data_8CBM # _model_server_result.job_id WljCSnDfvhpFnwmIInnxZg _model_server_result.datetime_utc '2025-02-28 18:31:30' _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 8cbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":501}' # _entry.id 8CBM # _exptl.entry_id 8CBM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 403.176 _entity.id 6 _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 8CBM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CBM _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,L,M,N,O,P,Q,R _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id L _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 hydrog WATSON-CRICK hydrog1 G N1 G 2 T G 2 1_555 G N3 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 G N2 G 2 T G 2 1_555 G O2 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 G O6 G 2 T G 2 1_555 G N4 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 G N1 A 3 T A 3 1_555 G N3 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 G N6 A 3 T A 3 1_555 G O4 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 G N1 A 4 T A 4 1_555 G N3 U 65 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 G N6 A 4 T A 4 1_555 G O4 U 65 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 G N1 A 4 T A 4 1_555 G N3 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 G N6 A 4 T A 4 1_555 G O4 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 G N1 A 5 T A 5 1_555 G N3 U 64 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 G N6 A 5 T A 5 1_555 G O4 U 64 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 G N3 U 6 T U 6 1_555 G N1 A 63 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 G O4 U 6 T U 6 1_555 G N6 A 63 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 G N1 A 7 T A 7 1_555 G N3 U 62 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 G N6 A 7 T A 7 1_555 G O4 U 62 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog16 G N3 U 8 T U 8 1_555 G N7 G 13 T G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 G N3 U 10 T U 10 1_555 G N1 A 21 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 G O4 U 10 T U 10 1_555 G N6 A 21 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 G N3 C 11 T C 11 1_555 G N1 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 G N4 C 11 T C 11 1_555 G O6 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 G O2 C 11 T C 11 1_555 G N2 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 G N3 U 12 T U 12 1_555 G N1 A 19 T A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 G O4 U 12 T U 12 1_555 G N6 A 19 T A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog24 G N2 G 13 T G 13 1_555 G N7 A 18 T A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog25 G N3 G 13 T G 13 1_555 G N6 A 18 T A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 G N3 U 23 T U 23 1_555 G N1 A 39 T A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 G O4 U 23 T U 23 1_555 G N6 A 39 T A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 G N3 U 24 T U 24 1_555 G N1 A 38 T A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 G O4 U 24 T U 24 1_555 G N6 A 38 T A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 G N1 A 25 T A 25 1_555 G N3 U 37 T U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 G N6 A 25 T A 25 1_555 G O4 U 37 T U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 G N3 C 26 T C 26 1_555 G N1 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 G N4 C 26 T C 26 1_555 G O6 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 G O2 C 26 T C 26 1_555 G N2 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 G N3 U 27 T U 27 1_555 G N1 A 35 T A 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 G O4 U 27 T U 27 1_555 G N6 A 35 T A 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 G N1 A 43 T A 43 1_555 G N3 U 52 T U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 G N6 A 43 T A 43 1_555 G O4 U 52 T U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 G N1 A 45 T A 45 1_555 G N3 U 61 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 G N6 A 45 T A 45 1_555 G O4 U 61 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 G N1 G 46 T G 46 1_555 G N3 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 G N2 G 46 T G 46 1_555 G O2 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 G O6 G 46 T G 46 1_555 G N4 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 G N1 G 47 T G 47 1_555 G N3 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 G N2 G 47 T G 47 1_555 G O2 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 G O6 G 47 T G 47 1_555 G N4 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog47 G N6 A 48 T A 48 1_555 G N3 C 58 T C 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 G N1 G 49 T G 49 1_555 G N3 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 G N2 G 49 T G 49 1_555 G O2 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog50 G O6 G 49 T G 49 1_555 G N4 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog51 G O2 C 50 T C 50 1_555 G N4 C 56 T C 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog52 G O2 U 51 T U 51 1_555 G N6 A 55 T A 55 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 8CBM _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 H 5 NAD A 1 301 301 NAD NAD . I 5 NAD B 1 301 301 NAD NAD . J 5 NAD C 1 301 301 NAD NAD . K 5 NAD D 1 301 301 NAD NAD . L 6 CDP E 1 501 501 CDP CDP . M 7 SAH F 1 501 401 SAH SAH . N 8 HOH A 1 401 7 HOH HOH . N 8 HOH A 2 402 2 HOH HOH . O 8 HOH B 1 401 8 HOH HOH . P 8 HOH C 1 401 6 HOH HOH . Q 8 HOH D 1 401 1 HOH HOH . Q 8 HOH D 2 402 3 HOH HOH . Q 8 HOH D 3 403 5 HOH HOH . R 8 HOH F 1 601 4 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 . . . L 6 160.554 127.088 75.037 1 217.58 ? O3B CDP 501 E 1 HETATM 2 P PB CDP . . . L 6 160.168 125.63 75.013 1 225.7 ? PB CDP 501 E 1 HETATM 3 O O1B CDP . . . L 6 159.402 125.251 73.77 1 216.8 ? O1B CDP 501 E 1 HETATM 4 O O2B CDP . . . L 6 161.339 124.715 75.276 1 217.97 ? O2B CDP 501 E 1 HETATM 5 O O3A CDP . . . L 6 159.156 125.415 76.227 1 222.42 ? O3A CDP 501 E 1 HETATM 6 P PA CDP . . . L 6 159.178 126.115 77.657 1 224.01 ? PA CDP 501 E 1 HETATM 7 O O1A CDP . . . L 6 158.997 127.584 77.47 1 215.16 ? O1A CDP 501 E 1 HETATM 8 O O2A CDP . . . L 6 160.382 125.637 78.398 1 215.33 ? O2A CDP 501 E 1 HETATM 9 O O5' CDP . . . L 6 157.862 125.503 78.335 1 214.79 ? O5' CDP 501 E 1 HETATM 10 C C5' CDP . . . L 6 157.961 124.178 78.906 1 212.91 ? C5' CDP 501 E 1 HETATM 11 C C4' CDP . . . L 6 157.395 123.179 77.929 1 215.13 ? C4' CDP 501 E 1 HETATM 12 O O4' CDP . . . L 6 156.407 122.372 78.61 1 214.79 ? O4' CDP 501 E 1 HETATM 13 C C3' CDP . . . L 6 156.664 123.77 76.716 1 215.88 ? C3' CDP 501 E 1 HETATM 14 O O3' CDP . . . L 6 157.525 123.901 75.593 1 217.43 ? O3' CDP 501 E 1 HETATM 15 C C2' CDP . . . L 6 155.59 122.73 76.391 1 215.15 ? C2' CDP 501 E 1 HETATM 16 O O2' CDP . . . L 6 155.953 121.81 75.386 1 214.63 ? O2' CDP 501 E 1 HETATM 17 C C1' CDP . . . L 6 155.363 122.026 77.731 1 215.27 ? C1' CDP 501 E 1 HETATM 18 N N1 CDP . . . L 6 154.081 122.44 78.345 1 214.37 ? N1 CDP 501 E 1 HETATM 19 C C2 CDP . . . L 6 153 121.623 78.069 1 213.02 ? C2 CDP 501 E 1 HETATM 20 O O2 CDP . . . L 6 153.167 120.621 77.359 1 212.11 ? O2 CDP 501 E 1 HETATM 21 N N3 CDP . . . L 6 151.825 121.959 78.599 1 212.42 ? N3 CDP 501 E 1 HETATM 22 C C4 CDP . . . L 6 151.715 123.058 79.363 1 212.56 ? C4 CDP 501 E 1 HETATM 23 N N4 CDP . . . L 6 150.525 123.358 79.843 1 213.69 ? N4 CDP 501 E 1 HETATM 24 C C5 CDP . . . L 6 152.82 123.904 79.643 1 211.21 ? C5 CDP 501 E 1 HETATM 25 C C6 CDP . . . L 6 153.993 123.564 79.103 1 212.07 ? C6 CDP 501 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #