data_3S8B # _model_server_result.job_id wZLhZwLVgoDlSvyOAWWk4Q _model_server_result.datetime_utc '2024-12-02 11:32:33' _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 3s8b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":889}' # _entry.id 3S8B # _exptl.entry_id 3S8B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 2 _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 3S8B _cell.length_a 107.869 _cell.length_b 117.567 _cell.length_c 64.967 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S8B _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 0 117.567 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 C O3A ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc2 C O1G ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc3 C O2A ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc4 C O1B ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? # _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 3S8B _atom_sites.fract_transf_matrix[1][1] 0.009271 _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] 0.008506 _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] 0.015392 _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 CDP A 1 889 1 CDP CDP . C 3 ANP A 1 890 1 ANP ANP . D 4 MG A 1 891 1 MG MG . E 5 HOH A 1 892 1 HOH HOH . E 5 HOH A 2 893 2 HOH HOH . E 5 HOH A 3 894 4 HOH HOH . E 5 HOH A 4 895 5 HOH HOH . E 5 HOH A 5 896 6 HOH HOH . E 5 HOH A 6 897 9 HOH HOH . E 5 HOH A 7 898 10 HOH HOH . E 5 HOH A 8 899 11 HOH HOH . E 5 HOH A 9 900 12 HOH HOH . E 5 HOH A 10 901 13 HOH HOH . E 5 HOH A 11 902 14 HOH HOH . E 5 HOH A 12 903 16 HOH HOH . E 5 HOH A 13 904 18 HOH HOH . E 5 HOH A 14 905 19 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 22 HOH HOH . E 5 HOH A 18 909 23 HOH HOH . E 5 HOH A 19 910 25 HOH HOH . E 5 HOH A 20 911 26 HOH HOH . E 5 HOH A 21 912 27 HOH HOH . E 5 HOH A 22 913 35 HOH HOH . E 5 HOH A 23 914 37 HOH HOH . E 5 HOH A 24 915 39 HOH HOH . E 5 HOH A 25 916 42 HOH HOH . E 5 HOH A 26 917 43 HOH HOH . E 5 HOH A 27 918 45 HOH HOH . E 5 HOH A 28 919 47 HOH HOH . E 5 HOH A 29 920 48 HOH HOH . E 5 HOH A 30 921 49 HOH HOH . E 5 HOH A 31 922 51 HOH HOH . E 5 HOH A 32 923 52 HOH HOH . E 5 HOH A 33 924 57 HOH HOH . E 5 HOH A 34 925 58 HOH HOH . E 5 HOH A 35 926 59 HOH HOH . E 5 HOH A 36 927 60 HOH HOH . E 5 HOH A 37 928 61 HOH HOH . E 5 HOH A 38 929 63 HOH HOH . E 5 HOH A 39 930 65 HOH HOH . E 5 HOH A 40 931 67 HOH HOH . E 5 HOH A 41 932 68 HOH HOH . E 5 HOH A 42 933 71 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 . . . B 2 28.235 53.377 16.111 1 82.8 ? O3B CDP 889 A 1 HETATM 2 P PB CDP . . . B 2 26.84 52.995 16.469 1 83.17 ? PB CDP 889 A 1 HETATM 3 O O1B CDP . . . B 2 25.774 53.406 15.301 1 83.04 ? O1B CDP 889 A 1 HETATM 4 O O2B CDP . . . B 2 26.322 53.721 17.848 1 82.89 ? O2B CDP 889 A 1 HETATM 5 O O3A CDP . . . B 2 26.711 51.398 16.794 1 82.94 ? O3A CDP 889 A 1 HETATM 6 P PA CDP . . . B 2 25.736 50.338 16.038 1 82.14 ? PA CDP 889 A 1 HETATM 7 O O1A CDP . . . B 2 26.501 49.083 15.899 1 82.01 ? O1A CDP 889 A 1 HETATM 8 O O2A CDP . . . B 2 25.072 50.936 14.85 1 81.99 ? O2A CDP 889 A 1 HETATM 9 O O5' CDP . . . B 2 24.593 50.021 17.142 1 81.47 ? O5' CDP 889 A 1 HETATM 10 C C5' CDP . . . B 2 24.239 50.992 18.126 1 80.97 ? C5' CDP 889 A 1 HETATM 11 C C4' CDP . . . B 2 22.752 50.941 18.491 1 80.49 ? C4' CDP 889 A 1 HETATM 12 O O4' CDP . . . B 2 22.164 52.233 18.135 1 80.3 ? O4' CDP 889 A 1 HETATM 13 C C3' CDP . . . B 2 21.961 49.885 17.719 1 79.72 ? C3' CDP 889 A 1 HETATM 14 O O3' CDP . . . B 2 21.998 48.635 18.407 1 78.92 ? O3' CDP 889 A 1 HETATM 15 C C2' CDP . . . B 2 20.559 50.492 17.727 1 79.68 ? C2' CDP 889 A 1 HETATM 16 O O2' CDP . . . B 2 19.898 50.288 18.996 1 78.53 ? O2' CDP 889 A 1 HETATM 17 C C1' CDP . . . B 2 20.861 51.994 17.523 1 79.99 ? C1' CDP 889 A 1 HETATM 18 N N1 CDP . . . B 2 20.942 52.426 16.094 1 80.29 ? N1 CDP 889 A 1 HETATM 19 C C2 CDP . . . B 2 20.156 53.506 15.64 1 80.18 ? C2 CDP 889 A 1 HETATM 20 O O2 CDP . . . B 2 19.398 54.095 16.415 1 79.92 ? O2 CDP 889 A 1 HETATM 21 N N3 CDP . . . B 2 20.244 53.904 14.286 1 80.1 ? N3 CDP 889 A 1 HETATM 22 C C4 CDP . . . B 2 21.11 53.229 13.399 1 80.07 ? C4 CDP 889 A 1 HETATM 23 N N4 CDP . . . B 2 21.196 53.6 12.128 1 79.92 ? N4 CDP 889 A 1 HETATM 24 C C5 CDP . . . B 2 21.884 52.164 13.847 1 80.31 ? C5 CDP 889 A 1 HETATM 25 C C6 CDP . . . B 2 21.806 51.77 15.18 1 80.42 ? C6 CDP 889 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #