data_3TB9
#
_model_server_result.job_id            HEOhDSMdupDlmOq_KVaavg 
_model_server_result.datetime_utc      '2024-12-03 12:11:28' 
_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          3tb9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":889}' 
#
_entry.id    3TB9 
#
_exptl.entry_id    3TB9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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            3TB9 
_cell.length_a            107.886 
_cell.length_b            116.959 
_cell.length_c            64.329 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TB9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 116.959 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 C O2A ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc2 C O1B ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? 
metalc ? metalc3 C O1G ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
#
_chem_comp.formula           'C9 H15 N3 O11 P2' 
_chem_comp.formula_weight    403.176 
_chem_comp.id                CDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-5'-DIPHOSPHATE" 
_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
O3B PB CDP sing 120 n n 
PB O1B CDP doub 121 n n 
PB O2B CDP sing 122 n n 
PB O3A CDP sing 123 n n 
O3A PA CDP sing 124 n n 
PA O1A CDP doub 125 n n 
PA O2A CDP sing 126 n n 
PA O5' CDP sing 127 n n 
O5' C5' CDP sing 128 n n 
C5' C4' CDP sing 129 n n 
C5' "H5'1" CDP sing 130 n n 
C5' "H5'2" CDP sing 131 n n 
C4' O4' CDP sing 132 n n 
C4' C3' CDP sing 133 n n 
C4' H4' CDP sing 134 n n 
O4' C1' CDP sing 135 n n 
C3' O3' CDP sing 136 n n 
C3' C2' CDP sing 137 n n 
C3' H3' CDP sing 138 n n 
O3' HA CDP sing 139 n n 
C2' O2' CDP sing 140 n n 
C2' C1' CDP sing 141 n n 
C2' H2' CDP sing 142 n n 
O2' HB CDP sing 143 n n 
C1' N1 CDP sing 144 n n 
C1' H1' CDP sing 145 n n 
N1 C2 CDP sing 146 n n 
N1 C6 CDP sing 147 n n 
C2 O2 CDP doub 148 n n 
C2 N3 CDP sing 149 n n 
N3 C4 CDP doub 150 n n 
C4 N4 CDP sing 151 n n 
C4 C5 CDP sing 152 n n 
N4 H4N1 CDP sing 153 n n 
N4 H4N2 CDP sing 154 n n 
C5 C6 CDP doub 155 n n 
C5 H5 CDP sing 156 n n 
C6 H6 CDP sing 157 n n 
HO1 O2A CDP sing 158 n n 
HO2 O2B CDP sing 159 n n 
HO3 O3B CDP sing 160 n n 
#
_atom_sites.entry_id                     3TB9 
_atom_sites.fract_transf_matrix[1][1]    0.009269 
_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]    0.00855 
_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]    0.015545 
_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 CDP A 1 889 889 CDP CDP . 
C 3 ANP A 1 890 890 ANP ANP . 
D 4 MG A 1 891 891 MG MG . 
E 5 HOH A 1 892 892 HOH HOH . 
E 5 HOH A 2 893 893 HOH HOH . 
E 5 HOH A 3 894 894 HOH HOH . 
E 5 HOH A 4 895 895 HOH HOH . 
E 5 HOH A 5 896 896 HOH HOH . 
E 5 HOH A 6 897 897 HOH HOH . 
E 5 HOH A 7 898 898 HOH HOH . 
E 5 HOH A 8 899 899 HOH HOH . 
E 5 HOH A 9 900 900 HOH HOH . 
E 5 HOH A 10 901 901 HOH HOH . 
E 5 HOH A 11 902 902 HOH HOH . 
E 5 HOH A 12 903 903 HOH HOH . 
E 5 HOH A 13 904 904 HOH HOH . 
E 5 HOH A 14 905 905 HOH HOH . 
E 5 HOH A 15 906 906 HOH HOH . 
E 5 HOH A 16 907 907 HOH HOH . 
E 5 HOH A 17 908 908 HOH HOH . 
E 5 HOH A 18 909 909 HOH HOH . 
E 5 HOH A 19 910 910 HOH HOH . 
E 5 HOH A 20 911 911 HOH HOH . 
E 5 HOH A 21 912 912 HOH HOH . 
E 5 HOH A 22 913 913 HOH HOH . 
E 5 HOH A 23 914 914 HOH HOH . 
E 5 HOH A 24 915 915 HOH HOH . 
E 5 HOH A 25 916 916 HOH HOH . 
E 5 HOH A 26 917 917 HOH HOH . 
E 5 HOH A 27 918 918 HOH HOH . 
E 5 HOH A 28 919 919 HOH HOH . 
E 5 HOH A 29 920 920 HOH HOH . 
E 5 HOH A 30 921 921 HOH HOH . 
E 5 HOH A 31 922 922 HOH HOH . 
E 5 HOH A 32 923 923 HOH HOH . 
E 5 HOH A 33 924 924 HOH HOH . 
E 5 HOH A 34 925 925 HOH HOH . 
E 5 HOH A 35 926 926 HOH HOH . 
E 5 HOH A 36 927 927 HOH HOH . 
E 5 HOH A 37 928 928 HOH HOH . 
E 5 HOH A 38 929 929 HOH HOH . 
E 5 HOH A 39 930 930 HOH HOH . 
E 5 HOH A 40 931 931 HOH HOH . 
E 5 HOH A 41 932 932 HOH HOH . 
E 5 HOH A 42 933 933 HOH HOH . 
E 5 HOH A 43 934 934 HOH HOH . 
E 5 HOH A 44 935 935 HOH HOH . 
E 5 HOH A 45 936 936 HOH HOH . 
E 5 HOH A 46 937 937 HOH HOH . 
E 5 HOH A 47 938 938 HOH HOH . 
E 5 HOH A 48 939 939 HOH HOH . 
E 5 HOH A 49 940 940 HOH HOH . 
E 5 HOH A 50 941 941 HOH HOH . 
E 5 HOH A 51 942 942 HOH HOH . 
E 5 HOH A 52 943 943 HOH HOH . 
E 5 HOH A 53 944 944 HOH HOH . 
E 5 HOH A 54 945 945 HOH HOH . 
E 5 HOH A 55 946 946 HOH HOH . 
E 5 HOH A 56 947 947 HOH HOH . 
E 5 HOH A 57 948 948 HOH HOH . 
E 5 HOH A 58 949 949 HOH HOH . 
E 5 HOH A 59 950 950 HOH HOH . 
E 5 HOH A 60 951 951 HOH HOH . 
E 5 HOH A 61 952 952 HOH HOH . 
E 5 HOH A 62 953 953 HOH HOH . 
E 5 HOH A 63 954 954 HOH HOH . 
E 5 HOH A 64 955 955 HOH HOH . 
E 5 HOH A 65 956 956 HOH HOH . 
E 5 HOH A 66 957 957 HOH HOH . 
E 5 HOH A 67 958 958 HOH HOH . 
E 5 HOH A 68 959 959 HOH HOH . 
E 5 HOH A 69 960 960 HOH HOH . 
E 5 HOH A 70 961 961 HOH HOH . 
E 5 HOH A 71 962 962 HOH HOH . 
E 5 HOH A 72 963 963 HOH HOH . 
E 5 HOH A 73 964 964 HOH HOH . 
E 5 HOH A 74 965 965 HOH HOH . 
E 5 HOH A 75 966 966 HOH HOH . 
E 5 HOH A 76 967 967 HOH HOH . 
E 5 HOH A 77 968 968 HOH HOH . 
E 5 HOH A 78 969 969 HOH HOH . 
E 5 HOH A 79 970 970 HOH HOH . 
E 5 HOH A 80 971 971 HOH HOH . 
E 5 HOH A 81 972 972 HOH HOH . 
E 5 HOH A 82 973 973 HOH HOH . 
E 5 HOH A 83 974 974 HOH HOH . 
E 5 HOH A 84 975 975 HOH HOH . 
E 5 HOH A 85 976 976 HOH HOH . 
E 5 HOH A 86 977 977 HOH HOH . 
E 5 HOH A 87 978 978 HOH HOH . 
E 5 HOH A 88 979 979 HOH HOH . 
E 5 HOH A 89 980 980 HOH HOH . 
E 5 HOH A 90 981 981 HOH HOH . 
E 5 HOH A 91 982 982 HOH HOH . 
E 5 HOH A 92 983 983 HOH HOH . 
E 5 HOH A 93 984 984 HOH HOH . 
E 5 HOH A 94 985 985 HOH HOH . 
E 5 HOH A 95 986 986 HOH HOH . 
E 5 HOH A 96 987 987 HOH HOH . 
E 5 HOH A 97 988 988 HOH HOH . 
E 5 HOH A 98 989 989 HOH HOH . 
E 5 HOH A 99 990 990 HOH HOH . 
E 5 HOH A 100 991 991 HOH HOH . 
E 5 HOH A 101 992 992 HOH HOH . 
E 5 HOH A 102 993 993 HOH HOH . 
E 5 HOH A 103 994 994 HOH HOH . 
E 5 HOH A 104 995 995 HOH HOH . 
E 5 HOH A 105 996 996 HOH HOH . 
E 5 HOH A 106 997 997 HOH HOH . 
E 5 HOH A 107 998 998 HOH HOH . 
E 5 HOH A 108 999 999 HOH HOH . 
E 5 HOH A 109 1000 1000 HOH HOH . 
E 5 HOH A 110 1001 1001 HOH HOH . 
E 5 HOH A 111 1002 1002 HOH HOH . 
E 5 HOH A 112 1003 1003 HOH HOH . 
E 5 HOH A 113 1004 1004 HOH HOH . 
E 5 HOH A 114 1005 1005 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 O3B CDP . . . B 2 26.555 54.124 15.612 1 47.46 ? O3B CDP 889 A 1 
HETATM 2 P PB CDP . . . B 2 27.178 52.902 16.246 1 46.45 ? PB CDP 889 A 1 
HETATM 3 O O1B CDP . . . B 2 28.343 52.344 15.449 1 47.22 ? O1B CDP 889 A 1 
HETATM 4 O O2B CDP . . . B 2 27.441 53.034 17.735 1 46.2 ? O2B CDP 889 A 1 
HETATM 5 O O3A CDP . . . B 2 25.942 51.846 16.223 1 46.04 ? O3A CDP 889 A 1 
HETATM 6 P PA CDP . . . B 2 25.872 50.295 15.749 1 46.33 ? PA CDP 889 A 1 
HETATM 7 O O1A CDP . . . B 2 26.95 49.467 16.412 1 42.94 ? O1A CDP 889 A 1 
HETATM 8 O O2A CDP . . . B 2 25.696 50.272 14.23 1 44.76 ? O2A CDP 889 A 1 
HETATM 9 O O5' CDP . . . B 2 24.469 49.845 16.399 1 46.52 ? O5' CDP 889 A 1 
HETATM 10 C C5' CDP . . . B 2 24.392 49.618 17.806 1 45.88 ? C5' CDP 889 A 1 
HETATM 11 C C4' CDP . . . B 2 23.018 50.016 18.345 1 47.34 ? C4' CDP 889 A 1 
HETATM 12 O O4' CDP . . . B 2 22.69 51.394 18.085 1 48.34 ? O4' CDP 889 A 1 
HETATM 13 C C3' CDP . . . B 2 21.887 49.191 17.746 1 47.44 ? C3' CDP 889 A 1 
HETATM 14 O O3' CDP . . . B 2 21.729 47.957 18.442 1 47.73 ? O3' CDP 889 A 1 
HETATM 15 C C2' CDP . . . B 2 20.672 50.113 17.799 1 48.95 ? C2' CDP 889 A 1 
HETATM 16 O O2' CDP . . . B 2 19.885 49.928 18.999 1 46.89 ? O2' CDP 889 A 1 
HETATM 17 C C1' CDP . . . B 2 21.3 51.516 17.723 1 52.15 ? C1' CDP 889 A 1 
HETATM 18 N N1 CDP . . . B 2 21.188 52.081 16.363 1 54.23 ? N1 CDP 889 A 1 
HETATM 19 C C2 CDP . . . B 2 20.198 53.058 16.064 1 55.8 ? C2 CDP 889 A 1 
HETATM 20 O O2 CDP . . . B 2 19.395 53.462 16.947 1 55.7 ? O2 CDP 889 A 1 
HETATM 21 N N3 CDP . . . B 2 20.114 53.558 14.798 1 56.02 ? N3 CDP 889 A 1 
HETATM 22 C C4 CDP . . . B 2 20.96 53.146 13.815 1 56.16 ? C4 CDP 889 A 1 
HETATM 23 N N4 CDP . . . B 2 20.864 53.659 12.558 1 55.93 ? N4 CDP 889 A 1 
HETATM 24 C C5 CDP . . . B 2 21.934 52.19 14.09 1 55.93 ? C5 CDP 889 A 1 
HETATM 25 C C6 CDP . . . B 2 22.026 51.677 15.383 1 55.34 ? C6 CDP 889 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#