data_5DV2 # _model_server_result.job_id KYYkaXFQW7FUvSjN2GkUZA _model_server_result.datetime_utc '2025-07-03 05:47:03' _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 5dv2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5DV2 # _exptl.entry_id 5DV2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-MONOPHOSPHATE" _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 5DV2 _cell.length_a 77.051 _cell.length_b 77.051 _cell.length_c 167.65 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DV2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id C5P _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-MONOPHOSPHATE" _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 O3P P C5P sing 70 n n O3P HOP3 C5P sing 71 n n P O1P C5P doub 72 n n P O2P C5P sing 73 n n P O5' C5P sing 74 n n O2P HOP2 C5P sing 75 n n O5' C5' C5P sing 76 n n C5' C4' C5P sing 77 n n C5' "H5'1" C5P sing 78 n n C5' "H5'2" C5P sing 79 n n C4' O4' C5P sing 80 n n C4' C3' C5P sing 81 n n C4' H4' C5P sing 82 n n O4' C1' C5P sing 83 n n C3' O3' C5P sing 84 n n C3' C2' C5P sing 85 n n C3' H3' C5P sing 86 n n O3' HO3' C5P sing 87 n n C2' O2' C5P sing 88 n n C2' C1' C5P sing 89 n n C2' "H2'1" C5P sing 90 n n O2' HO2' C5P sing 91 n n C1' N1 C5P sing 92 n n C1' H1' C5P sing 93 n n N1 C2 C5P sing 94 n n N1 C6 C5P sing 95 n n C2 N3 C5P sing 96 n n C2 O2 C5P doub 97 n n N3 C4 C5P doub 98 n n C4 C5 C5P sing 99 n n C4 N4 C5P sing 100 n n C5 C6 C5P doub 101 n n C5 H5 C5P sing 102 n n C6 H6 C5P sing 103 n n N4 HN41 C5P sing 104 n n N4 HN42 C5P sing 105 n n # _atom_sites.entry_id 5DV2 _atom_sites.fract_transf_matrix[1][1] 0.012978 _atom_sites.fract_transf_matrix[1][2] 0.007493 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014986 _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] 0.005965 _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 B 2 C5P A 1 601 541 C5P C5P . C 3 HOH A 1 701 147 HOH HOH . C 3 HOH A 2 702 192 HOH HOH . C 3 HOH A 3 703 165 HOH HOH . C 3 HOH A 4 704 31 HOH HOH . C 3 HOH A 5 705 109 HOH HOH . C 3 HOH A 6 706 144 HOH HOH . C 3 HOH A 7 707 83 HOH HOH . C 3 HOH A 8 708 75 HOH HOH . C 3 HOH A 9 709 66 HOH HOH . C 3 HOH A 10 710 71 HOH HOH . C 3 HOH A 11 711 52 HOH HOH . C 3 HOH A 12 712 124 HOH HOH . C 3 HOH A 13 713 145 HOH HOH . C 3 HOH A 14 714 182 HOH HOH . C 3 HOH A 15 715 2 HOH HOH . C 3 HOH A 16 716 30 HOH HOH . C 3 HOH A 17 717 129 HOH HOH . C 3 HOH A 18 718 35 HOH HOH . C 3 HOH A 19 719 48 HOH HOH . C 3 HOH A 20 720 74 HOH HOH . C 3 HOH A 21 721 110 HOH HOH . C 3 HOH A 22 722 168 HOH HOH . C 3 HOH A 23 723 131 HOH HOH . C 3 HOH A 24 724 148 HOH HOH . C 3 HOH A 25 725 62 HOH HOH . C 3 HOH A 26 726 6 HOH HOH . C 3 HOH A 27 727 164 HOH HOH . C 3 HOH A 28 728 64 HOH HOH . C 3 HOH A 29 729 108 HOH HOH . C 3 HOH A 30 730 46 HOH HOH . C 3 HOH A 31 731 25 HOH HOH . C 3 HOH A 32 732 32 HOH HOH . C 3 HOH A 33 733 72 HOH HOH . C 3 HOH A 34 734 96 HOH HOH . C 3 HOH A 35 735 36 HOH HOH . C 3 HOH A 36 736 82 HOH HOH . C 3 HOH A 37 737 18 HOH HOH . C 3 HOH A 38 738 4 HOH HOH . C 3 HOH A 39 739 9 HOH HOH . C 3 HOH A 40 740 55 HOH HOH . C 3 HOH A 41 741 12 HOH HOH . C 3 HOH A 42 742 27 HOH HOH . C 3 HOH A 43 743 57 HOH HOH . C 3 HOH A 44 744 11 HOH HOH . C 3 HOH A 45 745 114 HOH HOH . C 3 HOH A 46 746 185 HOH HOH . C 3 HOH A 47 747 61 HOH HOH . C 3 HOH A 48 748 97 HOH HOH . C 3 HOH A 49 749 81 HOH HOH . C 3 HOH A 50 750 37 HOH HOH . C 3 HOH A 51 751 155 HOH HOH . C 3 HOH A 52 752 73 HOH HOH . C 3 HOH A 53 753 29 HOH HOH . C 3 HOH A 54 754 107 HOH HOH . C 3 HOH A 55 755 77 HOH HOH . C 3 HOH A 56 756 78 HOH HOH . C 3 HOH A 57 757 86 HOH HOH . C 3 HOH A 58 758 116 HOH HOH . C 3 HOH A 59 759 3 HOH HOH . C 3 HOH A 60 760 47 HOH HOH . C 3 HOH A 61 761 67 HOH HOH . C 3 HOH A 62 762 80 HOH HOH . C 3 HOH A 63 763 34 HOH HOH . C 3 HOH A 64 764 137 HOH HOH . C 3 HOH A 65 765 56 HOH HOH . C 3 HOH A 66 766 26 HOH HOH . C 3 HOH A 67 767 146 HOH HOH . C 3 HOH A 68 768 1 HOH HOH . C 3 HOH A 69 769 122 HOH HOH . C 3 HOH A 70 770 16 HOH HOH . C 3 HOH A 71 771 22 HOH HOH . C 3 HOH A 72 772 7 HOH HOH . C 3 HOH A 73 773 142 HOH HOH . C 3 HOH A 74 774 128 HOH HOH . C 3 HOH A 75 775 15 HOH HOH . C 3 HOH A 76 776 132 HOH HOH . C 3 HOH A 77 777 49 HOH HOH . C 3 HOH A 78 778 191 HOH HOH . C 3 HOH A 79 779 13 HOH HOH . C 3 HOH A 80 780 23 HOH HOH . C 3 HOH A 81 781 33 HOH HOH . C 3 HOH A 82 782 113 HOH HOH . C 3 HOH A 83 783 28 HOH HOH . C 3 HOH A 84 784 58 HOH HOH . C 3 HOH A 85 785 104 HOH HOH . C 3 HOH A 86 786 17 HOH HOH . C 3 HOH A 87 787 50 HOH HOH . C 3 HOH A 88 788 44 HOH HOH . C 3 HOH A 89 789 53 HOH HOH . C 3 HOH A 90 790 112 HOH HOH . C 3 HOH A 91 791 5 HOH HOH . C 3 HOH A 92 792 95 HOH HOH . C 3 HOH A 93 793 154 HOH HOH . C 3 HOH A 94 794 136 HOH HOH . C 3 HOH A 95 795 69 HOH HOH . C 3 HOH A 96 796 19 HOH HOH . C 3 HOH A 97 797 24 HOH HOH . C 3 HOH A 98 798 90 HOH HOH . C 3 HOH A 99 799 106 HOH HOH . C 3 HOH A 100 800 84 HOH HOH . C 3 HOH A 101 801 8 HOH HOH . C 3 HOH A 102 802 70 HOH HOH . C 3 HOH A 103 803 51 HOH HOH . C 3 HOH A 104 804 20 HOH HOH . C 3 HOH A 105 805 43 HOH HOH . C 3 HOH A 106 806 115 HOH HOH . C 3 HOH A 107 807 111 HOH HOH . C 3 HOH A 108 808 172 HOH HOH . C 3 HOH A 109 809 54 HOH HOH . C 3 HOH A 110 810 163 HOH HOH . C 3 HOH A 111 811 153 HOH HOH . C 3 HOH A 112 812 59 HOH HOH . C 3 HOH A 113 813 189 HOH HOH . C 3 HOH A 114 814 42 HOH HOH . C 3 HOH A 115 815 161 HOH HOH . C 3 HOH A 116 816 126 HOH HOH . C 3 HOH A 117 817 176 HOH HOH . C 3 HOH A 118 818 173 HOH HOH . C 3 HOH A 119 819 91 HOH HOH . C 3 HOH A 120 820 140 HOH HOH . C 3 HOH A 121 821 41 HOH HOH . C 3 HOH A 122 822 98 HOH HOH . C 3 HOH A 123 823 38 HOH HOH . C 3 HOH A 124 824 186 HOH HOH . C 3 HOH A 125 825 94 HOH HOH . C 3 HOH A 126 826 121 HOH HOH . C 3 HOH A 127 827 102 HOH HOH . C 3 HOH A 128 828 187 HOH HOH . C 3 HOH A 129 829 178 HOH HOH . C 3 HOH A 130 830 167 HOH HOH . C 3 HOH A 131 831 14 HOH HOH . C 3 HOH A 132 832 65 HOH HOH . C 3 HOH A 133 833 120 HOH HOH . C 3 HOH A 134 834 181 HOH HOH . C 3 HOH A 135 835 117 HOH HOH . C 3 HOH A 136 836 141 HOH HOH . C 3 HOH A 137 837 151 HOH HOH . C 3 HOH A 138 838 190 HOH HOH . C 3 HOH A 139 839 79 HOH HOH . C 3 HOH A 140 840 60 HOH HOH . C 3 HOH A 141 841 76 HOH HOH . C 3 HOH A 142 842 130 HOH HOH . C 3 HOH A 143 843 150 HOH HOH . C 3 HOH A 144 844 92 HOH HOH . C 3 HOH A 145 845 125 HOH HOH . C 3 HOH A 146 846 179 HOH HOH . C 3 HOH A 147 847 143 HOH HOH . C 3 HOH A 148 848 180 HOH HOH . C 3 HOH A 149 849 170 HOH HOH . C 3 HOH A 150 850 135 HOH HOH . C 3 HOH A 151 851 105 HOH HOH . C 3 HOH A 152 852 139 HOH HOH . C 3 HOH A 153 853 162 HOH HOH . C 3 HOH A 154 854 152 HOH HOH . C 3 HOH A 155 855 159 HOH HOH . C 3 HOH A 156 856 174 HOH HOH . C 3 HOH A 157 857 68 HOH HOH . C 3 HOH A 158 858 133 HOH HOH . C 3 HOH A 159 859 157 HOH HOH . C 3 HOH A 160 860 63 HOH HOH . C 3 HOH A 161 861 156 HOH HOH . C 3 HOH A 162 862 184 HOH HOH . C 3 HOH A 163 863 123 HOH HOH . C 3 HOH A 164 864 127 HOH HOH . C 3 HOH A 165 865 175 HOH HOH . C 3 HOH A 166 866 188 HOH HOH . C 3 HOH A 167 867 171 HOH HOH . C 3 HOH A 168 868 10 HOH HOH . C 3 HOH A 169 869 99 HOH HOH . C 3 HOH A 170 870 100 HOH HOH . C 3 HOH A 171 871 118 HOH HOH . C 3 HOH A 172 872 177 HOH HOH . C 3 HOH A 173 873 21 HOH HOH . C 3 HOH A 174 874 149 HOH HOH . C 3 HOH A 175 875 85 HOH HOH . C 3 HOH A 176 876 119 HOH HOH . C 3 HOH A 177 877 134 HOH HOH . C 3 HOH A 178 878 40 HOH HOH . C 3 HOH A 179 879 166 HOH HOH . C 3 HOH A 180 880 45 HOH HOH . C 3 HOH A 181 881 183 HOH HOH . C 3 HOH A 182 882 158 HOH HOH . C 3 HOH A 183 883 160 HOH HOH . C 3 HOH A 184 884 103 HOH HOH . C 3 HOH A 185 885 87 HOH HOH . C 3 HOH A 186 886 93 HOH HOH . C 3 HOH A 187 887 89 HOH HOH . C 3 HOH A 188 888 39 HOH HOH . C 3 HOH A 189 889 101 HOH HOH . C 3 HOH A 190 890 138 HOH HOH . C 3 HOH A 191 891 169 HOH HOH . C 3 HOH A 192 892 88 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 O3P C5P . . . B 2 -34.011 12.682 11.587 1 78.07 ? O3P C5P 601 A 1 HETATM 2 P P C5P . . . B 2 -32.517 12.613 11.333 1 82.1 ? P C5P 601 A 1 HETATM 3 O O1P C5P . . . B 2 -32.146 13.638 10.251 1 81.62 ? O1P C5P 601 A 1 HETATM 4 O O2P C5P . . . B 2 -31.92 11.254 10.993 1 80.62 ? O2P C5P 601 A 1 HETATM 5 O O5' C5P . . . B 2 -31.81 13.055 12.69 1 75.83 ? O5' C5P 601 A 1 HETATM 6 C C5' C5P . . . B 2 -32.484 12.902 13.927 1 70.27 ? C5' C5P 601 A 1 HETATM 7 C C4' C5P . . . B 2 -31.65 13.38 15.087 1 67.73 ? C4' C5P 601 A 1 HETATM 8 O O4' C5P . . . B 2 -31.79 14.82 15.232 1 58.19 ? O4' C5P 601 A 1 HETATM 9 C C3' C5P . . . B 2 -32.051 12.827 16.447 1 61.99 ? C3' C5P 601 A 1 HETATM 10 O O3' C5P . . . B 2 -31.514 11.537 16.696 1 59.92 ? O3' C5P 601 A 1 HETATM 11 C C2' C5P . . . B 2 -31.542 13.89 17.41 1 55.54 ? C2' C5P 601 A 1 HETATM 12 O O2' C5P . . . B 2 -30.151 13.709 17.643 1 52.41 ? O2' C5P 601 A 1 HETATM 13 C C1' C5P . . . B 2 -31.749 15.173 16.594 1 55.86 ? C1' C5P 601 A 1 HETATM 14 N N1 C5P . . . B 2 -33.004 15.885 16.949 1 54.69 ? N1 C5P 601 A 1 HETATM 15 C C2 C5P . . . B 2 -32.992 16.639 18.213 1 55.28 ? C2 C5P 601 A 1 HETATM 16 N N3 C5P . . . B 2 -34.186 17.389 18.654 1 51.44 ? N3 C5P 601 A 1 HETATM 17 C C4 C5P . . . B 2 -35.35 17.407 17.874 1 44.14 ? C4 C5P 601 A 1 HETATM 18 C C5 C5P . . . B 2 -35.38 16.65 16.594 1 46.32 ? C5 C5P 601 A 1 HETATM 19 C C6 C5P . . . B 2 -34.187 15.89 16.141 1 44.58 ? C6 C5P 601 A 1 HETATM 20 O O2 C5P . . . B 2 -31.98 16.626 18.894 1 65.56 ? O2 C5P 601 A 1 HETATM 21 N N4 C5P . . . B 2 -36.487 18.173 18.363 1 50.5 ? N4 C5P 601 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #