data_3EE3 # _model_server_result.job_id yiIewiepE9qEiPtZRKSdwQ _model_server_result.datetime_utc '2024-11-27 13:13:07' _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 3ee3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":164}' # _entry.id 3EE3 # _exptl.entry_id 3EE3 _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 6 _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 3EE3 _cell.length_a 82.419 _cell.length_b 154.419 _cell.length_c 187.039 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EE3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,K,L,O,P,S,U,W 1 1,2 B,D,F,I,J,M,N,Q,R,T,V,X 2 1,3 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 164.838 0 93.5195 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q 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 metalc ? metalc1 G O3B CDP . A CDP 160 1_555 H MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 G O1A CDP . A CDP 160 1_555 H MG MG . A MG 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc3 I O3B CDP . B CDP 161 1_555 J MG MG . B MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc4 I O1A CDP . B CDP 161 1_555 J MG MG . B MG 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 K O3B CDP . C CDP 162 1_555 L MG MG . C MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc6 K O1A CDP . C CDP 162 1_555 L MG MG . C MG 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc7 M O1A CDP . D CDP 163 1_555 N MG MG . D MG 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc8 O O3B CDP . E CDP 164 1_555 P MG MG . E MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc9 O O1A CDP . E CDP 164 1_555 P MG MG . E MG 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc10 Q O3B CDP . F CDP 165 1_555 R MG MG . F MG 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc11 Q O1A CDP . F CDP 165 1_555 R MG MG . F MG 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _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 70 n n PB O1B CDP doub 71 n n PB O2B CDP sing 72 n n PB O3A CDP sing 73 n n O3A PA CDP sing 74 n n PA O1A CDP doub 75 n n PA O2A CDP sing 76 n n PA O5' CDP sing 77 n n O5' C5' CDP sing 78 n n C5' C4' CDP sing 79 n n C5' "H5'1" CDP sing 80 n n C5' "H5'2" CDP sing 81 n n C4' O4' CDP sing 82 n n C4' C3' CDP sing 83 n n C4' H4' CDP sing 84 n n O4' C1' CDP sing 85 n n C3' O3' CDP sing 86 n n C3' C2' CDP sing 87 n n C3' H3' CDP sing 88 n n O3' HA CDP sing 89 n n C2' O2' CDP sing 90 n n C2' C1' CDP sing 91 n n C2' H2' CDP sing 92 n n O2' HB CDP sing 93 n n C1' N1 CDP sing 94 n n C1' H1' CDP sing 95 n n N1 C2 CDP sing 96 n n N1 C6 CDP sing 97 n n C2 O2 CDP doub 98 n n C2 N3 CDP sing 99 n n N3 C4 CDP doub 100 n n C4 N4 CDP sing 101 n n C4 C5 CDP sing 102 n n N4 H4N1 CDP sing 103 n n N4 H4N2 CDP sing 104 n n C5 C6 CDP doub 105 n n C5 H5 CDP sing 106 n n C6 H6 CDP sing 107 n n HO1 O2A CDP sing 108 n n HO2 O2B CDP sing 109 n n HO3 O3B CDP sing 110 n n # _atom_sites.entry_id 3EE3 _atom_sites.fract_transf_matrix[1][1] 0.012133 _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] 0.006476 _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] 0.005346 _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 G 2 CDP A 1 160 160 CDP CDP . H 3 MG A 1 161 161 MG MG . I 2 CDP B 1 161 161 CDP CDP . J 3 MG B 1 162 162 MG MG . K 2 CDP C 1 162 162 CDP CDP . L 3 MG C 1 163 163 MG MG . M 2 CDP D 1 163 163 CDP CDP . N 3 MG D 1 164 164 MG MG . O 2 CDP E 1 164 164 CDP CDP . P 3 MG E 1 165 165 MG MG . Q 2 CDP F 1 165 165 CDP CDP . R 3 MG F 1 166 166 MG MG . S 4 HOH A 1 162 162 HOH HOH . S 4 HOH A 2 163 163 HOH HOH . S 4 HOH A 3 164 164 HOH HOH . S 4 HOH A 4 165 165 HOH HOH . S 4 HOH A 5 166 166 HOH HOH . S 4 HOH A 6 167 167 HOH HOH . S 4 HOH A 7 168 168 HOH HOH . S 4 HOH A 8 169 169 HOH HOH . S 4 HOH A 9 170 170 HOH HOH . S 4 HOH A 10 171 171 HOH HOH . S 4 HOH A 11 172 172 HOH HOH . S 4 HOH A 12 173 173 HOH HOH . S 4 HOH A 13 174 174 HOH HOH . S 4 HOH A 14 175 175 HOH HOH . S 4 HOH A 15 176 176 HOH HOH . S 4 HOH A 16 177 177 HOH HOH . S 4 HOH A 17 178 178 HOH HOH . S 4 HOH A 18 179 179 HOH HOH . S 4 HOH A 19 180 180 HOH HOH . S 4 HOH A 20 181 181 HOH HOH . S 4 HOH A 21 182 182 HOH HOH . S 4 HOH A 22 183 183 HOH HOH . S 4 HOH A 23 184 184 HOH HOH . S 4 HOH A 24 185 185 HOH HOH . S 4 HOH A 25 186 186 HOH HOH . S 4 HOH A 26 187 187 HOH HOH . S 4 HOH A 27 188 188 HOH HOH . S 4 HOH A 28 189 189 HOH HOH . S 4 HOH A 29 190 190 HOH HOH . S 4 HOH A 30 191 191 HOH HOH . S 4 HOH A 31 192 192 HOH HOH . S 4 HOH A 32 193 193 HOH HOH . T 4 HOH B 1 163 163 HOH HOH . T 4 HOH B 2 164 164 HOH HOH . T 4 HOH B 3 165 165 HOH HOH . T 4 HOH B 4 166 166 HOH HOH . T 4 HOH B 5 167 167 HOH HOH . T 4 HOH B 6 168 168 HOH HOH . T 4 HOH B 7 169 169 HOH HOH . T 4 HOH B 8 170 170 HOH HOH . T 4 HOH B 9 171 171 HOH HOH . T 4 HOH B 10 172 172 HOH HOH . T 4 HOH B 11 173 173 HOH HOH . T 4 HOH B 12 174 174 HOH HOH . T 4 HOH B 13 175 175 HOH HOH . T 4 HOH B 14 176 176 HOH HOH . T 4 HOH B 15 177 177 HOH HOH . T 4 HOH B 16 178 178 HOH HOH . T 4 HOH B 17 179 179 HOH HOH . T 4 HOH B 18 180 180 HOH HOH . T 4 HOH B 19 181 181 HOH HOH . T 4 HOH B 20 182 182 HOH HOH . T 4 HOH B 21 183 183 HOH HOH . U 4 HOH C 1 164 164 HOH HOH . U 4 HOH C 2 165 165 HOH HOH . U 4 HOH C 3 166 166 HOH HOH . U 4 HOH C 4 167 167 HOH HOH . U 4 HOH C 5 168 168 HOH HOH . U 4 HOH C 6 169 169 HOH HOH . U 4 HOH C 7 170 170 HOH HOH . U 4 HOH C 8 171 171 HOH HOH . U 4 HOH C 9 172 172 HOH HOH . U 4 HOH C 10 173 173 HOH HOH . U 4 HOH C 11 174 174 HOH HOH . U 4 HOH C 12 175 175 HOH HOH . U 4 HOH C 13 176 176 HOH HOH . U 4 HOH C 14 177 177 HOH HOH . U 4 HOH C 15 178 178 HOH HOH . U 4 HOH C 16 179 179 HOH HOH . U 4 HOH C 17 180 180 HOH HOH . U 4 HOH C 18 181 181 HOH HOH . U 4 HOH C 19 182 182 HOH HOH . U 4 HOH C 20 183 183 HOH HOH . U 4 HOH C 21 184 184 HOH HOH . U 4 HOH C 22 185 185 HOH HOH . U 4 HOH C 23 186 186 HOH HOH . U 4 HOH C 24 187 187 HOH HOH . U 4 HOH C 25 188 188 HOH HOH . U 4 HOH C 26 189 189 HOH HOH . U 4 HOH C 27 190 190 HOH HOH . U 4 HOH C 28 191 191 HOH HOH . U 4 HOH C 29 192 192 HOH HOH . U 4 HOH C 30 193 193 HOH HOH . U 4 HOH C 31 194 194 HOH HOH . U 4 HOH C 32 195 195 HOH HOH . U 4 HOH C 33 196 196 HOH HOH . U 4 HOH C 34 197 197 HOH HOH . U 4 HOH C 35 198 198 HOH HOH . V 4 HOH D 1 165 165 HOH HOH . V 4 HOH D 2 166 166 HOH HOH . V 4 HOH D 3 167 167 HOH HOH . V 4 HOH D 4 168 168 HOH HOH . V 4 HOH D 5 169 169 HOH HOH . V 4 HOH D 6 170 170 HOH HOH . V 4 HOH D 7 171 171 HOH HOH . V 4 HOH D 8 172 172 HOH HOH . V 4 HOH D 9 173 173 HOH HOH . V 4 HOH D 10 174 174 HOH HOH . V 4 HOH D 11 175 175 HOH HOH . V 4 HOH D 12 176 176 HOH HOH . V 4 HOH D 13 177 177 HOH HOH . V 4 HOH D 14 178 178 HOH HOH . V 4 HOH D 15 179 179 HOH HOH . V 4 HOH D 16 180 180 HOH HOH . V 4 HOH D 17 181 181 HOH HOH . V 4 HOH D 18 182 182 HOH HOH . V 4 HOH D 19 183 183 HOH HOH . V 4 HOH D 20 184 184 HOH HOH . V 4 HOH D 21 185 185 HOH HOH . V 4 HOH D 22 186 186 HOH HOH . W 4 HOH E 1 166 166 HOH HOH . W 4 HOH E 2 167 167 HOH HOH . W 4 HOH E 3 168 168 HOH HOH . W 4 HOH E 4 169 169 HOH HOH . W 4 HOH E 5 170 170 HOH HOH . W 4 HOH E 6 171 171 HOH HOH . W 4 HOH E 7 172 172 HOH HOH . W 4 HOH E 8 173 173 HOH HOH . W 4 HOH E 9 174 174 HOH HOH . W 4 HOH E 10 175 175 HOH HOH . W 4 HOH E 11 176 176 HOH HOH . W 4 HOH E 12 177 177 HOH HOH . W 4 HOH E 13 178 178 HOH HOH . W 4 HOH E 14 179 179 HOH HOH . W 4 HOH E 15 180 180 HOH HOH . W 4 HOH E 16 181 181 HOH HOH . W 4 HOH E 17 182 182 HOH HOH . W 4 HOH E 18 183 183 HOH HOH . W 4 HOH E 19 184 184 HOH HOH . W 4 HOH E 20 185 185 HOH HOH . W 4 HOH E 21 186 186 HOH HOH . W 4 HOH E 22 187 187 HOH HOH . W 4 HOH E 23 188 188 HOH HOH . W 4 HOH E 24 189 189 HOH HOH . W 4 HOH E 25 190 190 HOH HOH . W 4 HOH E 26 191 191 HOH HOH . W 4 HOH E 27 192 192 HOH HOH . X 4 HOH F 1 167 167 HOH HOH . X 4 HOH F 2 168 168 HOH HOH . X 4 HOH F 3 169 169 HOH HOH . X 4 HOH F 4 170 170 HOH HOH . X 4 HOH F 5 171 171 HOH HOH . X 4 HOH F 6 172 172 HOH HOH . X 4 HOH F 7 173 173 HOH HOH . X 4 HOH F 8 174 174 HOH HOH . X 4 HOH F 9 175 175 HOH HOH . X 4 HOH F 10 176 176 HOH HOH . X 4 HOH F 11 177 177 HOH HOH . X 4 HOH F 12 178 178 HOH HOH . X 4 HOH F 13 179 179 HOH HOH . X 4 HOH F 14 180 180 HOH HOH . X 4 HOH F 15 181 181 HOH HOH . X 4 HOH F 16 182 182 HOH HOH . X 4 HOH F 17 183 183 HOH HOH . X 4 HOH F 18 184 184 HOH HOH . X 4 HOH F 19 185 185 HOH HOH . X 4 HOH F 20 186 186 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 . . . O 2 22.691 16.581 14.798 1 51.21 ? O3B CDP 164 E 1 HETATM 2 P PB CDP . . . O 2 22.016 15.371 15.399 1 50.08 ? PB CDP 164 E 1 HETATM 3 O O1B CDP . . . O 2 20.517 15.517 15.394 1 49.54 ? O1B CDP 164 E 1 HETATM 4 O O2B CDP . . . O 2 22.703 14.094 14.916 1 48.77 ? O2B CDP 164 E 1 HETATM 5 O O3A CDP . . . O 2 22.215 15.313 17.019 1 51.96 ? O3A CDP 164 E 1 HETATM 6 P PA CDP . . . O 2 23.322 16.087 17.957 1 51.37 ? PA CDP 164 E 1 HETATM 7 O O1A CDP . . . O 2 24.274 16.873 17.084 1 49.6 ? O1A CDP 164 E 1 HETATM 8 O O2A CDP . . . O 2 22.483 16.709 19.052 1 49.63 ? O2A CDP 164 E 1 HETATM 9 O O5' CDP . . . O 2 24.182 14.902 18.61 1 50 ? O5' CDP 164 E 1 HETATM 10 C C5' CDP . . . O 2 24.96 14.078 17.756 1 48.9 ? C5' CDP 164 E 1 HETATM 11 C C4' CDP . . . O 2 24.607 12.638 18.109 1 50.48 ? C4' CDP 164 E 1 HETATM 12 O O4' CDP . . . O 2 25.009 12.361 19.461 1 49.48 ? O4' CDP 164 E 1 HETATM 13 C C3' CDP . . . O 2 23.098 12.309 18.04 1 49.74 ? C3' CDP 164 E 1 HETATM 14 O O3' CDP . . . O 2 22.654 11.959 16.719 1 48.07 ? O3' CDP 164 E 1 HETATM 15 C C2' CDP . . . O 2 23.007 11.129 18.994 1 50.05 ? C2' CDP 164 E 1 HETATM 16 O O2' CDP . . . O 2 23.205 9.898 18.28 1 48.09 ? O2' CDP 164 E 1 HETATM 17 C C1' CDP . . . O 2 24.149 11.363 20.012 1 49.37 ? C1' CDP 164 E 1 HETATM 18 N N1 CDP . . . O 2 23.554 11.821 21.273 1 48.54 ? N1 CDP 164 E 1 HETATM 19 C C2 CDP . . . O 2 23.485 10.954 22.397 1 48.47 ? C2 CDP 164 E 1 HETATM 20 O O2 CDP . . . O 2 23.972 9.794 22.376 1 47.51 ? O2 CDP 164 E 1 HETATM 21 N N3 CDP . . . O 2 22.906 11.413 23.533 1 47.97 ? N3 CDP 164 E 1 HETATM 22 C C4 CDP . . . O 2 22.385 12.658 23.603 1 47.74 ? C4 CDP 164 E 1 HETATM 23 N N4 CDP . . . O 2 21.805 13.074 24.754 1 48.82 ? N4 CDP 164 E 1 HETATM 24 C C5 CDP . . . O 2 22.427 13.515 22.513 1 46.55 ? C5 CDP 164 E 1 HETATM 25 C C6 CDP . . . O 2 23.025 13.061 21.35 1 48.46 ? C6 CDP 164 E 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #