data_1QF9 # _model_server_result.job_id d_G6Y7hp9PUKH2KhoVJ2eA _model_server_result.datetime_utc '2024-11-13 12:10:50' _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 1qf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":196}' # _entry.id 1QF9 # _exptl.entry_id 1QF9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 5 _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 90 _cell.entry_id 1QF9 _cell.length_a 78 _cell.length_b 78 _cell.length_c 100.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QF9 _symmetry.cell_setting tetragonal _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 5 _struct_asym.id E _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 NH2 ARG 148 A ARG 148 1_555 B AL ALF . A ALF 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.68 ? metalc ? metalc2 A NH1 ARG 148 A ARG 148 1_555 B AL ALF . A ALF 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.653 ? metalc ? metalc3 D O3B ADP . A ADP 195 1_555 B AL ALF . A ALF 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc4 D O2B ADP . A ADP 195 1_555 B AL ALF . A ALF 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.704 ? metalc ? metalc5 D O2B ADP . A ADP 195 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc6 E O3P C5P . A C5P 196 1_555 B AL ALF . A ALF 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc7 F O HOH . A HOH 198 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc8 F O HOH . A HOH 215 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc9 F O HOH . A HOH 220 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc10 F O HOH . A HOH 227 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc11 B F2 ALF . A ALF 499 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc12 B AL ALF . A ALF 499 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.405 ? metalc ? metalc13 B F3 ALF . A ALF 499 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? # _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 118 n n O3P HOP3 C5P sing 119 n n P O1P C5P doub 120 n n P O2P C5P sing 121 n n P O5' C5P sing 122 n n O2P HOP2 C5P sing 123 n n O5' C5' C5P sing 124 n n C5' C4' C5P sing 125 n n C5' "H5'1" C5P sing 126 n n C5' "H5'2" C5P sing 127 n n C4' O4' C5P sing 128 n n C4' C3' C5P sing 129 n n C4' H4' C5P sing 130 n n O4' C1' C5P sing 131 n n C3' O3' C5P sing 132 n n C3' C2' C5P sing 133 n n C3' H3' C5P sing 134 n n O3' HO3' C5P sing 135 n n C2' O2' C5P sing 136 n n C2' C1' C5P sing 137 n n C2' "H2'1" C5P sing 138 n n O2' HO2' C5P sing 139 n n C1' N1 C5P sing 140 n n C1' H1' C5P sing 141 n n N1 C2 C5P sing 142 n n N1 C6 C5P sing 143 n n C2 N3 C5P sing 144 n n C2 O2 C5P doub 145 n n N3 C4 C5P doub 146 n n C4 C5 C5P sing 147 n n C4 N4 C5P sing 148 n n C5 C6 C5P doub 149 n n C5 H5 C5P sing 150 n n C6 H6 C5P sing 151 n n N4 HN41 C5P sing 152 n n N4 HN42 C5P sing 153 n n # _atom_sites.entry_id 1QF9 _atom_sites.fract_transf_matrix[1][1] 0.01282 _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] 0.01282 _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] 0.00994 _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 ALF A 1 499 499 ALF ALF . C 3 MG A 1 500 500 MG MG . D 4 ADP A 1 195 195 ADP ADP . E 5 C5P A 1 196 196 C5P C5P . F 6 HOH A 1 197 197 HOH HOH . F 6 HOH A 2 198 198 HOH HOH . F 6 HOH A 3 200 200 HOH HOH . F 6 HOH A 4 201 201 HOH HOH . F 6 HOH A 5 202 202 HOH HOH . F 6 HOH A 6 203 203 HOH HOH . F 6 HOH A 7 204 204 HOH HOH . F 6 HOH A 8 206 206 HOH HOH . F 6 HOH A 9 207 207 HOH HOH . F 6 HOH A 10 208 208 HOH HOH . F 6 HOH A 11 210 210 HOH HOH . F 6 HOH A 12 211 211 HOH HOH . F 6 HOH A 13 212 212 HOH HOH . F 6 HOH A 14 214 214 HOH HOH . F 6 HOH A 15 215 215 HOH HOH . F 6 HOH A 16 216 216 HOH HOH . F 6 HOH A 17 218 218 HOH HOH . F 6 HOH A 18 220 220 HOH HOH . F 6 HOH A 19 221 221 HOH HOH . F 6 HOH A 20 222 222 HOH HOH . F 6 HOH A 21 223 223 HOH HOH . F 6 HOH A 22 226 226 HOH HOH . F 6 HOH A 23 227 227 HOH HOH . F 6 HOH A 24 228 228 HOH HOH . F 6 HOH A 25 229 229 HOH HOH . F 6 HOH A 26 231 231 HOH HOH . F 6 HOH A 27 232 232 HOH HOH . F 6 HOH A 28 233 233 HOH HOH . F 6 HOH A 29 234 234 HOH HOH . F 6 HOH A 30 236 236 HOH HOH . F 6 HOH A 31 238 238 HOH HOH . F 6 HOH A 32 239 239 HOH HOH . F 6 HOH A 33 242 242 HOH HOH . F 6 HOH A 34 244 244 HOH HOH . F 6 HOH A 35 245 245 HOH HOH . F 6 HOH A 36 509 509 HOH HOH . F 6 HOH A 37 512 512 HOH HOH . F 6 HOH A 38 528 528 HOH HOH . F 6 HOH A 39 531 531 HOH HOH . F 6 HOH A 40 532 532 HOH HOH . F 6 HOH A 41 533 533 HOH HOH . F 6 HOH A 42 536 536 HOH HOH . F 6 HOH A 43 538 538 HOH HOH . F 6 HOH A 44 543 543 HOH HOH . F 6 HOH A 45 553 553 HOH HOH . F 6 HOH A 46 558 558 HOH HOH . F 6 HOH A 47 562 562 HOH HOH . F 6 HOH A 48 563 563 HOH HOH . F 6 HOH A 49 564 564 HOH HOH . F 6 HOH A 50 566 566 HOH HOH . F 6 HOH A 51 568 568 HOH HOH . F 6 HOH A 52 569 569 HOH HOH . F 6 HOH A 53 577 577 HOH HOH . F 6 HOH A 54 580 580 HOH HOH . F 6 HOH A 55 582 582 HOH HOH . F 6 HOH A 56 591 591 HOH HOH . F 6 HOH A 57 599 599 HOH HOH . F 6 HOH A 58 601 601 HOH HOH . F 6 HOH A 59 602 602 HOH HOH . F 6 HOH A 60 603 603 HOH HOH . F 6 HOH A 61 604 604 HOH HOH . F 6 HOH A 62 605 605 HOH HOH . F 6 HOH A 63 606 606 HOH HOH . F 6 HOH A 64 607 607 HOH HOH . F 6 HOH A 65 608 608 HOH HOH . F 6 HOH A 66 610 610 HOH HOH . F 6 HOH A 67 611 611 HOH HOH . F 6 HOH A 68 612 612 HOH HOH . F 6 HOH A 69 613 613 HOH HOH . F 6 HOH A 70 614 614 HOH HOH . F 6 HOH A 71 619 619 HOH HOH . F 6 HOH A 72 620 620 HOH HOH . F 6 HOH A 73 621 621 HOH HOH . F 6 HOH A 74 622 622 HOH HOH . F 6 HOH A 75 623 623 HOH HOH . F 6 HOH A 76 624 624 HOH HOH . F 6 HOH A 77 625 625 HOH HOH . F 6 HOH A 78 640 640 HOH HOH . F 6 HOH A 79 650 650 HOH HOH . F 6 HOH A 80 664 664 HOH HOH . F 6 HOH A 81 670 670 HOH HOH . F 6 HOH A 82 712 712 HOH HOH . F 6 HOH A 83 717 717 HOH HOH . F 6 HOH A 84 727 727 HOH HOH . F 6 HOH A 85 732 732 HOH HOH . F 6 HOH A 86 737 737 HOH HOH . F 6 HOH A 87 739 739 HOH HOH . F 6 HOH A 88 741 741 HOH HOH . F 6 HOH A 89 744 744 HOH HOH . F 6 HOH A 90 746 746 HOH HOH . F 6 HOH A 91 747 747 HOH HOH . F 6 HOH A 92 750 750 HOH HOH . F 6 HOH A 93 751 751 HOH HOH . F 6 HOH A 94 759 759 HOH HOH . F 6 HOH A 95 767 767 HOH HOH . F 6 HOH A 96 778 778 HOH HOH . F 6 HOH A 97 779 779 HOH HOH . F 6 HOH A 98 786 786 HOH HOH . F 6 HOH A 99 797 797 HOH HOH . F 6 HOH A 100 801 801 HOH HOH . F 6 HOH A 101 810 810 HOH HOH . F 6 HOH A 102 814 814 HOH HOH . F 6 HOH A 103 824 824 HOH HOH . F 6 HOH A 104 826 826 HOH HOH . F 6 HOH A 105 827 827 HOH HOH . F 6 HOH A 106 833 833 HOH HOH . F 6 HOH A 107 838 838 HOH HOH . F 6 HOH A 108 839 839 HOH HOH . F 6 HOH A 109 840 840 HOH HOH . F 6 HOH A 110 843 843 HOH HOH . F 6 HOH A 111 844 844 HOH HOH . F 6 HOH A 112 845 845 HOH HOH . F 6 HOH A 113 848 848 HOH HOH . F 6 HOH A 114 853 853 HOH HOH . F 6 HOH A 115 861 861 HOH HOH . F 6 HOH A 116 864 864 HOH HOH . F 6 HOH A 117 874 874 HOH HOH . F 6 HOH A 118 877 877 HOH HOH . F 6 HOH A 119 878 878 HOH HOH . F 6 HOH A 120 880 880 HOH HOH . F 6 HOH A 121 881 881 HOH HOH . F 6 HOH A 122 882 882 HOH HOH . F 6 HOH A 123 883 883 HOH HOH . F 6 HOH A 124 891 891 HOH HOH . F 6 HOH A 125 900 900 HOH HOH . F 6 HOH A 126 903 903 HOH HOH . F 6 HOH A 127 907 907 HOH HOH . F 6 HOH A 128 908 908 HOH HOH . F 6 HOH A 129 909 909 HOH HOH . F 6 HOH A 130 910 910 HOH HOH . F 6 HOH A 131 911 911 HOH HOH . F 6 HOH A 132 912 912 HOH HOH . F 6 HOH A 133 913 913 HOH HOH . F 6 HOH A 134 915 915 HOH HOH . F 6 HOH A 135 916 916 HOH HOH . F 6 HOH A 136 917 917 HOH HOH . F 6 HOH A 137 918 918 HOH HOH . F 6 HOH A 138 919 919 HOH HOH . F 6 HOH A 139 920 920 HOH HOH . F 6 HOH A 140 923 923 HOH HOH . F 6 HOH A 141 925 925 HOH HOH . F 6 HOH A 142 928 928 HOH HOH . F 6 HOH A 143 930 930 HOH HOH . F 6 HOH A 144 931 931 HOH HOH . F 6 HOH A 145 932 932 HOH HOH . F 6 HOH A 146 933 933 HOH HOH . F 6 HOH A 147 934 934 HOH HOH . F 6 HOH A 148 935 935 HOH HOH . F 6 HOH A 149 936 936 HOH HOH . F 6 HOH A 150 937 937 HOH HOH . F 6 HOH A 151 938 938 HOH HOH . F 6 HOH A 152 939 939 HOH HOH . F 6 HOH A 153 940 940 HOH HOH . F 6 HOH A 154 941 941 HOH HOH . F 6 HOH A 155 942 942 HOH HOH . F 6 HOH A 156 950 950 HOH HOH . F 6 HOH A 157 951 951 HOH HOH . F 6 HOH A 158 952 952 HOH HOH . F 6 HOH A 159 953 953 HOH HOH . F 6 HOH A 160 955 955 HOH HOH . F 6 HOH A 161 956 956 HOH HOH . F 6 HOH A 162 957 957 HOH HOH . F 6 HOH A 163 961 961 HOH HOH . F 6 HOH A 164 963 963 HOH HOH . F 6 HOH A 165 965 965 HOH HOH . F 6 HOH A 166 966 966 HOH HOH . F 6 HOH A 167 969 969 HOH HOH . F 6 HOH A 168 970 970 HOH HOH . F 6 HOH A 169 974 974 HOH HOH . F 6 HOH A 170 975 975 HOH HOH . F 6 HOH A 171 976 976 HOH HOH . F 6 HOH A 172 977 977 HOH HOH . F 6 HOH A 173 978 978 HOH HOH . F 6 HOH A 174 979 979 HOH HOH . F 6 HOH A 175 982 982 HOH HOH . F 6 HOH A 176 983 983 HOH HOH . F 6 HOH A 177 985 985 HOH HOH . F 6 HOH A 178 986 986 HOH HOH . F 6 HOH A 179 987 987 HOH HOH . F 6 HOH A 180 989 989 HOH HOH . F 6 HOH A 181 993 993 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 . . . E 5 37.623 69.755 -14.254 1 16.13 ? O3P C5P 196 A 1 HETATM 2 P P C5P . . . E 5 38.712 70.74 -14.185 1 15.95 ? P C5P 196 A 1 HETATM 3 O O1P C5P . . . E 5 38.848 71.487 -12.93 1 16.27 ? O1P C5P 196 A 1 HETATM 4 O O2P C5P . . . E 5 40.055 70.038 -14.526 1 14.39 ? O2P C5P 196 A 1 HETATM 5 O O5' C5P . . . E 5 38.507 71.789 -15.355 1 13.84 ? O5' C5P 196 A 1 HETATM 6 C C5' C5P . . . E 5 37.4 72.72 -15.269 1 14.75 ? C5' C5P 196 A 1 HETATM 7 C C4' C5P . . . E 5 37.399 73.567 -16.508 1 14.14 ? C4' C5P 196 A 1 HETATM 8 O O4' C5P . . . E 5 38.573 74.417 -16.498 1 17.05 ? O4' C5P 196 A 1 HETATM 9 C C3' C5P . . . E 5 37.456 72.829 -17.823 1 15.14 ? C3' C5P 196 A 1 HETATM 10 O O3' C5P . . . E 5 36.234 72.261 -18.164 1 13.23 ? O3' C5P 196 A 1 HETATM 11 C C2' C5P . . . E 5 37.853 73.949 -18.749 1 15.01 ? C2' C5P 196 A 1 HETATM 12 O O2' C5P . . . E 5 36.789 74.822 -19.003 1 17.24 ? O2' C5P 196 A 1 HETATM 13 C C1' C5P . . . E 5 38.957 74.623 -17.898 1 17.57 ? C1' C5P 196 A 1 HETATM 14 N N1 C5P . . . E 5 40.235 74.042 -18.202 1 15.96 ? N1 C5P 196 A 1 HETATM 15 C C2 C5P . . . E 5 40.998 74.587 -19.259 1 16.76 ? C2 C5P 196 A 1 HETATM 16 N N3 C5P . . . E 5 42.237 74.139 -19.569 1 15.33 ? N3 C5P 196 A 1 HETATM 17 C C4 C5P . . . E 5 42.799 73.091 -18.905 1 13.86 ? C4 C5P 196 A 1 HETATM 18 C C5 C5P . . . E 5 42.129 72.634 -17.803 1 14.36 ? C5 C5P 196 A 1 HETATM 19 C C6 C5P . . . E 5 40.955 73.078 -17.39 1 13.96 ? C6 C5P 196 A 1 HETATM 20 O O2 C5P . . . E 5 40.453 75.568 -19.999 1 15.8 ? O2 C5P 196 A 1 HETATM 21 N N4 C5P . . . E 5 43.987 72.587 -19.319 1 13.94 ? N4 C5P 196 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #