data_3UKD
#
_model_server_result.job_id            KhgcyhjoKrhAuFIfeHDI0w 
_model_server_result.datetime_utc      '2024-11-13 06:15:10' 
_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          3ukd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":196}' 
#
_entry.id    3UKD 
#
_exptl.entry_id    3UKD 
_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            3UKD 
_cell.length_a            78.8 
_cell.length_b            78.8 
_cell.length_c            100.7 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3UKD 
_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,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                      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 NH2 ARG 148 A ARG 148 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.405 ? 
metalc ? metalc2 C O2B ADP . A ADP 195 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc3 C O3B ADP . A ADP 195 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc4 C O2B ADP . A ADP 195 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.648 ? 
metalc ? metalc5 D O3P C5P . A C5P 196 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc6 D O2P C5P . A C5P 196 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.698 ? 
metalc ? metalc7 F O HOH . A HOH 198 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc8 F O HOH . A HOH 198 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.458 ? 
metalc ? metalc9 F O HOH . A HOH 215 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc10 F O HOH . A HOH 220 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc11 F O HOH . A HOH 227 1_555 B MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? 
metalc ? metalc12 B MG MG . A MG 500 1_555 E F3 AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc13 B MG MG . A MG 500 1_555 E AL AF3 . A AF3 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.595 ? 
#
_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 117 n n 
O3P HOP3 C5P sing 118 n n 
P O1P C5P doub 119 n n 
P O2P C5P sing 120 n n 
P O5' C5P sing 121 n n 
O2P HOP2 C5P sing 122 n n 
O5' C5' C5P sing 123 n n 
C5' C4' C5P sing 124 n n 
C5' "H5'1" C5P sing 125 n n 
C5' "H5'2" C5P sing 126 n n 
C4' O4' C5P sing 127 n n 
C4' C3' C5P sing 128 n n 
C4' H4' C5P sing 129 n n 
O4' C1' C5P sing 130 n n 
C3' O3' C5P sing 131 n n 
C3' C2' C5P sing 132 n n 
C3' H3' C5P sing 133 n n 
O3' HO3' C5P sing 134 n n 
C2' O2' C5P sing 135 n n 
C2' C1' C5P sing 136 n n 
C2' "H2'1" C5P sing 137 n n 
O2' HO2' C5P sing 138 n n 
C1' N1 C5P sing 139 n n 
C1' H1' C5P sing 140 n n 
N1 C2 C5P sing 141 n n 
N1 C6 C5P sing 142 n n 
C2 N3 C5P sing 143 n n 
C2 O2 C5P doub 144 n n 
N3 C4 C5P doub 145 n n 
C4 C5 C5P sing 146 n n 
C4 N4 C5P sing 147 n n 
C5 C6 C5P doub 148 n n 
C5 H5 C5P sing 149 n n 
C6 H6 C5P sing 150 n n 
N4 HN41 C5P sing 151 n n 
N4 HN42 C5P sing 152 n n 
#
_atom_sites.entry_id                     3UKD 
_atom_sites.fract_transf_matrix[1][1]    0.01269 
_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]    0.01269 
_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]    0.00993 
_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 AF3 A 1 501 501 AF3 AF3 . 
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 11 209 209 HOH HOH . 
F 6 HOH A 12 210 210 HOH HOH . 
F 6 HOH A 13 211 211 HOH HOH . 
F 6 HOH A 14 212 212 HOH HOH . 
F 6 HOH A 15 214 214 HOH HOH . 
F 6 HOH A 16 215 215 HOH HOH . 
F 6 HOH A 17 216 216 HOH HOH . 
F 6 HOH A 18 218 218 HOH HOH . 
F 6 HOH A 19 220 220 HOH HOH . 
F 6 HOH A 20 221 221 HOH HOH . 
F 6 HOH A 21 222 222 HOH HOH . 
F 6 HOH A 22 223 223 HOH HOH . 
F 6 HOH A 23 226 226 HOH HOH . 
F 6 HOH A 24 227 227 HOH HOH . 
F 6 HOH A 25 228 228 HOH HOH . 
F 6 HOH A 26 229 229 HOH HOH . 
F 6 HOH A 27 231 231 HOH HOH . 
F 6 HOH A 28 232 232 HOH HOH . 
F 6 HOH A 29 233 233 HOH HOH . 
F 6 HOH A 30 234 234 HOH HOH . 
F 6 HOH A 31 236 236 HOH HOH . 
F 6 HOH A 32 238 238 HOH HOH . 
F 6 HOH A 33 239 239 HOH HOH . 
F 6 HOH A 34 242 242 HOH HOH . 
F 6 HOH A 35 244 244 HOH HOH . 
F 6 HOH A 36 245 245 HOH HOH . 
F 6 HOH A 37 509 509 HOH HOH . 
F 6 HOH A 38 512 512 HOH HOH . 
F 6 HOH A 39 528 528 HOH HOH . 
F 6 HOH A 40 531 531 HOH HOH . 
F 6 HOH A 41 532 532 HOH HOH . 
F 6 HOH A 42 533 533 HOH HOH . 
F 6 HOH A 43 536 536 HOH HOH . 
F 6 HOH A 44 538 538 HOH HOH . 
F 6 HOH A 45 543 543 HOH HOH . 
F 6 HOH A 46 553 553 HOH HOH . 
F 6 HOH A 47 558 558 HOH HOH . 
F 6 HOH A 48 559 559 HOH HOH . 
F 6 HOH A 49 562 562 HOH HOH . 
F 6 HOH A 50 563 563 HOH HOH . 
F 6 HOH A 51 564 564 HOH HOH . 
F 6 HOH A 52 565 565 HOH HOH . 
F 6 HOH A 53 566 566 HOH HOH . 
F 6 HOH A 54 568 568 HOH HOH . 
F 6 HOH A 55 569 569 HOH HOH . 
F 6 HOH A 56 577 577 HOH HOH . 
F 6 HOH A 57 580 580 HOH HOH . 
F 6 HOH A 58 582 582 HOH HOH . 
F 6 HOH A 59 591 591 HOH HOH . 
F 6 HOH A 60 592 592 HOH HOH . 
F 6 HOH A 61 597 597 HOH HOH . 
F 6 HOH A 62 599 599 HOH HOH . 
F 6 HOH A 63 601 601 HOH HOH . 
F 6 HOH A 64 602 602 HOH HOH . 
F 6 HOH A 65 603 603 HOH HOH . 
F 6 HOH A 66 604 604 HOH HOH . 
F 6 HOH A 67 605 605 HOH HOH . 
F 6 HOH A 68 606 606 HOH HOH . 
F 6 HOH A 69 608 608 HOH HOH . 
F 6 HOH A 70 616 616 HOH HOH . 
F 6 HOH A 71 640 640 HOH HOH . 
F 6 HOH A 72 646 646 HOH HOH . 
F 6 HOH A 73 650 650 HOH HOH . 
F 6 HOH A 74 664 664 HOH HOH . 
F 6 HOH A 75 670 670 HOH HOH . 
F 6 HOH A 76 712 712 HOH HOH . 
F 6 HOH A 77 717 717 HOH HOH . 
F 6 HOH A 78 727 727 HOH HOH . 
F 6 HOH A 79 732 732 HOH HOH . 
F 6 HOH A 80 734 734 HOH HOH . 
F 6 HOH A 81 737 737 HOH HOH . 
F 6 HOH A 82 739 739 HOH HOH . 
F 6 HOH A 83 741 741 HOH HOH . 
F 6 HOH A 84 744 744 HOH HOH . 
F 6 HOH A 85 746 746 HOH HOH . 
F 6 HOH A 86 747 747 HOH HOH . 
F 6 HOH A 87 750 750 HOH HOH . 
F 6 HOH A 88 751 751 HOH HOH . 
F 6 HOH A 89 752 752 HOH HOH . 
F 6 HOH A 90 753 753 HOH HOH . 
F 6 HOH A 91 759 759 HOH HOH . 
F 6 HOH A 92 767 767 HOH HOH . 
F 6 HOH A 93 769 769 HOH HOH . 
F 6 HOH A 94 771 771 HOH HOH . 
F 6 HOH A 95 774 774 HOH HOH . 
F 6 HOH A 96 778 778 HOH HOH . 
F 6 HOH A 97 779 779 HOH HOH . 
F 6 HOH A 98 781 781 HOH HOH . 
F 6 HOH A 99 786 786 HOH HOH . 
F 6 HOH A 100 793 793 HOH HOH . 
F 6 HOH A 101 797 797 HOH HOH . 
F 6 HOH A 102 801 801 HOH HOH . 
F 6 HOH A 103 809 809 HOH HOH . 
F 6 HOH A 104 810 810 HOH HOH . 
F 6 HOH A 105 814 814 HOH HOH . 
F 6 HOH A 106 816 816 HOH HOH . 
F 6 HOH A 107 817 817 HOH HOH . 
F 6 HOH A 108 818 818 HOH HOH . 
F 6 HOH A 109 819 819 HOH HOH . 
F 6 HOH A 110 822 822 HOH HOH . 
F 6 HOH A 111 823 823 HOH HOH . 
F 6 HOH A 112 824 824 HOH HOH . 
F 6 HOH A 113 826 826 HOH HOH . 
F 6 HOH A 114 827 827 HOH HOH . 
F 6 HOH A 115 828 828 HOH HOH . 
F 6 HOH A 116 829 829 HOH HOH . 
F 6 HOH A 117 833 833 HOH HOH . 
F 6 HOH A 118 838 838 HOH HOH . 
F 6 HOH A 119 839 839 HOH HOH . 
F 6 HOH A 120 840 840 HOH HOH . 
F 6 HOH A 121 843 843 HOH HOH . 
F 6 HOH A 122 844 844 HOH HOH . 
F 6 HOH A 123 845 845 HOH HOH . 
F 6 HOH A 124 848 848 HOH HOH . 
F 6 HOH A 125 849 849 HOH HOH . 
F 6 HOH A 126 853 853 HOH HOH . 
F 6 HOH A 127 855 855 HOH HOH . 
F 6 HOH A 128 856 856 HOH HOH . 
F 6 HOH A 129 857 857 HOH HOH . 
F 6 HOH A 130 858 858 HOH HOH . 
F 6 HOH A 131 861 861 HOH HOH . 
F 6 HOH A 132 862 862 HOH HOH . 
F 6 HOH A 133 863 863 HOH HOH . 
F 6 HOH A 134 864 864 HOH HOH . 
F 6 HOH A 135 865 865 HOH HOH . 
F 6 HOH A 136 868 868 HOH HOH . 
F 6 HOH A 137 869 869 HOH HOH . 
F 6 HOH A 138 870 870 HOH HOH . 
F 6 HOH A 139 871 871 HOH HOH . 
F 6 HOH A 140 872 872 HOH HOH . 
F 6 HOH A 141 873 873 HOH HOH . 
F 6 HOH A 142 874 874 HOH HOH . 
F 6 HOH A 143 877 877 HOH HOH . 
F 6 HOH A 144 878 878 HOH HOH . 
F 6 HOH A 145 879 879 HOH HOH . 
F 6 HOH A 146 880 880 HOH HOH . 
F 6 HOH A 147 881 881 HOH HOH . 
F 6 HOH A 148 882 882 HOH HOH . 
F 6 HOH A 149 883 883 HOH HOH . 
F 6 HOH A 150 890 890 HOH HOH . 
F 6 HOH A 151 891 891 HOH HOH . 
F 6 HOH A 152 892 892 HOH HOH . 
F 6 HOH A 153 893 893 HOH HOH . 
F 6 HOH A 154 894 894 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 37.864 70.432 -14.284 1 17.56 ? O3P C5P 196 A 1 
HETATM 2 P P C5P . . . D 4 39.087 71.346 -14.214 1 18.75 ? P C5P 196 A 1 
HETATM 3 O O1P C5P . . . D 4 39.035 72.13 -12.963 1 18.58 ? O1P C5P 196 A 1 
HETATM 4 O O2P C5P . . . D 4 40.268 70.556 -14.444 1 18.05 ? O2P C5P 196 A 1 
HETATM 5 O O5' C5P . . . D 4 38.852 72.334 -15.438 1 15.82 ? O5' C5P 196 A 1 
HETATM 6 C C5' C5P . . . D 4 37.85 73.357 -15.404 1 17.93 ? C5' C5P 196 A 1 
HETATM 7 C C4' C5P . . . D 4 37.885 74.195 -16.675 1 16.03 ? C4' C5P 196 A 1 
HETATM 8 O O4' C5P . . . D 4 39.057 74.939 -16.64 1 16.48 ? O4' C5P 196 A 1 
HETATM 9 C C3' C5P . . . D 4 38.004 73.393 -17.926 1 16.16 ? C3' C5P 196 A 1 
HETATM 10 O O3' C5P . . . D 4 36.774 72.768 -18.261 1 15.04 ? O3' C5P 196 A 1 
HETATM 11 C C2' C5P . . . D 4 38.347 74.562 -18.832 1 14.65 ? C2' C5P 196 A 1 
HETATM 12 O O2' C5P . . . D 4 37.23 75.453 -19.05 1 15.77 ? O2' C5P 196 A 1 
HETATM 13 C C1' C5P . . . D 4 39.442 75.212 -17.989 1 16.09 ? C1' C5P 196 A 1 
HETATM 14 N N1 C5P . . . D 4 40.718 74.632 -18.287 1 15.62 ? N1 C5P 196 A 1 
HETATM 15 C C2 C5P . . . D 4 41.459 75.131 -19.354 1 14.92 ? C2 C5P 196 A 1 
HETATM 16 N N3 C5P . . . D 4 42.655 74.666 -19.674 1 14.35 ? N3 C5P 196 A 1 
HETATM 17 C C4 C5P . . . D 4 43.223 73.642 -19.005 1 16.41 ? C4 C5P 196 A 1 
HETATM 18 C C5 C5P . . . D 4 42.594 73.242 -17.879 1 16.06 ? C5 C5P 196 A 1 
HETATM 19 C C6 C5P . . . D 4 41.446 73.695 -17.461 1 15.01 ? C6 C5P 196 A 1 
HETATM 20 O O2 C5P . . . D 4 40.919 76.081 -20.103 1 17.27 ? O2 C5P 196 A 1 
HETATM 21 N N4 C5P . . . D 4 44.391 73.104 -19.418 1 15.81 ? N4 C5P 196 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           21 
#