36 HOH HOH . E 5 HOH A 26 917 42 HOH HOH . E 5 HOH A 27 918 45 HOH HOH . E 5 HOH A 28 919 48 HOH HOH . E 5 HOH A 29 920 52 HOH HOH . E 5 HOH A 30 921 54 HOH HOH . E 5 HOH A 31 922 55 HOH HOH . E 5 HOH A 32 923 57 HOH HOH . E 5 HOH A 33 924 59 HOH HOH . E 5 HOH A 34 925 67 HOH HOH . E 5 HOH A 35 926 69 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 O O3B CDP . . . D 4 27.453 52.439 17.549 1 66.75 ? O3B CDP 891 A 1 HETATM 2 P PB CDP . . . D 4 27.381 52.637 16.051 1 66.58 ? PB CDP 891 A 1 HETATM 3 O O1B CDP . . . D 4 28.807 52.213 15.365 1 64.92 ? O1B CDP 891 A 1 HETATM 4 O O2B CDP . . . D 4 27.123 54.136 15.601 1 65.73 ? O2B CDP 891 A 1 HETATM 5 O O3A CDP . . . D 4 26.151 51.866 15.286 1 68.47 ? O3A CDP 891 A 1 HETATM 6 P PA CDP . . . D 4 25.889 50.237 15.463 1 70.26 ? PA CDP 891 A 1 HETATM 7 O O1A CDP . . . D 4 26.768 49.578 16.458 1 66.97 ? O1A CDP 891 A 1 HETATM 8 O O2A CDP . . . D 4 25.792 49.695 14.089 1 70.57 ? O2A CDP 891 A 1 HETATM 9 O O5' CDP . . . D 4 24.438 50.226 16.075 1 71.71 ? O5' CDP 891 A 1 HETATM 10 C C5' CDP . . . D 4 23.4 51.019 15.512 1 73.13 ? C5' CDP 891 A 1 HETATM 11 C C4' CDP . . . D 4 22.409 51.234 16.65 1 76.19 ? C4' CDP 891 A 1 HETATM 12 O O4' CDP . . . D 4 22.946 52.13 17.71 1 76.46 ? O4' CDP 891 A 1 HETATM 13 C C3' CDP . . . D 4 21.14 51.877 16.124 1 77.47 ? C3' CDP 891 A 1 HETATM 14 O O3' CDP . . . D 4 20.169 50.85 15.973 1 79.43 ? O3' CDP 891 A 1 HETATM 15 C C2' CDP . . . D 4 20.731 52.696 17.316 1 77.51 ? C2' CDP 891 A 1 HETATM 16 O O2' CDP . . . D 4 20.229 51.771 18.289 1 78.25 ? O2' CDP 891 A 1 HETATM 17 C C1' CDP . . . D 4 22.062 53.28 17.795 1 76.33 ? C1' CDP 891 A 1 HETATM 18 N N1 CDP . . . D 4 22.445 54.534 17.026 1 75.92 ? N1 CDP 891 A 1 HETATM 19 C C2 CDP . . . D 4 21.964 55.787 17.48 1 75.88 ? C2 CDP 891 A 1 HETATM 20 O O2 CDP . . . D 4 21.242 55.85 18.48 1 74.58 ? O2 CDP 891 A 1 HETATM 21 N N3 CDP . . . D 4 22.314 56.961 16.764 1 75.54 ? N3 CDP 891 A 1 HETATM 22 C C4 CDP . . . D 4 23.145 56.89 15.6 1 75.9 ? C4 CDP 891 A 1 HETATM 23 N N4 CDP . . . D 4 23.468 58.003 14.94 1 75.41 ? N4 CDP 891 A 1 HETATM 24 C C5 CDP . . . D 4 23.633 55.665 15.154 1 74.66 ? C5 CDP 891 A 1 HETATM 25 C C6 CDP . . . D 4 23.267 54.513 15.859 1 76.16 ? C6 CDP 891 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #