data_9LJS # _model_server_result.job_id xTESG4-HjJ4xW0u2DGghoA _model_server_result.datetime_utc '2025-08-15 02:53:37' _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 9ljs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 9LJS # _exptl.entry_id 9LJS _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 120 _cell.entry_id 9LJS _cell.length_a 139.003 _cell.length_b 139.003 _cell.length_c 92.986 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LJS _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,F,G _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 x,y,z _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 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 A OD1 ASP 221 A ASP 220 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc2 A OD1 ASP 221 A ASP 220 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 A O THR 222 A THR 221 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc4 A OD1 ASP 319 A ASP 318 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc5 A OD2 ASP 319 A ASP 318 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc6 D O2A CDP . A CDP 602 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc7 D O2B CDP . A CDP 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc8 D O2A CDP . A CDP 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc9 F MN MN . A MN 604 1_555 G O HOH . A HOH 721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? # _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 9LJS _atom_sites.fract_transf_matrix[1][1] 0.007194 _atom_sites.fract_transf_matrix[1][2] 0.004154 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008307 _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] 0.010754 _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 C 3 FAD A 1 601 601 FAD FAD . D 4 CDP A 1 602 602 CDP CDP . E 5 MN A 1 603 1 MN MN . F 5 MN A 1 604 2 MN MN . G 6 HOH A 1 701 69 HOH HOH . G 6 HOH A 2 702 5 HOH HOH . G 6 HOH A 3 703 77 HOH HOH . G 6 HOH A 4 704 67 HOH HOH . G 6 HOH A 5 705 27 HOH HOH . G 6 HOH A 6 706 50 HOH HOH . G 6 HOH A 7 707 33 HOH HOH . G 6 HOH A 8 708 39 HOH HOH . G 6 HOH A 9 709 2 HOH HOH . G 6 HOH A 10 710 29 HOH HOH . G 6 HOH A 11 711 9 HOH HOH . G 6 HOH A 12 712 44 HOH HOH . G 6 HOH A 13 713 14 HOH HOH . G 6 HOH A 14 714 48 HOH HOH . G 6 HOH A 15 715 21 HOH HOH . G 6 HOH A 16 716 61 HOH HOH . G 6 HOH A 17 717 15 HOH HOH . G 6 HOH A 18 718 78 HOH HOH . G 6 HOH A 19 719 62 HOH HOH . G 6 HOH A 20 720 16 HOH HOH . G 6 HOH A 21 721 68 HOH HOH . G 6 HOH A 22 722 23 HOH HOH . G 6 HOH A 23 723 53 HOH HOH . G 6 HOH A 24 724 31 HOH HOH . G 6 HOH A 25 725 71 HOH HOH . G 6 HOH A 26 726 35 HOH HOH . G 6 HOH A 27 727 24 HOH HOH . G 6 HOH A 28 728 40 HOH HOH . G 6 HOH A 29 729 30 HOH HOH . G 6 HOH A 30 730 36 HOH HOH . G 6 HOH A 31 731 49 HOH HOH . G 6 HOH A 32 732 65 HOH HOH . G 6 HOH A 33 733 45 HOH HOH . G 6 HOH A 34 734 43 HOH HOH . G 6 HOH A 35 735 32 HOH HOH . G 6 HOH A 36 736 72 HOH HOH . G 6 HOH A 37 737 70 HOH HOH . G 6 HOH A 38 738 66 HOH HOH . G 6 HOH A 39 739 34 HOH HOH . G 6 HOH A 40 740 59 HOH HOH . G 6 HOH A 41 741 47 HOH HOH . G 6 HOH A 42 742 20 HOH HOH . G 6 HOH A 43 743 79 HOH HOH . G 6 HOH A 44 744 58 HOH HOH . G 6 HOH A 45 745 41 HOH HOH . G 6 HOH A 46 746 80 HOH HOH . G 6 HOH A 47 747 63 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 56.22 -16.666 13.777 1 49.91 ? O3B CDP 602 A 1 HETATM 2 P PB CDP . . . D 4 56.955 -15.355 13.606 1 59.83 ? PB CDP 602 A 1 HETATM 3 O O1B CDP . . . D 4 55.961 -14.253 13.241 1 58.09 ? O1B CDP 602 A 1 HETATM 4 O O2B CDP . . . D 4 57.73 -14.997 14.863 1 48.64 ? O2B CDP 602 A 1 HETATM 5 O O3A CDP . . . D 4 57.989 -15.597 12.338 1 56.57 ? O3A CDP 602 A 1 HETATM 6 P PA CDP . . . D 4 59.632 -15.611 12.375 1 58.65 ? PA CDP 602 A 1 HETATM 7 O O1A CDP . . . D 4 60.095 -16.611 11.342 1 53.37 ? O1A CDP 602 A 1 HETATM 8 O O2A CDP . . . D 4 60.123 -15.958 13.75 1 57.78 ? O2A CDP 602 A 1 HETATM 9 O O5' CDP . . . D 4 60.202 -14.087 12.016 1 56.46 ? O5' CDP 602 A 1 HETATM 10 C C5' CDP . . . D 4 59.809 -13.033 12.869 1 53.08 ? C5' CDP 602 A 1 HETATM 11 C C4' CDP . . . D 4 59.508 -11.803 12.085 1 54.83 ? C4' CDP 602 A 1 HETATM 12 O O4' CDP . . . D 4 60.164 -11.751 10.954 1 52.85 ? O4' CDP 602 A 1 HETATM 13 C C3' CDP . . . D 4 57.913 -11.789 11.623 1 51.01 ? C3' CDP 602 A 1 HETATM 14 O O3' CDP . . . D 4 57.028 -11.759 12.817 1 42.61 ? O3' CDP 602 A 1 HETATM 15 C C2' CDP . . . D 4 57.864 -10.861 10.765 1 49.28 ? C2' CDP 602 A 1 HETATM 16 O O2' CDP . . . D 4 57.741 -9.429 11.223 1 46.68 ? O2' CDP 602 A 1 HETATM 17 C C1' CDP . . . D 4 59.282 -10.983 10.007 1 47.68 ? C1' CDP 602 A 1 HETATM 18 N N1 CDP . . . D 4 59.045 -11.674 8.918 1 54.09 ? N1 CDP 602 A 1 HETATM 19 C C2 CDP . . . D 4 58.506 -10.994 7.702 1 59.79 ? C2 CDP 602 A 1 HETATM 20 O O2 CDP . . . D 4 58.318 -9.814 7.713 1 59.32 ? O2 CDP 602 A 1 HETATM 21 N N3 CDP . . . D 4 58.211 -11.787 6.471 1 53.32 ? N3 CDP 602 A 1 HETATM 22 C C4 CDP . . . D 4 58.442 -13.204 6.469 1 48.08 ? C4 CDP 602 A 1 HETATM 23 N N4 CDP . . . D 4 58.155 -14.002 5.277 1 61.13 ? N4 CDP 602 A 1 HETATM 24 C C5 CDP . . . D 4 58.973 -13.877 7.664 1 47.46 ? C5 CDP 602 A 1 HETATM 25 C C6 CDP . . . D 4 59.267 -13.107 8.89 1 51.78 ? C6 CDP 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #