data_8GZR # _model_server_result.job_id o3aPzpqq6IphY5HDN-icIQ _model_server_result.datetime_utc '2024-10-20 03:28:24' _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 8gzr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":702}' # _entry.id 8GZR # _exptl.entry_id 8GZR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 403.176 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 8GZR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GZR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J,K _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 ? _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 ? 7 I N N ? 7 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 metalc ? metalc1 A OE2 GLU 445 A GLU 437 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc2 A NE2 HIS 449 A HIS 441 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 A SG CYS 454 A CYS 446 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 A SG CYS 457 A CYS 449 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc5 A OD1 ASP 541 A ASP 533 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc6 A OD2 ASP 541 A ASP 533 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc7 A O THR 542 A THR 534 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc8 A OD2 ASP 671 A ASP 663 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc9 A OD1 ASP 671 A ASP 663 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc10 A OD1 ASP 672 A ASP 664 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc11 A NE2 HIS 720 A HIS 712 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc12 A NE2 HIS 722 A HIS 714 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc13 A SG CYS 736 A CYS 728 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc14 A SG CYS 855 A CYS 847 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc15 D MN MN . A MN 1001 1_555 I O2A CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc16 D MN MN . A MN 1001 1_555 I O2B CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc17 E MN MN . A MN 1002 1_555 I O2A CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc18 B OG1 THR 255 B THR 201 1_555 J MN MN . B MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc19 J MN MN . B MN 701 1_555 K O1B CDP . B CDP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? hydrog WATSON-CRICK hydrog1 C N1 A 17 C A 17 1_555 C N3 U 40 C U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N6 A 17 C A 17 1_555 C O4 U 40 C U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N1 A 18 C A 18 1_555 C N3 U 39 C U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N6 A 18 C A 18 1_555 C O4 U 39 C U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N3 C 19 C C 19 1_555 C N1 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N4 C 19 C C 19 1_555 C O6 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C O2 C 19 C C 19 1_555 C N2 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N1 A 20 C A 20 1_555 C N3 U 37 C U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N6 A 20 C A 20 1_555 C O4 U 37 C U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N1 G 21 C G 21 1_555 C N3 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N2 G 21 C G 21 1_555 C O2 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O6 G 21 C G 21 1_555 C N4 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N1 G 22 C G 22 1_555 C N3 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N2 G 22 C G 22 1_555 C O2 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O6 G 22 C G 22 1_555 C N4 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N3 U 23 C U 23 1_555 C N1 A 34 C A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O4 U 23 C U 23 1_555 C N6 A 34 C A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N3 U 24 C U 24 1_555 C N1 A 33 C A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C O4 U 24 C U 24 1_555 C N6 A 33 C A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N3 C 25 C C 25 1_555 C N1 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N4 C 25 C C 25 1_555 C O6 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O2 C 25 C C 25 1_555 C N2 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N3 U 26 C U 26 1_555 C N1 A 31 C A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C O4 U 26 C U 26 1_555 C N6 A 31 C A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog25 C N2 G 27 C G 27 1_555 C N7 A 30 C A 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 145 n n PB O1B CDP doub 146 n n PB O2B CDP sing 147 n n PB O3A CDP sing 148 n n O3A PA CDP sing 149 n n PA O1A CDP doub 150 n n PA O2A CDP sing 151 n n PA O5' CDP sing 152 n n O5' C5' CDP sing 153 n n C5' C4' CDP sing 154 n n C5' "H5'1" CDP sing 155 n n C5' "H5'2" CDP sing 156 n n C4' O4' CDP sing 157 n n C4' C3' CDP sing 158 n n C4' H4' CDP sing 159 n n O4' C1' CDP sing 160 n n C3' O3' CDP sing 161 n n C3' C2' CDP sing 162 n n C3' H3' CDP sing 163 n n O3' HA CDP sing 164 n n C2' O2' CDP sing 165 n n C2' C1' CDP sing 166 n n C2' H2' CDP sing 167 n n O2' HB CDP sing 168 n n C1' N1 CDP sing 169 n n C1' H1' CDP sing 170 n n N1 C2 CDP sing 171 n n N1 C6 CDP sing 172 n n C2 O2 CDP doub 173 n n C2 N3 CDP sing 174 n n N3 C4 CDP doub 175 n n C4 N4 CDP sing 176 n n C4 C5 CDP sing 177 n n N4 H4N1 CDP sing 178 n n N4 H4N2 CDP sing 179 n n C5 C6 CDP doub 180 n n C5 H5 CDP sing 181 n n C6 H6 CDP sing 182 n n HO1 O2A CDP sing 183 n n HO2 O2B CDP sing 184 n n HO3 O3B CDP sing 185 n n # _atom_sites.entry_id 8GZR _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 D 4 MN A 1 1001 1 MN MN . E 4 MN A 1 1002 2 MN MN . F 5 ZN A 1 1003 4 ZN ZN . G 5 ZN A 1 1004 5 ZN ZN . H 6 SAH A 1 1005 6 SAH SAH . I 7 CDP A 1 1006 7 CDP CDP . J 4 MN B 1 701 3 MN MN . K 7 CDP B 1 702 8 CDP CDP . # 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 . . . K 7 57.167 87.451 109.921 1 75.64 ? O3B CDP 702 B 1 HETATM 2 P PB CDP . . . K 7 56.787 88.65 109.092 1 75.64 ? PB CDP 702 B 1 HETATM 3 O O1B CDP . . . K 7 57.979 89.101 108.285 1 75.64 ? O1B CDP 702 B 1 HETATM 4 O O2B CDP . . . K 7 56.338 89.757 110.006 1 75.64 ? O2B CDP 702 B 1 HETATM 5 O O3A CDP . . . K 7 55.557 88.245 108.078 1 75.64 ? O3A CDP 702 B 1 HETATM 6 P PA CDP . . . K 7 55.205 89.044 106.684 1 75.64 ? PA CDP 702 B 1 HETATM 7 O O1A CDP . . . K 7 56.101 88.555 105.574 1 75.64 ? O1A CDP 702 B 1 HETATM 8 O O2A CDP . . . K 7 55.424 90.52 106.877 1 75.64 ? O2A CDP 702 B 1 HETATM 9 O O5' CDP . . . K 7 53.633 88.768 106.285 1 75.64 ? O5' CDP 702 B 1 HETATM 10 C C5' CDP . . . K 7 52.644 88.971 107.252 1 75.64 ? C5' CDP 702 B 1 HETATM 11 C C4' CDP . . . K 7 51.381 88.241 106.841 1 75.64 ? C4' CDP 702 B 1 HETATM 12 O O4' CDP . . . K 7 51.01 88.599 105.308 1 75.64 ? O4' CDP 702 B 1 HETATM 13 C C3' CDP . . . K 7 51.566 86.948 106.91 1 75.64 ? C3' CDP 702 B 1 HETATM 14 O O3' CDP . . . K 7 50.468 86.32 107.705 1 75.64 ? O3' CDP 702 B 1 HETATM 15 C C2' CDP . . . K 7 51.51 86.432 105.462 1 75.64 ? C2' CDP 702 B 1 HETATM 16 O O2' CDP . . . K 7 50.921 85.214 105.418 1 75.64 ? O2' CDP 702 B 1 HETATM 17 C C1' CDP . . . K 7 50.63 87.478 104.765 1 75.64 ? C1' CDP 702 B 1 HETATM 18 N N1 CDP . . . K 7 50.881 87.487 103.314 1 75.64 ? N1 CDP 702 B 1 HETATM 19 C C2 CDP . . . K 7 49.75 87.716 102.38 1 75.64 ? C2 CDP 702 B 1 HETATM 20 O O2 CDP . . . K 7 48.66 87.888 102.808 1 75.64 ? O2 CDP 702 B 1 HETATM 21 N N3 CDP . . . K 7 49.984 87.73 100.916 1 75.64 ? N3 CDP 702 B 1 HETATM 22 C C4 CDP . . . K 7 51.316 87.519 100.39 1 75.64 ? C4 CDP 702 B 1 HETATM 23 N N4 CDP . . . K 7 51.536 87.534 98.956 1 75.64 ? N4 CDP 702 B 1 HETATM 24 C C5 CDP . . . K 7 52.455 87.289 101.322 1 75.64 ? C5 CDP 702 B 1 HETATM 25 C C6 CDP . . . K 7 52.22 87.275 102.795 1 75.64 ? C6 CDP 702 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #