data_9LJR # _model_server_result.job_id aK94wyO0Z23i8pQNG8VBYg _model_server_result.datetime_utc '2025-08-14 21:36:55' _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 9ljr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 9LJR # _exptl.entry_id 9LJR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 3 _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 9LJR _cell.length_a 138.876 _cell.length_b 138.876 _cell.length_c 93.227 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9LJR _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,H _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 3 _struct_asym.id C _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc2 A OD1 ASP 221 A ASP 220 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc3 A O THR 222 A THR 221 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc4 A OD2 ASP 319 A ASP 318 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc5 A OD1 ASP 319 A ASP 318 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc6 A OD1 ASP 320 A ASP 319 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc7 C O1B CDP . A CDP 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc8 C O2A CDP . A CDP 601 1_555 E MN MN . A MN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc9 C O2A CDP . A CDP 601 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc10 D O3B FAD . A FAD 602 1_555 F MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc11 E MN MN . A MN 603 1_555 G O HOH . A HOH 791 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _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 106 n n PB O1B CDP doub 107 n n PB O2B CDP sing 108 n n PB O3A CDP sing 109 n n O3A PA CDP sing 110 n n PA O1A CDP doub 111 n n PA O2A CDP sing 112 n n PA O5' CDP sing 113 n n O5' C5' CDP sing 114 n n C5' C4' CDP sing 115 n n C5' "H5'1" CDP sing 116 n n C5' "H5'2" CDP sing 117 n n C4' O4' CDP sing 118 n n C4' C3' CDP sing 119 n n C4' H4' CDP sing 120 n n O4' C1' CDP sing 121 n n C3' O3' CDP sing 122 n n C3' C2' CDP sing 123 n n C3' H3' CDP sing 124 n n O3' HA CDP sing 125 n n C2' O2' CDP sing 126 n n C2' C1' CDP sing 127 n n C2' H2' CDP sing 128 n n O2' HB CDP sing 129 n n C1' N1 CDP sing 130 n n C1' H1' CDP sing 131 n n N1 C2 CDP sing 132 n n N1 C6 CDP sing 133 n n C2 O2 CDP doub 134 n n C2 N3 CDP sing 135 n n N3 C4 CDP doub 136 n n C4 N4 CDP sing 137 n n C4 C5 CDP sing 138 n n N4 H4N1 CDP sing 139 n n N4 H4N2 CDP sing 140 n n C5 C6 CDP doub 141 n n C5 H5 CDP sing 142 n n C6 H6 CDP sing 143 n n HO1 O2A CDP sing 144 n n HO2 O2B CDP sing 145 n n HO3 O3B CDP sing 146 n n # _atom_sites.entry_id 9LJR _atom_sites.fract_transf_matrix[1][1] 0.007201 _atom_sites.fract_transf_matrix[1][2] 0.004157 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008315 _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] 0.010727 _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 CDP A 1 601 601 CDP CDP . D 4 FAD A 1 602 602 FAD FAD . E 5 MN A 1 603 1 MN MN . F 5 MN A 1 604 2 MN MN . G 6 HOH A 1 701 61 HOH HOH . G 6 HOH A 2 702 13 HOH HOH . G 6 HOH A 3 703 4 HOH HOH . G 6 HOH A 4 704 25 HOH HOH . G 6 HOH A 5 705 95 HOH HOH . G 6 HOH A 6 706 11 HOH HOH . G 6 HOH A 7 707 96 HOH HOH . G 6 HOH A 8 708 66 HOH HOH . G 6 HOH A 9 709 6 HOH HOH . G 6 HOH A 10 710 103 HOH HOH . G 6 HOH A 11 711 129 HOH HOH . G 6 HOH A 12 712 126 HOH HOH . G 6 HOH A 13 713 89 HOH HOH . G 6 HOH A 14 714 23 HOH HOH . G 6 HOH A 15 715 8 HOH HOH . G 6 HOH A 16 716 130 HOH HOH . G 6 HOH A 17 717 15 HOH HOH . G 6 HOH A 18 718 86 HOH HOH . G 6 HOH A 19 719 45 HOH HOH . G 6 HOH A 20 720 36 HOH HOH . G 6 HOH A 21 721 76 HOH HOH . G 6 HOH A 22 722 26 HOH HOH . G 6 HOH A 23 723 33 HOH HOH . G 6 HOH A 24 724 2 HOH HOH . G 6 HOH A 25 725 75 HOH HOH . G 6 HOH A 26 726 39 HOH HOH . G 6 HOH A 27 727 91 HOH HOH . G 6 HOH A 28 728 87 HOH HOH . G 6 HOH A 29 729 55 HOH HOH . G 6 HOH A 30 730 78 HOH HOH . G 6 HOH A 31 731 5 HOH HOH . G 6 HOH A 32 732 54 HOH HOH . G 6 HOH A 33 733 35 HOH HOH . G 6 HOH A 34 734 7 HOH HOH . G 6 HOH A 35 735 111 HOH HOH . G 6 HOH A 36 736 3 HOH HOH . G 6 HOH A 37 737 28 HOH HOH . G 6 HOH A 38 738 16 HOH HOH . G 6 HOH A 39 739 80 HOH HOH . G 6 HOH A 40 740 62 HOH HOH . G 6 HOH A 41 741 110 HOH HOH . G 6 HOH A 42 742 1 HOH HOH . G 6 HOH A 43 743 79 HOH HOH . G 6 HOH A 44 744 64 HOH HOH . G 6 HOH A 45 745 108 HOH HOH . G 6 HOH A 46 746 27 HOH HOH . G 6 HOH A 47 747 84 HOH HOH . G 6 HOH A 48 748 115 HOH HOH . G 6 HOH A 49 749 72 HOH HOH . G 6 HOH A 50 750 31 HOH HOH . G 6 HOH A 51 751 48 HOH HOH . G 6 HOH A 52 752 46 HOH HOH . G 6 HOH A 53 753 56 HOH HOH . G 6 HOH A 54 754 43 HOH HOH . G 6 HOH A 55 755 44 HOH HOH . G 6 HOH A 56 756 90 HOH HOH . G 6 HOH A 57 757 9 HOH HOH . G 6 HOH A 58 758 12 HOH HOH . G 6 HOH A 59 759 42 HOH HOH . G 6 HOH A 60 760 49 HOH HOH . G 6 HOH A 61 761 32 HOH HOH . G 6 HOH A 62 762 98 HOH HOH . G 6 HOH A 63 763 63 HOH HOH . G 6 HOH A 64 764 21 HOH HOH . G 6 HOH A 65 765 53 HOH HOH . G 6 HOH A 66 766 29 HOH HOH . G 6 HOH A 67 767 114 HOH HOH . G 6 HOH A 68 768 22 HOH HOH . G 6 HOH A 69 769 58 HOH HOH . G 6 HOH A 70 770 38 HOH HOH . G 6 HOH A 71 771 41 HOH HOH . G 6 HOH A 72 772 52 HOH HOH . G 6 HOH A 73 773 83 HOH HOH . G 6 HOH A 74 774 60 HOH HOH . G 6 HOH A 75 775 17 HOH HOH . G 6 HOH A 76 776 77 HOH HOH . G 6 HOH A 77 777 30 HOH HOH . G 6 HOH A 78 778 19 HOH HOH . G 6 HOH A 79 779 37 HOH HOH . G 6 HOH A 80 780 67 HOH HOH . G 6 HOH A 81 781 107 HOH HOH . G 6 HOH A 82 782 101 HOH HOH . G 6 HOH A 83 783 85 HOH HOH . G 6 HOH A 84 784 40 HOH HOH . G 6 HOH A 85 785 69 HOH HOH . G 6 HOH A 86 786 99 HOH HOH . G 6 HOH A 87 787 20 HOH HOH . G 6 HOH A 88 788 112 HOH HOH . G 6 HOH A 89 789 102 HOH HOH . G 6 HOH A 90 790 82 HOH HOH . G 6 HOH A 91 791 128 HOH HOH . G 6 HOH A 92 792 24 HOH HOH . G 6 HOH A 93 793 34 HOH HOH . G 6 HOH A 94 794 47 HOH HOH . G 6 HOH A 95 795 14 HOH HOH . G 6 HOH A 96 796 57 HOH HOH . G 6 HOH A 97 797 94 HOH HOH . G 6 HOH A 98 798 117 HOH HOH . G 6 HOH A 99 799 93 HOH HOH . G 6 HOH A 100 800 68 HOH HOH . G 6 HOH A 101 801 50 HOH HOH . G 6 HOH A 102 802 59 HOH HOH . G 6 HOH A 103 803 105 HOH HOH . G 6 HOH A 104 804 113 HOH HOH . G 6 HOH A 105 805 65 HOH HOH . G 6 HOH A 106 806 127 HOH HOH . G 6 HOH A 107 807 104 HOH HOH . G 6 HOH A 108 808 70 HOH HOH . G 6 HOH A 109 809 97 HOH HOH . G 6 HOH A 110 810 106 HOH HOH . G 6 HOH A 111 811 88 HOH HOH . G 6 HOH A 112 812 92 HOH HOH . G 6 HOH A 113 813 73 HOH HOH . G 6 HOH A 114 814 74 HOH HOH . G 6 HOH A 115 815 100 HOH HOH . G 6 HOH A 116 816 109 HOH HOH . H 6 HOH T 1 101 71 HOH HOH . H 6 HOH T 2 102 51 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 . . . C 3 40.431 -41.516 3.159 1 39.75 ? O3B CDP 601 A 1 HETATM 2 P PB CDP . . . C 3 41.838 -41.612 2.587 1 40.18 ? PB CDP 601 A 1 HETATM 3 O O1B CDP . . . C 3 41.826 -42.583 1.429 1 35.52 ? O1B CDP 601 A 1 HETATM 4 O O2B CDP . . . C 3 42.383 -40.246 2.196 1 36.87 ? O2B CDP 601 A 1 HETATM 5 O O3A CDP . . . C 3 42.8 -42.185 3.796 1 45.27 ? O3A CDP 601 A 1 HETATM 6 P PA CDP . . . C 3 43.264 -43.746 3.939 1 41.44 ? PA CDP 601 A 1 HETATM 7 O O1A CDP . . . C 3 44.462 -43.775 4.858 1 40.05 ? O1A CDP 601 A 1 HETATM 8 O O2A CDP . . . C 3 43.613 -44.254 2.564 1 47.51 ? O2A CDP 601 A 1 HETATM 9 O O5' CDP . . . C 3 42.022 -44.698 4.505 1 42.49 ? O5' CDP 601 A 1 HETATM 10 C C5' CDP . . . C 3 41.112 -45.291 3.596 1 38.41 ? C5' CDP 601 A 1 HETATM 11 C C4' CDP . . . C 3 39.876 -45.638 4.342 1 40.75 ? C4' CDP 601 A 1 HETATM 12 O O4' CDP . . . C 3 40.135 -46.247 5.484 1 43.24 ? O4' CDP 601 A 1 HETATM 13 C C3' CDP . . . C 3 39.105 -44.237 4.792 1 41.07 ? C3' CDP 601 A 1 HETATM 14 O O3' CDP . . . C 3 38.595 -43.523 3.587 1 38.6 ? O3' CDP 601 A 1 HETATM 15 C C2' CDP . . . C 3 38.281 -44.635 5.648 1 36.8 ? C2' CDP 601 A 1 HETATM 16 O O2' CDP . . . C 3 37.075 -45.336 5.07 1 38.11 ? O2' CDP 601 A 1 HETATM 17 C C1' CDP . . . C 3 39.121 -45.738 6.481 1 34.57 ? C1' CDP 601 A 1 HETATM 18 N N1 CDP . . . C 3 39.666 -45.153 7.529 1 36.22 ? N1 CDP 601 A 1 HETATM 19 C C2 CDP . . . C 3 38.856 -44.964 8.755 1 41.27 ? C2 CDP 601 A 1 HETATM 20 O O2 CDP . . . C 3 37.74 -45.372 8.787 1 40.9 ? O2 CDP 601 A 1 HETATM 21 N N3 CDP . . . C 3 39.438 -44.289 9.944 1 36.86 ? N3 CDP 601 A 1 HETATM 22 C C4 CDP . . . C 3 40.79 -43.802 9.917 1 39.7 ? C4 CDP 601 A 1 HETATM 23 N N4 CDP . . . C 3 41.366 -43.126 11.095 1 42.33 ? N4 CDP 601 A 1 HETATM 24 C C5 CDP . . . C 3 41.602 -43.984 8.691 1 35.62 ? C5 CDP 601 A 1 HETATM 25 C C6 CDP . . . C 3 41.027 -44.661 7.511 1 36.09 ? C6 CDP 601 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #