data_6CDZ
#
_model_server_result.job_id            BQhKok2zmvKV7l7tJ-bmDA 
_model_server_result.datetime_utc      '2024-11-23 19:52:17' 
_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          6cdz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    6CDZ 
#
_exptl.entry_id    6CDZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              310.198 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-deoxy-5'-uridylic acid" 
_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          103.5 
_cell.angle_gamma         90 
_cell.entry_id            6CDZ 
_cell.length_a            67.658 
_cell.length_b            80.451 
_cell.length_c            94.08 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6CDZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             F 
_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
covale ? covale1 A C CXM 1 A CXM 1 1_555 A N LYS 2 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 B C CXM 1 B CXM 1 1_555 B N LYS 2 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_chem_comp.formula           'C9 H15 N2 O8 P' 
_chem_comp.formula_weight    310.198 
_chem_comp.id                UMC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-deoxy-5'-uridylic acid" 
_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
O5' P UMC sing 440 n n 
O2P P UMC doub 441 n n 
P O1P UMC sing 442 n n 
P O3P UMC sing 443 n n 
C2 N1 UMC sing 444 n n 
C1' N1 UMC sing 445 n n 
N1 C6 UMC sing 446 n n 
O2 C2 UMC doub 447 n n 
C2 N3 UMC sing 448 n n 
HN3 N3 UMC sing 449 n n 
N3 C4 UMC sing 450 n n 
O4 C4 UMC doub 451 n n 
C4 C5 UMC sing 452 n n 
H5A C5 UMC sing 453 n n 
C5 C6 UMC sing 454 n n 
C5 H5 UMC sing 455 n n 
C6 H6 UMC sing 456 n n 
C6 H6A UMC sing 457 n n 
H1' C1' UMC sing 458 n n 
C1' C2' UMC sing 459 n n 
C1' O4' UMC sing 460 n n 
O1P HO1P UMC sing 461 n n 
"H2'A" C2' UMC sing 462 n n 
C2' C3' UMC sing 463 n n 
C2' H2' UMC sing 464 n n 
O3' C3' UMC sing 465 n n 
C3' H3' UMC sing 466 n n 
C3' C4' UMC sing 467 n n 
HO3' O3' UMC sing 468 n n 
O3P HO3P UMC sing 469 n n 
O4' C4' UMC sing 470 n n 
H4' C4' UMC sing 471 n n 
C4' C5' UMC sing 472 n n 
C5' H5' UMC sing 473 n n 
C5' "H5'A" UMC sing 474 n n 
C5' O5' UMC sing 475 n n 
#
_atom_sites.entry_id                     6CDZ 
_atom_sites.fract_transf_matrix[1][1]    0.01478 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003548 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01243 
_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]    0.010931 
_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 CB3 A 1 701 701 CB3 CB3 . 
D 3 UMP A 1 702 703 UMP UMP . 
E 2 CB3 B 1 301 702 CB3 CB3 . 
F 4 UMC B 1 302 704 UMC UMC . 
G 5 HOH A 1 801 27 HOH HOH . 
G 5 HOH A 2 802 118 HOH HOH . 
G 5 HOH A 3 803 61 HOH HOH . 
G 5 HOH A 4 804 98 HOH HOH . 
G 5 HOH A 5 805 122 HOH HOH . 
G 5 HOH A 6 806 67 HOH HOH . 
G 5 HOH A 7 807 9 HOH HOH . 
G 5 HOH A 8 808 54 HOH HOH . 
G 5 HOH A 9 809 1 HOH HOH . 
G 5 HOH A 10 810 109 HOH HOH . 
G 5 HOH A 11 811 32 HOH HOH . 
G 5 HOH A 12 812 34 HOH HOH . 
G 5 HOH A 13 813 26 HOH HOH . 
G 5 HOH A 14 814 13 HOH HOH . 
G 5 HOH A 15 815 5 HOH HOH . 
G 5 HOH A 16 816 56 HOH HOH . 
G 5 HOH A 17 817 65 HOH HOH . 
G 5 HOH A 18 818 152 HOH HOH . 
G 5 HOH A 19 819 60 HOH HOH . 
G 5 HOH A 20 820 53 HOH HOH . 
G 5 HOH A 21 821 161 HOH HOH . 
G 5 HOH A 22 822 165 HOH HOH . 
G 5 HOH A 23 823 11 HOH HOH . 
G 5 HOH A 24 824 23 HOH HOH . 
G 5 HOH A 25 825 78 HOH HOH . 
G 5 HOH A 26 826 16 HOH HOH . 
G 5 HOH A 27 827 157 HOH HOH . 
G 5 HOH A 28 828 162 HOH HOH . 
G 5 HOH A 29 829 138 HOH HOH . 
G 5 HOH A 30 830 89 HOH HOH . 
G 5 HOH A 31 831 92 HOH HOH . 
G 5 HOH A 32 832 21 HOH HOH . 
G 5 HOH A 33 833 31 HOH HOH . 
G 5 HOH A 34 834 42 HOH HOH . 
G 5 HOH A 35 835 63 HOH HOH . 
G 5 HOH A 36 836 15 HOH HOH . 
G 5 HOH A 37 837 77 HOH HOH . 
G 5 HOH A 38 838 4 HOH HOH . 
G 5 HOH A 39 839 124 HOH HOH . 
G 5 HOH A 40 840 90 HOH HOH . 
G 5 HOH A 41 841 46 HOH HOH . 
G 5 HOH A 42 842 108 HOH HOH . 
G 5 HOH A 43 843 28 HOH HOH . 
G 5 HOH A 44 844 69 HOH HOH . 
G 5 HOH A 45 845 166 HOH HOH . 
G 5 HOH A 46 846 70 HOH HOH . 
G 5 HOH A 47 847 75 HOH HOH . 
G 5 HOH A 48 848 86 HOH HOH . 
G 5 HOH A 49 849 12 HOH HOH . 
G 5 HOH A 50 850 128 HOH HOH . 
G 5 HOH A 51 851 19 HOH HOH . 
G 5 HOH A 52 852 3 HOH HOH . 
G 5 HOH A 53 853 119 HOH HOH . 
G 5 HOH A 54 854 139 HOH HOH . 
G 5 HOH A 55 855 37 HOH HOH . 
G 5 HOH A 56 856 68 HOH HOH . 
G 5 HOH A 57 857 130 HOH HOH . 
G 5 HOH A 58 858 48 HOH HOH . 
G 5 HOH A 59 859 58 HOH HOH . 
G 5 HOH A 60 860 147 HOH HOH . 
G 5 HOH A 61 861 49 HOH HOH . 
G 5 HOH A 62 862 163 HOH HOH . 
G 5 HOH A 63 863 47 HOH HOH . 
G 5 HOH A 64 864 8 HOH HOH . 
G 5 HOH A 65 865 20 HOH HOH . 
G 5 HOH A 66 866 112 HOH HOH . 
G 5 HOH A 67 867 59 HOH HOH . 
G 5 HOH A 68 868 135 HOH HOH . 
G 5 HOH A 69 869 137 HOH HOH . 
G 5 HOH A 70 870 66 HOH HOH . 
G 5 HOH A 71 871 125 HOH HOH . 
G 5 HOH A 72 872 38 HOH HOH . 
G 5 HOH A 73 873 111 HOH HOH . 
G 5 HOH A 74 874 156 HOH HOH . 
G 5 HOH A 75 875 116 HOH HOH . 
G 5 HOH A 76 876 133 HOH HOH . 
G 5 HOH A 77 877 84 HOH HOH . 
G 5 HOH A 78 878 64 HOH HOH . 
G 5 HOH A 79 879 144 HOH HOH . 
G 5 HOH A 80 880 91 HOH HOH . 
G 5 HOH A 81 881 97 HOH HOH . 
G 5 HOH A 82 882 41 HOH HOH . 
G 5 HOH A 83 883 94 HOH HOH . 
G 5 HOH A 84 884 146 HOH HOH . 
G 5 HOH A 85 885 115 HOH HOH . 
G 5 HOH A 86 886 95 HOH HOH . 
G 5 HOH A 87 887 110 HOH HOH . 
G 5 HOH A 88 888 151 HOH HOH . 
G 5 HOH A 89 889 149 HOH HOH . 
G 5 HOH A 90 890 141 HOH HOH . 
H 5 HOH B 1 401 160 HOH HOH . 
H 5 HOH B 2 402 154 HOH HOH . 
H 5 HOH B 3 403 72 HOH HOH . 
H 5 HOH B 4 404 35 HOH HOH . 
H 5 HOH B 5 405 164 HOH HOH . 
H 5 HOH B 6 406 52 HOH HOH . 
H 5 HOH B 7 407 131 HOH HOH . 
H 5 HOH B 8 408 57 HOH HOH . 
H 5 HOH B 9 409 55 HOH HOH . 
H 5 HOH B 10 410 18 HOH HOH . 
H 5 HOH B 11 411 74 HOH HOH . 
H 5 HOH B 12 412 167 HOH HOH . 
H 5 HOH B 13 413 40 HOH HOH . 
H 5 HOH B 14 414 83 HOH HOH . 
H 5 HOH B 15 415 105 HOH HOH . 
H 5 HOH B 16 416 96 HOH HOH . 
H 5 HOH B 17 417 2 HOH HOH . 
H 5 HOH B 18 418 6 HOH HOH . 
H 5 HOH B 19 419 140 HOH HOH . 
H 5 HOH B 20 420 117 HOH HOH . 
H 5 HOH B 21 421 159 HOH HOH . 
H 5 HOH B 22 422 62 HOH HOH . 
H 5 HOH B 23 423 80 HOH HOH . 
H 5 HOH B 24 424 148 HOH HOH . 
H 5 HOH B 25 425 158 HOH HOH . 
H 5 HOH B 26 426 85 HOH HOH . 
H 5 HOH B 27 427 25 HOH HOH . 
H 5 HOH B 28 428 22 HOH HOH . 
H 5 HOH B 29 429 106 HOH HOH . 
H 5 HOH B 30 430 10 HOH HOH . 
H 5 HOH B 31 431 44 HOH HOH . 
H 5 HOH B 32 432 82 HOH HOH . 
H 5 HOH B 33 433 79 HOH HOH . 
H 5 HOH B 34 434 145 HOH HOH . 
H 5 HOH B 35 435 30 HOH HOH . 
H 5 HOH B 36 436 33 HOH HOH . 
H 5 HOH B 37 437 14 HOH HOH . 
H 5 HOH B 38 438 99 HOH HOH . 
H 5 HOH B 39 439 81 HOH HOH . 
H 5 HOH B 40 440 143 HOH HOH . 
H 5 HOH B 41 441 39 HOH HOH . 
H 5 HOH B 42 442 45 HOH HOH . 
H 5 HOH B 43 443 29 HOH HOH . 
H 5 HOH B 44 444 155 HOH HOH . 
H 5 HOH B 45 445 129 HOH HOH . 
H 5 HOH B 46 446 17 HOH HOH . 
H 5 HOH B 47 447 36 HOH HOH . 
H 5 HOH B 48 448 7 HOH HOH . 
H 5 HOH B 49 449 121 HOH HOH . 
H 5 HOH B 50 450 51 HOH HOH . 
H 5 HOH B 51 451 127 HOH HOH . 
H 5 HOH B 52 452 43 HOH HOH . 
H 5 HOH B 53 453 71 HOH HOH . 
H 5 HOH B 54 454 113 HOH HOH . 
H 5 HOH B 55 455 87 HOH HOH . 
H 5 HOH B 56 456 50 HOH HOH . 
H 5 HOH B 57 457 120 HOH HOH . 
H 5 HOH B 58 458 107 HOH HOH . 
H 5 HOH B 59 459 102 HOH HOH . 
H 5 HOH B 60 460 93 HOH HOH . 
H 5 HOH B 61 461 142 HOH HOH . 
H 5 HOH B 62 462 88 HOH HOH . 
H 5 HOH B 63 463 103 HOH HOH . 
H 5 HOH B 64 464 24 HOH HOH . 
H 5 HOH B 65 465 114 HOH HOH . 
H 5 HOH B 66 466 104 HOH HOH . 
H 5 HOH B 67 467 136 HOH HOH . 
H 5 HOH B 68 468 132 HOH HOH . 
H 5 HOH B 69 469 126 HOH HOH . 
H 5 HOH B 70 470 150 HOH HOH . 
H 5 HOH B 71 471 153 HOH HOH . 
H 5 HOH B 72 472 123 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 P P UMC . . . F 4 18.674 -11.438 14.53 1 31.87 ? P UMC 302 B 1 
HETATM 2 N N1 UMC . . . F 4 22.146 -6.139 13.678 1 29.03 ? N1 UMC 302 B 1 
HETATM 3 C C2 UMC . . . F 4 22.639 -5.109 14.35 1 28.94 ? C2 UMC 302 B 1 
HETATM 4 O O2 UMC . . . F 4 23.389 -5.28 15.296 1 27.34 ? O2 UMC 302 B 1 
HETATM 5 N N3 UMC . . . F 4 22.296 -3.881 13.977 1 29.68 ? N3 UMC 302 B 1 
HETATM 6 C C4 UMC . . . F 4 21.507 -3.642 12.929 1 33.69 ? C4 UMC 302 B 1 
HETATM 7 O O4 UMC . . . F 4 21.214 -2.5 12.612 1 34.69 ? O4 UMC 302 B 1 
HETATM 8 C C5 UMC . . . F 4 20.963 -4.789 12.101 1 33.01 ? C5 UMC 302 B 1 
HETATM 9 C C6 UMC . . . F 4 20.986 -6.138 12.809 1 30.91 ? C6 UMC 302 B 1 
HETATM 10 C C1' UMC . . . F 4 22.748 -7.461 13.794 1 30.65 ? C1' UMC 302 B 1 
HETATM 11 O O1P UMC . . . F 4 18.455 -12.915 14.311 1 39.75 ? O1P UMC 302 B 1 
HETATM 12 C C2' UMC . . . F 4 22.378 -8.007 15.165 1 30.38 ? C2' UMC 302 B 1 
HETATM 13 O O2P UMC . . . F 4 17.765 -10.55 13.714 1 35.32 ? O2P UMC 302 B 1 
HETATM 14 C C3' UMC . . . F 4 22.153 -9.482 14.91 1 32.42 ? C3' UMC 302 B 1 
HETATM 15 O O3' UMC . . . F 4 23.315 -10.221 15.285 1 32.12 ? O3' UMC 302 B 1 
HETATM 16 O O3P UMC . . . F 4 18.811 -11.06 15.985 1 32.16 ? O3P UMC 302 B 1 
HETATM 17 C C4' UMC . . . F 4 21.903 -9.634 13.419 1 32.42 ? C4' UMC 302 B 1 
HETATM 18 O O4' UMC . . . F 4 22.249 -8.382 12.813 1 29.25 ? O4' UMC 302 B 1 
HETATM 19 C C5' UMC . . . F 4 20.455 -10.029 13.143 1 31.52 ? C5' UMC 302 B 1 
HETATM 20 O O5' UMC . . . F 4 20.154 -11.165 13.952 1 34.79 ? O5' UMC 302 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           38 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#