data_1ZPR
#
_model_server_result.job_id            L8y8CkBBi-GQSu31qv2VzA 
_model_server_result.datetime_utc      '2024-11-06 00:16:14' 
_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          1zpr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    1ZPR 
#
_exptl.entry_id    1ZPR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_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         120 
_cell.entry_id            1ZPR 
_cell.length_a            127.221 
_cell.length_b            127.221 
_cell.length_c            68.178 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1ZPR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63' 
#
_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 
_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
? 2 C N N 
? 2 E N 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
covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale2 A SG CYS 146 A CYS 146 1_555 C C6 UMP . A UMP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
covale ? covale3 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
#
_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 
#
_atom_sites.entry_id                     1ZPR 
_atom_sites.fract_transf_matrix[1][1]    0.00786 
_atom_sites.fract_transf_matrix[1][2]    0.004538 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009076 
_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]    0.014667 
_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 UMP A 1 301 301 UMP UMP . 
D 3 CB3 A 1 300 300 CB3 CB3 . 
E 2 UMP B 1 301 301 UMP UMP . 
F 3 CB3 B 1 300 300 CB3 CB3 . 
G 4 HOH A 1 701 701 HOH HOH . 
G 4 HOH A 2 702 702 HOH HOH . 
G 4 HOH A 3 703 703 HOH HOH . 
G 4 HOH A 4 704 704 HOH HOH . 
G 4 HOH A 5 705 705 HOH HOH . 
G 4 HOH A 6 706 706 HOH HOH . 
G 4 HOH A 7 707 707 HOH HOH . 
G 4 HOH A 8 708 708 HOH HOH . 
G 4 HOH A 9 710 710 HOH HOH . 
G 4 HOH A 10 715 715 HOH HOH . 
G 4 HOH A 11 716 716 HOH HOH . 
G 4 HOH A 12 717 717 HOH HOH . 
G 4 HOH A 13 718 718 HOH HOH . 
G 4 HOH A 14 720 720 HOH HOH . 
G 4 HOH A 15 723 723 HOH HOH . 
G 4 HOH A 16 724 724 HOH HOH . 
G 4 HOH A 17 725 725 HOH HOH . 
G 4 HOH A 18 726 726 HOH HOH . 
G 4 HOH A 19 727 727 HOH HOH . 
G 4 HOH A 20 729 729 HOH HOH . 
G 4 HOH A 21 731 731 HOH HOH . 
G 4 HOH A 22 732 732 HOH HOH . 
G 4 HOH A 23 734 734 HOH HOH . 
G 4 HOH A 24 735 735 HOH HOH . 
G 4 HOH A 25 736 736 HOH HOH . 
G 4 HOH A 26 738 738 HOH HOH . 
G 4 HOH A 27 739 739 HOH HOH . 
G 4 HOH A 28 740 740 HOH HOH . 
G 4 HOH A 29 741 741 HOH HOH . 
G 4 HOH A 30 742 742 HOH HOH . 
G 4 HOH A 31 743 743 HOH HOH . 
G 4 HOH A 32 744 744 HOH HOH . 
G 4 HOH A 33 748 748 HOH HOH . 
G 4 HOH A 34 749 749 HOH HOH . 
G 4 HOH A 35 750 750 HOH HOH . 
G 4 HOH A 36 751 751 HOH HOH . 
G 4 HOH A 37 752 752 HOH HOH . 
G 4 HOH A 38 753 753 HOH HOH . 
G 4 HOH A 39 754 754 HOH HOH . 
G 4 HOH A 40 755 755 HOH HOH . 
G 4 HOH A 41 756 756 HOH HOH . 
G 4 HOH A 42 757 757 HOH HOH . 
G 4 HOH A 43 758 758 HOH HOH . 
G 4 HOH A 44 759 759 HOH HOH . 
G 4 HOH A 45 760 760 HOH HOH . 
G 4 HOH A 46 761 761 HOH HOH . 
G 4 HOH A 47 763 763 HOH HOH . 
G 4 HOH A 48 764 764 HOH HOH . 
G 4 HOH A 49 765 765 HOH HOH . 
G 4 HOH A 50 769 769 HOH HOH . 
G 4 HOH A 51 770 770 HOH HOH . 
G 4 HOH A 52 771 771 HOH HOH . 
G 4 HOH A 53 776 776 HOH HOH . 
G 4 HOH A 54 785 785 HOH HOH . 
G 4 HOH A 55 787 787 HOH HOH . 
G 4 HOH A 56 790 790 HOH HOH . 
G 4 HOH A 57 791 791 HOH HOH . 
G 4 HOH A 58 792 792 HOH HOH . 
G 4 HOH A 59 793 793 HOH HOH . 
G 4 HOH A 60 800 800 HOH HOH . 
G 4 HOH A 61 802 802 HOH HOH . 
G 4 HOH A 62 803 803 HOH HOH . 
G 4 HOH A 63 805 805 HOH HOH . 
G 4 HOH A 64 806 806 HOH HOH . 
G 4 HOH A 65 809 809 HOH HOH . 
G 4 HOH A 66 815 815 HOH HOH . 
G 4 HOH A 67 816 816 HOH HOH . 
G 4 HOH A 68 817 817 HOH HOH . 
G 4 HOH A 69 818 818 HOH HOH . 
G 4 HOH A 70 819 819 HOH HOH . 
G 4 HOH A 71 821 821 HOH HOH . 
G 4 HOH A 72 822 822 HOH HOH . 
G 4 HOH A 73 823 823 HOH HOH . 
G 4 HOH A 74 824 824 HOH HOH . 
G 4 HOH A 75 825 825 HOH HOH . 
G 4 HOH A 76 826 826 HOH HOH . 
G 4 HOH A 77 831 831 HOH HOH . 
G 4 HOH A 78 832 832 HOH HOH . 
G 4 HOH A 79 834 834 HOH HOH . 
G 4 HOH A 80 836 836 HOH HOH . 
G 4 HOH A 81 837 837 HOH HOH . 
G 4 HOH A 82 839 839 HOH HOH . 
G 4 HOH A 83 842 842 HOH HOH . 
G 4 HOH A 84 843 843 HOH HOH . 
G 4 HOH A 85 844 844 HOH HOH . 
G 4 HOH A 86 846 846 HOH HOH . 
G 4 HOH A 87 847 847 HOH HOH . 
G 4 HOH A 88 849 849 HOH HOH . 
G 4 HOH A 89 856 856 HOH HOH . 
G 4 HOH A 90 857 857 HOH HOH . 
G 4 HOH A 91 858 858 HOH HOH . 
G 4 HOH A 92 859 859 HOH HOH . 
G 4 HOH A 93 860 860 HOH HOH . 
G 4 HOH A 94 861 861 HOH HOH . 
G 4 HOH A 95 862 862 HOH HOH . 
G 4 HOH A 96 863 863 HOH HOH . 
G 4 HOH A 97 864 864 HOH HOH . 
G 4 HOH A 98 868 868 HOH HOH . 
G 4 HOH A 99 869 869 HOH HOH . 
G 4 HOH A 100 870 870 HOH HOH . 
G 4 HOH A 101 871 871 HOH HOH . 
G 4 HOH A 102 875 875 HOH HOH . 
G 4 HOH A 103 876 876 HOH HOH . 
G 4 HOH A 104 877 877 HOH HOH . 
G 4 HOH A 105 878 878 HOH HOH . 
G 4 HOH A 106 879 879 HOH HOH . 
G 4 HOH A 107 881 881 HOH HOH . 
G 4 HOH A 108 886 886 HOH HOH . 
G 4 HOH A 109 887 887 HOH HOH . 
G 4 HOH A 110 888 888 HOH HOH . 
G 4 HOH A 111 890 890 HOH HOH . 
G 4 HOH A 112 891 891 HOH HOH . 
G 4 HOH A 113 892 892 HOH HOH . 
H 4 HOH B 1 711 711 HOH HOH . 
H 4 HOH B 2 712 713 HOH HOH . 
H 4 HOH B 3 713 719 HOH HOH . 
H 4 HOH B 4 714 721 HOH HOH . 
H 4 HOH B 5 715 722 HOH HOH . 
H 4 HOH B 6 716 730 HOH HOH . 
H 4 HOH B 7 717 737 HOH HOH . 
H 4 HOH B 8 718 745 HOH HOH . 
H 4 HOH B 9 719 747 HOH HOH . 
H 4 HOH B 10 720 762 HOH HOH . 
H 4 HOH B 11 721 766 HOH HOH . 
H 4 HOH B 12 722 767 HOH HOH . 
H 4 HOH B 13 723 768 HOH HOH . 
H 4 HOH B 14 724 772 HOH HOH . 
H 4 HOH B 15 725 773 HOH HOH . 
H 4 HOH B 16 726 774 HOH HOH . 
H 4 HOH B 17 727 775 HOH HOH . 
H 4 HOH B 18 728 777 HOH HOH . 
H 4 HOH B 19 729 778 HOH HOH . 
H 4 HOH B 20 730 779 HOH HOH . 
H 4 HOH B 21 731 780 HOH HOH . 
H 4 HOH B 22 732 781 HOH HOH . 
H 4 HOH B 23 733 782 HOH HOH . 
H 4 HOH B 24 734 783 HOH HOH . 
H 4 HOH B 25 735 784 HOH HOH . 
H 4 HOH B 26 736 786 HOH HOH . 
H 4 HOH B 27 737 788 HOH HOH . 
H 4 HOH B 28 738 789 HOH HOH . 
H 4 HOH B 29 739 794 HOH HOH . 
H 4 HOH B 30 740 795 HOH HOH . 
H 4 HOH B 31 741 796 HOH HOH . 
H 4 HOH B 32 742 797 HOH HOH . 
H 4 HOH B 33 743 798 HOH HOH . 
H 4 HOH B 34 744 799 HOH HOH . 
H 4 HOH B 35 745 801 HOH HOH . 
H 4 HOH B 36 746 804 HOH HOH . 
H 4 HOH B 37 747 807 HOH HOH . 
H 4 HOH B 38 748 808 HOH HOH . 
H 4 HOH B 39 749 811 HOH HOH . 
H 4 HOH B 40 750 812 HOH HOH . 
H 4 HOH B 41 751 813 HOH HOH . 
H 4 HOH B 42 752 814 HOH HOH . 
H 4 HOH B 43 753 820 HOH HOH . 
H 4 HOH B 44 754 827 HOH HOH . 
H 4 HOH B 45 755 828 HOH HOH . 
H 4 HOH B 46 756 829 HOH HOH . 
H 4 HOH B 47 757 830 HOH HOH . 
H 4 HOH B 48 758 833 HOH HOH . 
H 4 HOH B 49 759 835 HOH HOH . 
H 4 HOH B 50 760 838 HOH HOH . 
H 4 HOH B 51 761 840 HOH HOH . 
H 4 HOH B 52 762 841 HOH HOH . 
H 4 HOH B 53 763 845 HOH HOH . 
H 4 HOH B 54 764 852 HOH HOH . 
H 4 HOH B 55 765 855 HOH HOH . 
H 4 HOH B 56 766 865 HOH HOH . 
H 4 HOH B 57 767 866 HOH HOH . 
H 4 HOH B 58 768 867 HOH HOH . 
H 4 HOH B 59 769 873 HOH HOH . 
H 4 HOH B 60 770 882 HOH HOH . 
H 4 HOH B 61 771 883 HOH HOH . 
H 4 HOH B 62 772 884 HOH HOH . 
H 4 HOH B 63 773 885 HOH HOH . 
H 4 HOH B 64 774 889 HOH HOH . 
H 4 HOH B 65 775 7 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 . . . E 2 44.287 34.364 25.028 1 43.87 ? N1 UMP 301 B 1 
HETATM 2 C C2 UMP . . . E 2 43.366 34.858 25.958 1 42.54 ? C2 UMP 301 B 1 
HETATM 3 N N3 UMP . . . E 2 42.224 35.413 25.429 1 44.61 ? N3 UMP 301 B 1 
HETATM 4 C C4 UMP . . . E 2 41.916 35.484 24.079 1 46.46 ? C4 UMP 301 B 1 
HETATM 5 C C5 UMP . . . E 2 42.929 34.974 23.197 1 47.57 ? C5 UMP 301 B 1 
HETATM 6 C C6 UMP . . . E 2 44.077 34.409 23.732 1 46.42 ? C6 UMP 301 B 1 
HETATM 7 O O2 UMP . . . E 2 43.558 34.973 27.154 1 42.48 ? O2 UMP 301 B 1 
HETATM 8 O O4 UMP . . . E 2 40.815 35.842 23.706 1 49.1 ? O4 UMP 301 B 1 
HETATM 9 C C1' UMP . . . E 2 45.487 33.587 25.413 1 44.9 ? C1' UMP 301 B 1 
HETATM 10 C C2' UMP . . . E 2 45.189 32.463 26.388 1 45.15 ? C2' UMP 301 B 1 
HETATM 11 C C3' UMP . . . E 2 46.477 31.643 26.4 1 44.92 ? C3' UMP 301 B 1 
HETATM 12 C C4' UMP . . . E 2 46.715 31.577 24.859 1 43.79 ? C4' UMP 301 B 1 
HETATM 13 O O3' UMP . . . E 2 47.511 32.415 27.057 1 44 ? O3' UMP 301 B 1 
HETATM 14 O O4' UMP . . . E 2 46.233 32.871 24.345 1 45.18 ? O4' UMP 301 B 1 
HETATM 15 C C5' UMP . . . E 2 45.914 30.438 24.145 1 38.36 ? C5' UMP 301 B 1 
HETATM 16 O O5' UMP . . . E 2 46.746 29.23 24.113 1 29.86 ? O5' UMP 301 B 1 
HETATM 17 P P UMP . . . E 2 46.359 27.737 24.516 1 23.49 ? P UMP 301 B 1 
HETATM 18 O OP1 UMP . . . E 2 45.609 27.813 25.772 1 22.53 ? OP1 UMP 301 B 1 
HETATM 19 O OP2 UMP . . . E 2 45.642 27.005 23.457 1 19.28 ? OP2 UMP 301 B 1 
HETATM 20 O OP3 UMP . . . E 2 47.563 26.943 24.8 1 27.07 ? OP3 UMP 301 B 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           79 
_model_server_stats.create_model_time_ms    42 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#