data_1SYN
#
_model_server_result.job_id            I7rBvW8cQwGabQ4AnHsaag 
_model_server_result.datetime_utc      '2025-02-27 01:34:12' 
_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          1syn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":300}' 
#
_entry.id    1SYN 
#
_exptl.entry_id    1SYN 
_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            1SYN 
_cell.length_a            127.346 
_cell.length_b            127.346 
_cell.length_c            68.164 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1SYN 
_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 FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A O2 FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? 
covale ? covale3 B O1 FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
covale ? covale4 B C FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
#
_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 427 n n 
N1 C6 UMP sing 428 n n 
N1 C1' UMP sing 429 n n 
C2 N3 UMP sing 430 n n 
C2 O2 UMP doub 431 n n 
N3 C4 UMP sing 432 n n 
N3 HN3 UMP sing 433 n n 
C4 C5 UMP sing 434 n n 
C4 O4 UMP doub 435 n n 
C5 C6 UMP doub 436 n n 
C5 H5 UMP sing 437 n n 
C6 H6 UMP sing 438 n n 
C1' C2' UMP sing 439 n n 
C1' O4' UMP sing 440 n n 
C1' H1' UMP sing 441 n n 
C2' C3' UMP sing 442 n n 
C2' H2' UMP sing 443 n n 
C2' "H2''" UMP sing 444 n n 
C3' C4' UMP sing 445 n n 
C3' O3' UMP sing 446 n n 
C3' H3' UMP sing 447 n n 
C4' O4' UMP sing 448 n n 
C4' C5' UMP sing 449 n n 
C4' H4' UMP sing 450 n n 
O3' HO3' UMP sing 451 n n 
C5' O5' UMP sing 452 n n 
C5' H5' UMP sing 453 n n 
C5' "H5''" UMP sing 454 n n 
O5' P UMP sing 455 n n 
P OP1 UMP doub 456 n n 
P OP2 UMP sing 457 n n 
P OP3 UMP sing 458 n n 
OP2 HOP2 UMP sing 459 n n 
OP3 HOP3 UMP sing 460 n n 
#
_atom_sites.entry_id                     1SYN 
_atom_sites.fract_transf_matrix[1][1]    0.007853 
_atom_sites.fract_transf_matrix[1][2]    0.004534 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009067 
_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]    0.014671 
_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 1 300 300 UMP UMP . 
D 3 F89 A 1 301 301 F89 F89 . 
E 2 UMP B 1 300 300 UMP UMP . 
F 3 F89 B 1 301 301 F89 F89 . 
G 4 HOH A 1 751 751 HOH HOH . 
G 4 HOH A 2 756 756 HOH HOH . 
G 4 HOH A 3 757 757 HOH HOH . 
G 4 HOH A 4 759 759 HOH HOH . 
G 4 HOH A 5 761 761 HOH HOH . 
G 4 HOH A 6 766 766 HOH HOH . 
G 4 HOH A 7 767 767 HOH HOH . 
G 4 HOH A 8 768 768 HOH HOH . 
G 4 HOH A 9 769 769 HOH HOH . 
G 4 HOH A 10 770 770 HOH HOH . 
G 4 HOH A 11 771 771 HOH HOH . 
G 4 HOH A 12 780 780 HOH HOH . 
G 4 HOH A 13 781 781 HOH HOH . 
G 4 HOH A 14 785 785 HOH HOH . 
G 4 HOH A 15 788 788 HOH HOH . 
G 4 HOH A 16 789 789 HOH HOH . 
G 4 HOH A 17 791 791 HOH HOH . 
G 4 HOH A 18 792 792 HOH HOH . 
G 4 HOH A 19 797 797 HOH HOH . 
G 4 HOH A 20 798 798 HOH HOH . 
G 4 HOH A 21 799 799 HOH HOH . 
G 4 HOH A 22 800 800 HOH HOH . 
G 4 HOH A 23 801 801 HOH HOH . 
G 4 HOH A 24 802 802 HOH HOH . 
G 4 HOH A 25 803 803 HOH HOH . 
G 4 HOH A 26 804 804 HOH HOH . 
G 4 HOH A 27 807 807 HOH HOH . 
G 4 HOH A 28 808 808 HOH HOH . 
G 4 HOH A 29 809 809 HOH HOH . 
G 4 HOH A 30 810 810 HOH HOH . 
G 4 HOH A 31 811 811 HOH HOH . 
G 4 HOH A 32 812 812 HOH HOH . 
G 4 HOH A 33 813 813 HOH HOH . 
G 4 HOH A 34 814 814 HOH HOH . 
G 4 HOH A 35 815 815 HOH HOH . 
G 4 HOH A 36 816 816 HOH HOH . 
G 4 HOH A 37 817 817 HOH HOH . 
G 4 HOH A 38 818 818 HOH HOH . 
G 4 HOH A 39 819 819 HOH HOH . 
G 4 HOH A 40 820 820 HOH HOH . 
G 4 HOH A 41 821 821 HOH HOH . 
G 4 HOH A 42 822 822 HOH HOH . 
G 4 HOH A 43 824 824 HOH HOH . 
G 4 HOH A 44 826 826 HOH HOH . 
G 4 HOH A 45 827 827 HOH HOH . 
G 4 HOH A 46 831 831 HOH HOH . 
G 4 HOH A 47 832 832 HOH HOH . 
G 4 HOH A 48 833 833 HOH HOH . 
G 4 HOH A 49 834 834 HOH HOH . 
G 4 HOH A 50 837 837 HOH HOH . 
G 4 HOH A 51 845 845 HOH HOH . 
G 4 HOH A 52 848 848 HOH HOH . 
G 4 HOH A 53 850 850 HOH HOH . 
G 4 HOH A 54 852 852 HOH HOH . 
G 4 HOH A 55 856 856 HOH HOH . 
G 4 HOH A 56 857 857 HOH HOH . 
G 4 HOH A 57 861 861 HOH HOH . 
G 4 HOH A 58 862 862 HOH HOH . 
G 4 HOH A 59 863 863 HOH HOH . 
G 4 HOH A 60 864 864 HOH HOH . 
G 4 HOH A 61 865 865 HOH HOH . 
G 4 HOH A 62 868 868 HOH HOH . 
G 4 HOH A 63 869 869 HOH HOH . 
G 4 HOH A 64 872 872 HOH HOH . 
G 4 HOH A 65 874 874 HOH HOH . 
G 4 HOH A 66 875 875 HOH HOH . 
G 4 HOH A 67 876 876 HOH HOH . 
G 4 HOH A 68 877 877 HOH HOH . 
G 4 HOH A 69 878 878 HOH HOH . 
G 4 HOH A 70 879 879 HOH HOH . 
G 4 HOH A 71 882 882 HOH HOH . 
G 4 HOH A 72 883 883 HOH HOH . 
G 4 HOH A 73 884 884 HOH HOH . 
G 4 HOH A 74 885 885 HOH HOH . 
G 4 HOH A 75 887 887 HOH HOH . 
G 4 HOH A 76 889 889 HOH HOH . 
G 4 HOH A 77 890 890 HOH HOH . 
G 4 HOH A 78 891 891 HOH HOH . 
G 4 HOH A 79 894 894 HOH HOH . 
G 4 HOH A 80 895 895 HOH HOH . 
G 4 HOH A 81 899 899 HOH HOH . 
G 4 HOH A 82 900 900 HOH HOH . 
G 4 HOH A 83 901 901 HOH HOH . 
G 4 HOH A 84 904 904 HOH HOH . 
G 4 HOH A 85 905 905 HOH HOH . 
G 4 HOH A 86 907 907 HOH HOH . 
G 4 HOH A 87 908 908 HOH HOH . 
G 4 HOH A 88 909 909 HOH HOH . 
G 4 HOH A 89 911 911 HOH HOH . 
G 4 HOH A 90 912 912 HOH HOH . 
G 4 HOH A 91 913 913 HOH HOH . 
G 4 HOH A 92 914 914 HOH HOH . 
G 4 HOH A 93 915 915 HOH HOH . 
G 4 HOH A 94 917 917 HOH HOH . 
G 4 HOH A 95 918 918 HOH HOH . 
G 4 HOH A 96 919 919 HOH HOH . 
G 4 HOH A 97 920 920 HOH HOH . 
G 4 HOH A 98 921 921 HOH HOH . 
G 4 HOH A 99 922 922 HOH HOH . 
G 4 HOH A 100 923 923 HOH HOH . 
G 4 HOH A 101 924 924 HOH HOH . 
G 4 HOH A 102 925 925 HOH HOH . 
H 4 HOH B 1 750 750 HOH HOH . 
H 4 HOH B 2 752 752 HOH HOH . 
H 4 HOH B 3 753 753 HOH HOH . 
H 4 HOH B 4 754 754 HOH HOH . 
H 4 HOH B 5 755 755 HOH HOH . 
H 4 HOH B 6 758 758 HOH HOH . 
H 4 HOH B 7 760 760 HOH HOH . 
H 4 HOH B 8 762 762 HOH HOH . 
H 4 HOH B 9 763 763 HOH HOH . 
H 4 HOH B 10 764 764 HOH HOH . 
H 4 HOH B 11 765 765 HOH HOH . 
H 4 HOH B 12 772 772 HOH HOH . 
H 4 HOH B 13 773 773 HOH HOH . 
H 4 HOH B 14 774 774 HOH HOH . 
H 4 HOH B 15 775 775 HOH HOH . 
H 4 HOH B 16 776 776 HOH HOH . 
H 4 HOH B 17 777 777 HOH HOH . 
H 4 HOH B 18 778 778 HOH HOH . 
H 4 HOH B 19 779 779 HOH HOH . 
H 4 HOH B 20 782 782 HOH HOH . 
H 4 HOH B 21 783 783 HOH HOH . 
H 4 HOH B 22 784 784 HOH HOH . 
H 4 HOH B 23 786 786 HOH HOH . 
H 4 HOH B 24 787 787 HOH HOH . 
H 4 HOH B 25 790 790 HOH HOH . 
H 4 HOH B 26 793 793 HOH HOH . 
H 4 HOH B 27 794 794 HOH HOH . 
H 4 HOH B 28 795 795 HOH HOH . 
H 4 HOH B 29 796 796 HOH HOH . 
H 4 HOH B 30 805 805 HOH HOH . 
H 4 HOH B 31 823 823 HOH HOH . 
H 4 HOH B 32 825 825 HOH HOH . 
H 4 HOH B 33 828 828 HOH HOH . 
H 4 HOH B 34 829 829 HOH HOH . 
H 4 HOH B 35 830 830 HOH HOH . 
H 4 HOH B 36 835 835 HOH HOH . 
H 4 HOH B 37 836 836 HOH HOH . 
H 4 HOH B 38 838 838 HOH HOH . 
H 4 HOH B 39 839 839 HOH HOH . 
H 4 HOH B 40 840 840 HOH HOH . 
H 4 HOH B 41 841 841 HOH HOH . 
H 4 HOH B 42 842 842 HOH HOH . 
H 4 HOH B 43 843 843 HOH HOH . 
H 4 HOH B 44 844 844 HOH HOH . 
H 4 HOH B 45 846 846 HOH HOH . 
H 4 HOH B 46 847 847 HOH HOH . 
H 4 HOH B 47 851 851 HOH HOH . 
H 4 HOH B 48 853 853 HOH HOH . 
H 4 HOH B 49 854 854 HOH HOH . 
H 4 HOH B 50 855 855 HOH HOH . 
H 4 HOH B 51 858 858 HOH HOH . 
H 4 HOH B 52 859 859 HOH HOH . 
H 4 HOH B 53 860 860 HOH HOH . 
H 4 HOH B 54 866 866 HOH HOH . 
H 4 HOH B 55 867 867 HOH HOH . 
H 4 HOH B 56 870 870 HOH HOH . 
H 4 HOH B 57 871 871 HOH HOH . 
H 4 HOH B 58 873 873 HOH HOH . 
H 4 HOH B 59 880 880 HOH HOH . 
H 4 HOH B 60 881 881 HOH HOH . 
H 4 HOH B 61 886 886 HOH HOH . 
H 4 HOH B 62 888 888 HOH HOH . 
H 4 HOH B 63 892 892 HOH HOH . 
H 4 HOH B 64 893 893 HOH HOH . 
H 4 HOH B 65 896 896 HOH HOH . 
H 4 HOH B 66 897 897 HOH HOH . 
H 4 HOH B 67 898 898 HOH HOH . 
H 4 HOH B 68 902 902 HOH HOH . 
H 4 HOH B 69 903 903 HOH HOH . 
H 4 HOH B 70 906 906 HOH HOH . 
H 4 HOH B 71 910 910 HOH HOH . 
H 4 HOH B 72 916 916 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 44.519 34.411 24.549 1 22.35 ? N1 UMP 300 B 1 
HETATM 2 C C2 UMP . . . E 2 43.656 35.209 25.282 1 22.56 ? C2 UMP 300 B 1 
HETATM 3 N N3 UMP . . . E 2 42.653 35.812 24.557 1 22.73 ? N3 UMP 300 B 1 
HETATM 4 C C4 UMP . . . E 2 42.453 35.669 23.2 1 22.9 ? C4 UMP 300 B 1 
HETATM 5 C C5 UMP . . . E 2 43.405 34.815 22.519 1 22.11 ? C5 UMP 300 B 1 
HETATM 6 C C6 UMP . . . E 2 44.424 34.219 23.249 1 22.51 ? C6 UMP 300 B 1 
HETATM 7 O O2 UMP . . . E 2 43.669 35.273 26.5 1 19.03 ? O2 UMP 300 B 1 
HETATM 8 O O4 UMP . . . E 2 41.462 36.149 22.659 1 24.07 ? O4 UMP 300 B 1 
HETATM 9 C C1' UMP . . . E 2 45.633 33.731 25.233 1 23.28 ? C1' UMP 300 B 1 
HETATM 10 C C2' UMP . . . E 2 45.214 32.501 26.02 1 23.6 ? C2' UMP 300 B 1 
HETATM 11 C C3' UMP . . . E 2 46.549 31.879 26.382 1 22.22 ? C3' UMP 300 B 1 
HETATM 12 C C4' UMP . . . E 2 47.188 31.96 24.971 1 21.46 ? C4' UMP 300 B 1 
HETATM 13 O O3' UMP . . . E 2 47.187 32.763 27.314 1 18.79 ? O3' UMP 300 B 1 
HETATM 14 O O4' UMP . . . E 2 46.723 33.222 24.384 1 23.98 ? O4' UMP 300 B 1 
HETATM 15 C C5' UMP . . . E 2 46.735 30.809 24.053 1 20.31 ? C5' UMP 300 B 1 
HETATM 16 O O5' UMP . . . E 2 47.387 29.565 24.486 1 14.21 ? O5' UMP 300 B 1 
HETATM 17 P P UMP . . . E 2 46.638 28.213 24.572 1 14.28 ? P UMP 300 B 1 
HETATM 18 O OP1 UMP . . . E 2 45.604 28.397 25.582 1 8.35 ? OP1 UMP 300 B 1 
HETATM 19 O OP2 UMP . . . E 2 46.015 27.872 23.303 1 7.18 ? OP2 UMP 300 B 1 
HETATM 20 O OP3 UMP . . . E 2 47.551 27.142 24.982 1 10.04 ? OP3 UMP 300 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#