data_7F3Z
#
_model_server_result.job_id            hZwobjnAtb6I3gdn4K5chA 
_model_server_result.datetime_utc      '2024-11-12 21:47:23' 
_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          7f3z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":702}' 
#
_entry.id    7F3Z 
#
_exptl.entry_id    7F3Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            7F3Z 
_cell.length_a            56.332 
_cell.length_b            153.739 
_cell.length_c            164.119 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7F3Z 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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,I,J,K,L 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 H N N 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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
N1 C2 UMP sing 493 n n 
N1 C6 UMP sing 494 n n 
N1 C1' UMP sing 495 n n 
C2 N3 UMP sing 496 n n 
C2 O2 UMP doub 497 n n 
N3 C4 UMP sing 498 n n 
N3 HN3 UMP sing 499 n n 
C4 C5 UMP sing 500 n n 
C4 O4 UMP doub 501 n n 
C5 C6 UMP doub 502 n n 
C5 H5 UMP sing 503 n n 
C6 H6 UMP sing 504 n n 
C1' C2' UMP sing 505 n n 
C1' O4' UMP sing 506 n n 
C1' H1' UMP sing 507 n n 
C2' C3' UMP sing 508 n n 
C2' H2' UMP sing 509 n n 
C2' "H2''" UMP sing 510 n n 
C3' C4' UMP sing 511 n n 
C3' O3' UMP sing 512 n n 
C3' H3' UMP sing 513 n n 
C4' O4' UMP sing 514 n n 
C4' C5' UMP sing 515 n n 
C4' H4' UMP sing 516 n n 
O3' HO3' UMP sing 517 n n 
C5' O5' UMP sing 518 n n 
C5' H5' UMP sing 519 n n 
C5' "H5''" UMP sing 520 n n 
O5' P UMP sing 521 n n 
P OP1 UMP doub 522 n n 
P OP2 UMP sing 523 n n 
P OP3 UMP sing 524 n n 
OP2 HOP2 UMP sing 525 n n 
OP3 HOP3 UMP sing 526 n n 
#
_atom_sites.entry_id                     7F3Z 
_atom_sites.fract_transf_matrix[1][1]    0.017752 
_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]    0.006505 
_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]    0.006093 
_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 2 NDP A 1 701 701 NDP NDP . 
D 3 UMP A 1 702 702 UMP UMP . 
E 4 TOP A 1 703 703 TOP TOP . 
F 5 GOL A 1 704 704 GOL GOL . 
G 2 NDP B 1 701 701 NDP NDP . 
H 3 UMP B 1 702 702 UMP UMP . 
I 4 TOP B 1 703 703 TOP TOP . 
J 5 GOL B 1 704 704 GOL GOL . 
K 6 HOH A 1 801 185 HOH HOH . 
K 6 HOH A 2 802 157 HOH HOH . 
K 6 HOH A 3 803 89 HOH HOH . 
K 6 HOH A 4 804 63 HOH HOH . 
K 6 HOH A 5 805 41 HOH HOH . 
K 6 HOH A 6 806 95 HOH HOH . 
K 6 HOH A 7 807 144 HOH HOH . 
K 6 HOH A 8 808 5 HOH HOH . 
K 6 HOH A 9 809 60 HOH HOH . 
K 6 HOH A 10 810 168 HOH HOH . 
K 6 HOH A 11 811 149 HOH HOH . 
K 6 HOH A 12 812 49 HOH HOH . 
K 6 HOH A 13 813 53 HOH HOH . 
K 6 HOH A 14 814 70 HOH HOH . 
K 6 HOH A 15 815 176 HOH HOH . 
K 6 HOH A 16 816 73 HOH HOH . 
K 6 HOH A 17 817 90 HOH HOH . 
K 6 HOH A 18 818 24 HOH HOH . 
K 6 HOH A 19 819 43 HOH HOH . 
K 6 HOH A 20 820 74 HOH HOH . 
K 6 HOH A 21 821 135 HOH HOH . 
K 6 HOH A 22 822 195 HOH HOH . 
K 6 HOH A 23 823 33 HOH HOH . 
K 6 HOH A 24 824 153 HOH HOH . 
K 6 HOH A 25 825 94 HOH HOH . 
K 6 HOH A 26 826 40 HOH HOH . 
K 6 HOH A 27 827 190 HOH HOH . 
K 6 HOH A 28 828 148 HOH HOH . 
K 6 HOH A 29 829 162 HOH HOH . 
K 6 HOH A 30 830 15 HOH HOH . 
K 6 HOH A 31 831 4 HOH HOH . 
K 6 HOH A 32 832 170 HOH HOH . 
K 6 HOH A 33 833 127 HOH HOH . 
K 6 HOH A 34 834 75 HOH HOH . 
K 6 HOH A 35 835 126 HOH HOH . 
K 6 HOH A 36 836 151 HOH HOH . 
K 6 HOH A 37 837 50 HOH HOH . 
K 6 HOH A 38 838 36 HOH HOH . 
K 6 HOH A 39 839 180 HOH HOH . 
K 6 HOH A 40 840 160 HOH HOH . 
K 6 HOH A 41 841 174 HOH HOH . 
K 6 HOH A 42 842 188 HOH HOH . 
K 6 HOH A 43 843 12 HOH HOH . 
K 6 HOH A 44 844 137 HOH HOH . 
K 6 HOH A 45 845 57 HOH HOH . 
K 6 HOH A 46 846 19 HOH HOH . 
K 6 HOH A 47 847 122 HOH HOH . 
K 6 HOH A 48 848 178 HOH HOH . 
K 6 HOH A 49 849 146 HOH HOH . 
K 6 HOH A 50 850 173 HOH HOH . 
K 6 HOH A 51 851 45 HOH HOH . 
K 6 HOH A 52 852 3 HOH HOH . 
K 6 HOH A 53 853 171 HOH HOH . 
K 6 HOH A 54 854 29 HOH HOH . 
K 6 HOH A 55 855 102 HOH HOH . 
K 6 HOH A 56 856 98 HOH HOH . 
K 6 HOH A 57 857 101 HOH HOH . 
K 6 HOH A 58 858 21 HOH HOH . 
K 6 HOH A 59 859 115 HOH HOH . 
K 6 HOH A 60 860 136 HOH HOH . 
K 6 HOH A 61 861 169 HOH HOH . 
K 6 HOH A 62 862 199 HOH HOH . 
K 6 HOH A 63 863 38 HOH HOH . 
K 6 HOH A 64 864 147 HOH HOH . 
K 6 HOH A 65 865 2 HOH HOH . 
K 6 HOH A 66 866 104 HOH HOH . 
K 6 HOH A 67 867 161 HOH HOH . 
K 6 HOH A 68 868 196 HOH HOH . 
K 6 HOH A 69 869 26 HOH HOH . 
K 6 HOH A 70 870 100 HOH HOH . 
K 6 HOH A 71 871 87 HOH HOH . 
K 6 HOH A 72 872 83 HOH HOH . 
K 6 HOH A 73 873 107 HOH HOH . 
K 6 HOH A 74 874 156 HOH HOH . 
K 6 HOH A 75 875 132 HOH HOH . 
K 6 HOH A 76 876 175 HOH HOH . 
K 6 HOH A 77 877 181 HOH HOH . 
K 6 HOH A 78 878 145 HOH HOH . 
K 6 HOH A 79 879 72 HOH HOH . 
K 6 HOH A 80 880 125 HOH HOH . 
K 6 HOH A 81 881 193 HOH HOH . 
K 6 HOH A 82 882 48 HOH HOH . 
K 6 HOH A 83 883 79 HOH HOH . 
K 6 HOH A 84 884 47 HOH HOH . 
K 6 HOH A 85 885 109 HOH HOH . 
K 6 HOH A 86 886 68 HOH HOH . 
K 6 HOH A 87 887 141 HOH HOH . 
K 6 HOH A 88 888 117 HOH HOH . 
K 6 HOH A 89 889 97 HOH HOH . 
K 6 HOH A 90 890 120 HOH HOH . 
K 6 HOH A 91 891 99 HOH HOH . 
K 6 HOH A 92 892 179 HOH HOH . 
K 6 HOH A 93 893 54 HOH HOH . 
K 6 HOH A 94 894 124 HOH HOH . 
K 6 HOH A 95 895 155 HOH HOH . 
K 6 HOH A 96 896 78 HOH HOH . 
K 6 HOH A 97 897 177 HOH HOH . 
K 6 HOH A 98 898 202 HOH HOH . 
K 6 HOH A 99 899 205 HOH HOH . 
K 6 HOH A 100 900 167 HOH HOH . 
K 6 HOH A 101 901 92 HOH HOH . 
K 6 HOH A 102 902 142 HOH HOH . 
K 6 HOH A 103 903 140 HOH HOH . 
K 6 HOH A 104 904 172 HOH HOH . 
K 6 HOH A 105 905 61 HOH HOH . 
K 6 HOH A 106 906 197 HOH HOH . 
L 6 HOH B 1 801 27 HOH HOH . 
L 6 HOH B 2 802 187 HOH HOH . 
L 6 HOH B 3 803 128 HOH HOH . 
L 6 HOH B 4 804 66 HOH HOH . 
L 6 HOH B 5 805 30 HOH HOH . 
L 6 HOH B 6 806 59 HOH HOH . 
L 6 HOH B 7 807 150 HOH HOH . 
L 6 HOH B 8 808 44 HOH HOH . 
L 6 HOH B 9 809 131 HOH HOH . 
L 6 HOH B 10 810 86 HOH HOH . 
L 6 HOH B 11 811 186 HOH HOH . 
L 6 HOH B 12 812 32 HOH HOH . 
L 6 HOH B 13 813 184 HOH HOH . 
L 6 HOH B 14 814 34 HOH HOH . 
L 6 HOH B 15 815 96 HOH HOH . 
L 6 HOH B 16 816 203 HOH HOH . 
L 6 HOH B 17 817 25 HOH HOH . 
L 6 HOH B 18 818 14 HOH HOH . 
L 6 HOH B 19 819 206 HOH HOH . 
L 6 HOH B 20 820 51 HOH HOH . 
L 6 HOH B 21 821 39 HOH HOH . 
L 6 HOH B 22 822 93 HOH HOH . 
L 6 HOH B 23 823 159 HOH HOH . 
L 6 HOH B 24 824 76 HOH HOH . 
L 6 HOH B 25 825 42 HOH HOH . 
L 6 HOH B 26 826 130 HOH HOH . 
L 6 HOH B 27 827 52 HOH HOH . 
L 6 HOH B 28 828 119 HOH HOH . 
L 6 HOH B 29 829 133 HOH HOH . 
L 6 HOH B 30 830 192 HOH HOH . 
L 6 HOH B 31 831 10 HOH HOH . 
L 6 HOH B 32 832 164 HOH HOH . 
L 6 HOH B 33 833 1 HOH HOH . 
L 6 HOH B 34 834 110 HOH HOH . 
L 6 HOH B 35 835 183 HOH HOH . 
L 6 HOH B 36 836 121 HOH HOH . 
L 6 HOH B 37 837 208 HOH HOH . 
L 6 HOH B 38 838 8 HOH HOH . 
L 6 HOH B 39 839 165 HOH HOH . 
L 6 HOH B 40 840 189 HOH HOH . 
L 6 HOH B 41 841 105 HOH HOH . 
L 6 HOH B 42 842 55 HOH HOH . 
L 6 HOH B 43 843 143 HOH HOH . 
L 6 HOH B 44 844 207 HOH HOH . 
L 6 HOH B 45 845 7 HOH HOH . 
L 6 HOH B 46 846 18 HOH HOH . 
L 6 HOH B 47 847 198 HOH HOH . 
L 6 HOH B 48 848 82 HOH HOH . 
L 6 HOH B 49 849 9 HOH HOH . 
L 6 HOH B 50 850 13 HOH HOH . 
L 6 HOH B 51 851 111 HOH HOH . 
L 6 HOH B 52 852 118 HOH HOH . 
L 6 HOH B 53 853 17 HOH HOH . 
L 6 HOH B 54 854 16 HOH HOH . 
L 6 HOH B 55 855 113 HOH HOH . 
L 6 HOH B 56 856 123 HOH HOH . 
L 6 HOH B 57 857 103 HOH HOH . 
L 6 HOH B 58 858 64 HOH HOH . 
L 6 HOH B 59 859 91 HOH HOH . 
L 6 HOH B 60 860 163 HOH HOH . 
L 6 HOH B 61 861 204 HOH HOH . 
L 6 HOH B 62 862 129 HOH HOH . 
L 6 HOH B 63 863 77 HOH HOH . 
L 6 HOH B 64 864 154 HOH HOH . 
L 6 HOH B 65 865 191 HOH HOH . 
L 6 HOH B 66 866 6 HOH HOH . 
L 6 HOH B 67 867 200 HOH HOH . 
L 6 HOH B 68 868 20 HOH HOH . 
L 6 HOH B 69 869 71 HOH HOH . 
L 6 HOH B 70 870 108 HOH HOH . 
L 6 HOH B 71 871 69 HOH HOH . 
L 6 HOH B 72 872 80 HOH HOH . 
L 6 HOH B 73 873 138 HOH HOH . 
L 6 HOH B 74 874 201 HOH HOH . 
L 6 HOH B 75 875 35 HOH HOH . 
L 6 HOH B 76 876 65 HOH HOH . 
L 6 HOH B 77 877 11 HOH HOH . 
L 6 HOH B 78 878 62 HOH HOH . 
L 6 HOH B 79 879 58 HOH HOH . 
L 6 HOH B 80 880 182 HOH HOH . 
L 6 HOH B 81 881 67 HOH HOH . 
L 6 HOH B 82 882 114 HOH HOH . 
L 6 HOH B 83 883 116 HOH HOH . 
L 6 HOH B 84 884 139 HOH HOH . 
L 6 HOH B 85 885 37 HOH HOH . 
L 6 HOH B 86 886 112 HOH HOH . 
L 6 HOH B 87 887 194 HOH HOH . 
L 6 HOH B 88 888 56 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 N N1 UMP . . . D 3 -16.509 20.177 -19.501 1 85.57 0 N1 UMP 702 A 1 
HETATM 2 C C2 UMP . . . D 3 -15.725 19.611 -20.496 1 83.77 0 C2 UMP 702 A 1 
HETATM 3 N N3 UMP . . . D 3 -14.951 20.513 -21.189 1 92.57 0 N3 UMP 702 A 1 
HETATM 4 C C4 UMP . . . D 3 -14.888 21.884 -21.005 1 96.54 0 C4 UMP 702 A 1 
HETATM 5 C C5 UMP . . . D 3 -15.748 22.391 -19.979 1 98.3 0 C5 UMP 702 A 1 
HETATM 6 C C6 UMP . . . D 3 -16.515 21.538 -19.285 1 96.24 0 C6 UMP 702 A 1 
HETATM 7 O O2 UMP . . . D 3 -15.688 18.408 -20.738 1 60.68 0 O2 UMP 702 A 1 
HETATM 8 O O4 UMP . . . D 3 -14.129 22.559 -21.7 1 99 0 O4 UMP 702 A 1 
HETATM 9 C C1' UMP . . . D 3 -17.428 19.307 -18.726 1 82.34 0 C1' UMP 702 A 1 
HETATM 10 C C2' UMP . . . D 3 -16.809 18.12 -18.01 1 79.07 0 C2' UMP 702 A 1 
HETATM 11 C C3' UMP . . . D 3 -17.884 17.825 -16.973 1 73.01 0 C3' UMP 702 A 1 
HETATM 12 C C4' UMP . . . D 3 -18.347 19.23 -16.573 1 72.77 0 C4' UMP 702 A 1 
HETATM 13 O O3' UMP . . . D 3 -18.934 17.075 -17.575 1 57.89 0 O3' UMP 702 A 1 
HETATM 14 O O4' UMP . . . D 3 -18.008 20.088 -17.686 1 78.04 0 O4' UMP 702 A 1 
HETATM 15 C C5' UMP . . . D 3 -17.714 19.804 -15.323 1 76.6 0 C5' UMP 702 A 1 
HETATM 16 O O5' UMP . . . D 3 -18.259 19.168 -14.115 1 74.47 0 O5' UMP 702 A 1 
HETATM 17 P P UMP . . . D 3 -17.415 19.253 -12.735 1 62.5 0 P UMP 702 A 1 
HETATM 18 O OP1 UMP . . . D 3 -18.097 18.445 -11.657 1 71.4 0 OP1 UMP 702 A 1 
HETATM 19 O OP2 UMP . . . D 3 -16.108 18.621 -13.121 1 78.81 0 OP2 UMP 702 A 1 
HETATM 20 O OP3 UMP . . . D 3 -17.283 20.72 -12.383 1 61.01 0 OP3 UMP 702 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#