data_2UKD # _model_server_result.job_id MNcSNNQXOyFCOMNWDSqLuw _model_server_result.datetime_utc '2024-10-18 23:26:25' _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 2ukd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":196}' # _entry.id 2UKD # _exptl.entry_id 2UKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 4 _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 2UKD _cell.length_a 78.7 _cell.length_b 78.7 _cell.length_c 100.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2UKD _symmetry.cell_setting ? _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 _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 C O2B ADP . A ADP 195 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc2 E O HOH . A HOH 198 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc3 E O HOH . A HOH 215 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc4 E O HOH . A HOH 220 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc5 E O HOH . A HOH 227 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc6 B MG MG . A MG 500 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? # _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 114 n n O3P HOP3 C5P sing 115 n n P O1P C5P doub 116 n n P O2P C5P sing 117 n n P O5' C5P sing 118 n n O2P HOP2 C5P sing 119 n n O5' C5' C5P sing 120 n n C5' C4' C5P sing 121 n n C5' "H5'1" C5P sing 122 n n C5' "H5'2" C5P sing 123 n n C4' O4' C5P sing 124 n n C4' C3' C5P sing 125 n n C4' H4' C5P sing 126 n n O4' C1' C5P sing 127 n n C3' O3' C5P sing 128 n n C3' C2' C5P sing 129 n n C3' H3' C5P sing 130 n n O3' HO3' C5P sing 131 n n C2' O2' C5P sing 132 n n C2' C1' C5P sing 133 n n C2' "H2'1" C5P sing 134 n n O2' HO2' C5P sing 135 n n C1' N1 C5P sing 136 n n C1' H1' C5P sing 137 n n N1 C2 C5P sing 138 n n N1 C6 C5P sing 139 n n C2 N3 C5P sing 140 n n C2 O2 C5P doub 141 n n N3 C4 C5P doub 142 n n C4 C5 C5P sing 143 n n C4 N4 C5P sing 144 n n C5 C6 C5P doub 145 n n C5 H5 C5P sing 146 n n C6 H6 C5P sing 147 n n N4 HN41 C5P sing 148 n n N4 HN42 C5P sing 149 n n # _atom_sites.entry_id 2UKD _atom_sites.fract_transf_matrix[1][1] 0.012706 _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] 0.012706 _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] 0.00999 _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 MG A 1 500 500 MG MG . C 3 ADP A 1 195 195 ADP ADP . D 4 C5P A 1 196 196 C5P C5P . E 5 HOH A 1 197 197 HOH HOH . E 5 HOH A 2 198 198 HOH HOH . E 5 HOH A 3 200 200 HOH HOH . E 5 HOH A 4 201 201 HOH HOH . E 5 HOH A 5 202 202 HOH HOH . E 5 HOH A 6 203 203 HOH HOH . E 5 HOH A 7 204 204 HOH HOH . E 5 HOH A 8 206 206 HOH HOH . E 5 HOH A 9 207 207 HOH HOH . E 5 HOH A 10 208 208 HOH HOH . E 5 HOH A 11 209 209 HOH HOH . E 5 HOH A 12 210 210 HOH HOH . E 5 HOH A 13 211 211 HOH HOH . E 5 HOH A 14 212 212 HOH HOH . E 5 HOH A 15 214 214 HOH HOH . E 5 HOH A 16 215 215 HOH HOH . E 5 HOH A 17 216 216 HOH HOH . E 5 HOH A 18 218 218 HOH HOH . E 5 HOH A 19 220 220 HOH HOH . E 5 HOH A 20 221 221 HOH HOH . E 5 HOH A 21 222 222 HOH HOH . E 5 HOH A 22 223 223 HOH HOH . E 5 HOH A 23 226 226 HOH HOH . E 5 HOH A 24 227 227 HOH HOH . E 5 HOH A 25 228 228 HOH HOH . E 5 HOH A 26 229 229 HOH HOH . E 5 HOH A 27 231 231 HOH HOH . E 5 HOH A 28 232 232 HOH HOH . E 5 HOH A 29 233 233 HOH HOH . E 5 HOH A 30 234 234 HOH HOH . E 5 HOH A 31 236 236 HOH HOH . E 5 HOH A 32 238 238 HOH HOH . E 5 HOH A 33 239 239 HOH HOH . E 5 HOH A 34 242 242 HOH HOH . E 5 HOH A 35 244 244 HOH HOH . E 5 HOH A 36 245 245 HOH HOH . E 5 HOH A 37 501 501 HOH HOH . E 5 HOH A 38 509 509 HOH HOH . E 5 HOH A 39 512 512 HOH HOH . E 5 HOH A 40 528 528 HOH HOH . E 5 HOH A 41 531 531 HOH HOH . E 5 HOH A 42 532 532 HOH HOH . E 5 HOH A 43 533 533 HOH HOH . E 5 HOH A 44 536 536 HOH HOH . E 5 HOH A 45 538 538 HOH HOH . E 5 HOH A 46 543 543 HOH HOH . E 5 HOH A 47 553 553 HOH HOH . E 5 HOH A 48 558 558 HOH HOH . E 5 HOH A 49 559 559 HOH HOH . E 5 HOH A 50 562 562 HOH HOH . E 5 HOH A 51 563 563 HOH HOH . E 5 HOH A 52 564 564 HOH HOH . E 5 HOH A 53 565 565 HOH HOH . E 5 HOH A 54 566 566 HOH HOH . E 5 HOH A 55 568 568 HOH HOH . E 5 HOH A 56 569 569 HOH HOH . E 5 HOH A 57 577 577 HOH HOH . E 5 HOH A 58 580 580 HOH HOH . E 5 HOH A 59 582 582 HOH HOH . E 5 HOH A 60 591 591 HOH HOH . E 5 HOH A 61 597 597 HOH HOH . E 5 HOH A 62 601 601 HOH HOH . E 5 HOH A 63 602 602 HOH HOH . E 5 HOH A 64 603 603 HOH HOH . E 5 HOH A 65 604 604 HOH HOH . E 5 HOH A 66 605 605 HOH HOH . E 5 HOH A 67 608 608 HOH HOH . E 5 HOH A 68 616 616 HOH HOH . E 5 HOH A 69 640 640 HOH HOH . E 5 HOH A 70 650 650 HOH HOH . E 5 HOH A 71 664 664 HOH HOH . E 5 HOH A 72 670 670 HOH HOH . E 5 HOH A 73 717 717 HOH HOH . E 5 HOH A 74 727 727 HOH HOH . E 5 HOH A 75 732 732 HOH HOH . E 5 HOH A 76 737 737 HOH HOH . E 5 HOH A 77 739 739 HOH HOH . E 5 HOH A 78 741 741 HOH HOH . E 5 HOH A 79 744 744 HOH HOH . E 5 HOH A 80 746 746 HOH HOH . E 5 HOH A 81 747 747 HOH HOH . E 5 HOH A 82 750 750 HOH HOH . E 5 HOH A 83 751 751 HOH HOH . E 5 HOH A 84 752 752 HOH HOH . E 5 HOH A 85 753 753 HOH HOH . E 5 HOH A 86 767 767 HOH HOH . E 5 HOH A 87 769 769 HOH HOH . E 5 HOH A 88 774 774 HOH HOH . E 5 HOH A 89 778 778 HOH HOH . E 5 HOH A 90 779 779 HOH HOH . E 5 HOH A 91 781 781 HOH HOH . E 5 HOH A 92 786 786 HOH HOH . E 5 HOH A 93 797 797 HOH HOH . E 5 HOH A 94 801 801 HOH HOH . E 5 HOH A 95 807 807 HOH HOH . E 5 HOH A 96 810 810 HOH HOH . E 5 HOH A 97 816 816 HOH HOH . E 5 HOH A 98 818 818 HOH HOH . E 5 HOH A 99 819 819 HOH HOH . E 5 HOH A 100 823 823 HOH HOH . E 5 HOH A 101 824 824 HOH HOH . E 5 HOH A 102 825 825 HOH HOH . E 5 HOH A 103 826 826 HOH HOH . E 5 HOH A 104 827 827 HOH HOH . E 5 HOH A 105 828 828 HOH HOH . E 5 HOH A 106 829 829 HOH HOH . E 5 HOH A 107 832 832 HOH HOH . E 5 HOH A 108 833 833 HOH HOH . E 5 HOH A 109 837 837 HOH HOH . E 5 HOH A 110 838 838 HOH HOH . E 5 HOH A 111 839 839 HOH HOH . E 5 HOH A 112 840 840 HOH HOH . E 5 HOH A 113 843 843 HOH HOH . E 5 HOH A 114 844 844 HOH HOH . E 5 HOH A 115 845 845 HOH HOH . E 5 HOH A 116 848 848 HOH HOH . E 5 HOH A 117 849 849 HOH HOH . E 5 HOH A 118 853 853 HOH HOH . E 5 HOH A 119 857 857 HOH HOH . E 5 HOH A 120 863 863 HOH HOH . E 5 HOH A 121 864 864 HOH HOH . E 5 HOH A 122 870 870 HOH HOH . E 5 HOH A 123 871 871 HOH HOH . E 5 HOH A 124 872 872 HOH HOH . E 5 HOH A 125 874 874 HOH HOH . E 5 HOH A 126 877 877 HOH HOH . E 5 HOH A 127 879 879 HOH HOH . E 5 HOH A 128 881 881 HOH HOH . E 5 HOH A 129 882 882 HOH HOH . E 5 HOH A 130 883 883 HOH HOH . E 5 HOH A 131 890 890 HOH HOH . E 5 HOH A 132 900 900 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 . . . D 4 37.848 70.392 -15.119 1 20.42 ? O3P C5P 196 A 1 HETATM 2 P P C5P . . . D 4 39.072 71.195 -14.69 1 20.03 ? P C5P 196 A 1 HETATM 3 O O1P C5P . . . D 4 38.901 71.626 -13.308 1 22.39 ? O1P C5P 196 A 1 HETATM 4 O O2P C5P . . . D 4 40.228 70.406 -14.972 1 19.41 ? O2P C5P 196 A 1 HETATM 5 O O5' C5P . . . D 4 39.059 72.502 -15.597 1 19.63 ? O5' C5P 196 A 1 HETATM 6 C C5' C5P . . . D 4 37.949 73.454 -15.596 1 17.36 ? C5' C5P 196 A 1 HETATM 7 C C4' C5P . . . D 4 37.905 74.258 -16.911 1 16.92 ? C4' C5P 196 A 1 HETATM 8 O O4' C5P . . . D 4 39.112 75.013 -16.963 1 16.66 ? O4' C5P 196 A 1 HETATM 9 C C3' C5P . . . D 4 38.024 73.42 -18.157 1 16.92 ? C3' C5P 196 A 1 HETATM 10 O O3' C5P . . . D 4 36.824 72.816 -18.501 1 15.55 ? O3' C5P 196 A 1 HETATM 11 C C2' C5P . . . D 4 38.394 74.519 -19.118 1 16.78 ? C2' C5P 196 A 1 HETATM 12 O O2' C5P . . . D 4 37.283 75.368 -19.416 1 17.44 ? O2' C5P 196 A 1 HETATM 13 C C1' C5P . . . D 4 39.493 75.213 -18.318 1 16.52 ? C1' C5P 196 A 1 HETATM 14 N N1 C5P . . . D 4 40.799 74.6 -18.591 1 17.63 ? N1 C5P 196 A 1 HETATM 15 C C2 C5P . . . D 4 41.614 75.139 -19.59 1 18.04 ? C2 C5P 196 A 1 HETATM 16 N N3 C5P . . . D 4 42.855 74.674 -19.841 1 17.45 ? N3 C5P 196 A 1 HETATM 17 C C4 C5P . . . D 4 43.359 73.627 -19.168 1 16.99 ? C4 C5P 196 A 1 HETATM 18 C C5 C5P . . . D 4 42.642 73.181 -18.14 1 17.5 ? C5 C5P 196 A 1 HETATM 19 C C6 C5P . . . D 4 41.468 73.632 -17.78 1 16.4 ? C6 C5P 196 A 1 HETATM 20 O O2 C5P . . . D 4 41.12 76.142 -20.349 1 19.49 ? O2 C5P 196 A 1 HETATM 21 N N4 C5P . . . D 4 44.53 73.102 -19.499 1 17 ? 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 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #