data_2CVU
#
_model_server_result.job_id            bWXQxC3i3BC3s8iz2zhpxw 
_model_server_result.datetime_utc      '2024-12-03 10:45:45' 
_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          2cvu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1002}' 
#
_entry.id    2CVU 
#
_exptl.entry_id    2CVU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          4 
_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            2CVU 
_cell.length_a            107.759 
_cell.length_b            117.509 
_cell.length_c            64.584 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2CVU 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 0 117.509 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? 
metalc ? metalc2 C O2B ANP . A ANP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc3 C O2G ANP . A ANP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
#
_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                     2CVU 
_atom_sites.fract_transf_matrix[1][1]    0.00928 
_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]    0.00851 
_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]    0.015484 
_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 MG A 1 2001 2001 MG MG . 
C 3 ANP A 1 1001 1001 ANP ANP . 
D 4 CDP A 1 1002 1002 CDP CDP . 
E 5 HOH A 1 2002 1 HOH HOH . 
E 5 HOH A 2 2003 2 HOH HOH . 
E 5 HOH A 3 2004 3 HOH HOH . 
E 5 HOH A 4 2005 4 HOH HOH . 
E 5 HOH A 5 2006 5 HOH HOH . 
E 5 HOH A 6 2007 6 HOH HOH . 
E 5 HOH A 7 2008 7 HOH HOH . 
E 5 HOH A 8 2009 8 HOH HOH . 
E 5 HOH A 9 2010 9 HOH HOH . 
E 5 HOH A 10 2011 10 HOH HOH . 
E 5 HOH A 11 2012 11 HOH HOH . 
E 5 HOH A 12 2013 12 HOH HOH . 
E 5 HOH A 13 2014 13 HOH HOH . 
E 5 HOH A 14 2015 14 HOH HOH . 
E 5 HOH A 15 2016 15 HOH HOH . 
E 5 HOH A 16 2017 16 HOH HOH . 
E 5 HOH A 17 2018 17 HOH HOH . 
E 5 HOH A 18 2019 18 HOH HOH . 
E 5 HOH A 19 2020 19 HOH HOH . 
E 5 HOH A 20 2021 20 HOH HOH . 
E 5 HOH A 21 2022 21 HOH HOH . 
E 5 HOH A 22 2023 22 HOH HOH . 
E 5 HOH A 23 2024 23 HOH HOH . 
E 5 HOH A 24 2025 24 HOH HOH . 
E 5 HOH A 25 2026 25 HOH HOH . 
E 5 HOH A 26 2027 26 HOH HOH . 
E 5 HOH A 27 2028 27 HOH HOH . 
E 5 HOH A 28 2029 28 HOH HOH . 
E 5 HOH A 29 2030 29 HOH HOH . 
E 5 HOH A 30 2031 30 HOH HOH . 
E 5 HOH A 31 2032 31 HOH HOH . 
E 5 HOH A 32 2033 32 HOH HOH . 
E 5 HOH A 33 2034 33 HOH HOH . 
E 5 HOH A 34 2035 34 HOH HOH . 
E 5 HOH A 35 2036 35 HOH HOH . 
E 5 HOH A 36 2037 36 HOH HOH . 
E 5 HOH A 37 2038 37 HOH HOH . 
E 5 HOH A 38 2039 38 HOH HOH . 
E 5 HOH A 39 2040 39 HOH HOH . 
E 5 HOH A 40 2041 40 HOH HOH . 
E 5 HOH A 41 2042 41 HOH HOH . 
E 5 HOH A 42 2043 42 HOH HOH . 
E 5 HOH A 43 2044 43 HOH HOH . 
E 5 HOH A 44 2045 44 HOH HOH . 
E 5 HOH A 45 2046 45 HOH HOH . 
E 5 HOH A 46 2047 46 HOH HOH . 
E 5 HOH A 47 2048 47 HOH HOH . 
E 5 HOH A 48 2049 48 HOH HOH . 
E 5 HOH A 49 2050 49 HOH HOH . 
E 5 HOH A 50 2051 50 HOH HOH . 
E 5 HOH A 51 2052 51 HOH HOH . 
E 5 HOH A 52 2053 52 HOH HOH . 
E 5 HOH A 53 2054 53 HOH HOH . 
E 5 HOH A 54 2055 54 HOH HOH . 
E 5 HOH A 55 2056 55 HOH HOH . 
E 5 HOH A 56 2057 56 HOH HOH . 
E 5 HOH A 57 2058 57 HOH HOH . 
E 5 HOH A 58 2059 58 HOH HOH . 
E 5 HOH A 59 2060 59 HOH HOH . 
E 5 HOH A 60 2061 60 HOH HOH . 
E 5 HOH A 61 2062 61 HOH HOH . 
E 5 HOH A 62 2063 62 HOH HOH . 
E 5 HOH A 63 2064 63 HOH HOH . 
E 5 HOH A 64 2065 64 HOH HOH . 
E 5 HOH A 65 2066 65 HOH HOH . 
E 5 HOH A 66 2067 66 HOH HOH . 
E 5 HOH A 67 2068 67 HOH HOH . 
E 5 HOH A 68 2069 68 HOH HOH . 
E 5 HOH A 69 2070 69 HOH HOH . 
E 5 HOH A 70 2071 70 HOH HOH . 
E 5 HOH A 71 2072 71 HOH HOH . 
E 5 HOH A 72 2073 72 HOH HOH . 
E 5 HOH A 73 2074 73 HOH HOH . 
E 5 HOH A 74 2075 74 HOH HOH . 
E 5 HOH A 75 2076 75 HOH HOH . 
E 5 HOH A 76 2077 76 HOH HOH . 
E 5 HOH A 77 2078 77 HOH HOH . 
E 5 HOH A 78 2079 78 HOH HOH . 
E 5 HOH A 79 2080 79 HOH HOH . 
E 5 HOH A 80 2081 80 HOH HOH . 
E 5 HOH A 81 2082 81 HOH HOH . 
E 5 HOH A 82 2083 82 HOH HOH . 
E 5 HOH A 83 2084 83 HOH HOH . 
E 5 HOH A 84 2085 84 HOH HOH . 
E 5 HOH A 85 2086 85 HOH HOH . 
E 5 HOH A 86 2087 86 HOH HOH . 
E 5 HOH A 87 2088 87 HOH HOH . 
E 5 HOH A 88 2089 88 HOH HOH . 
E 5 HOH A 89 2090 89 HOH HOH . 
E 5 HOH A 90 2091 90 HOH HOH . 
E 5 HOH A 91 2092 91 HOH HOH . 
E 5 HOH A 92 2093 92 HOH HOH . 
E 5 HOH A 93 2094 93 HOH HOH . 
E 5 HOH A 94 2095 94 HOH HOH . 
E 5 HOH A 95 2096 95 HOH HOH . 
E 5 HOH A 96 2097 96 HOH HOH . 
E 5 HOH A 97 2098 97 HOH HOH . 
E 5 HOH A 98 2099 98 HOH HOH . 
E 5 HOH A 99 2100 99 HOH HOH . 
E 5 HOH A 100 2101 100 HOH HOH . 
E 5 HOH A 101 2102 101 HOH HOH . 
E 5 HOH A 102 2103 102 HOH HOH . 
E 5 HOH A 103 2104 103 HOH HOH . 
E 5 HOH A 104 2105 104 HOH HOH . 
E 5 HOH A 105 2106 105 HOH HOH . 
E 5 HOH A 106 2107 106 HOH HOH . 
E 5 HOH A 107 2108 107 HOH HOH . 
E 5 HOH A 108 2109 108 HOH HOH . 
E 5 HOH A 109 2110 109 HOH HOH . 
E 5 HOH A 110 2111 110 HOH HOH . 
E 5 HOH A 111 2112 111 HOH HOH . 
E 5 HOH A 112 2113 112 HOH HOH . 
E 5 HOH A 113 2114 113 HOH HOH . 
E 5 HOH A 114 2115 114 HOH HOH . 
E 5 HOH A 115 2116 115 HOH HOH . 
E 5 HOH A 116 2117 116 HOH HOH . 
E 5 HOH A 117 2118 117 HOH HOH . 
E 5 HOH A 118 2119 118 HOH HOH . 
E 5 HOH A 119 2120 119 HOH HOH . 
E 5 HOH A 120 2121 120 HOH HOH . 
E 5 HOH A 121 2122 121 HOH HOH . 
E 5 HOH A 122 2123 122 HOH HOH . 
E 5 HOH A 123 2124 123 HOH HOH . 
E 5 HOH A 124 2125 124 HOH HOH . 
E 5 HOH A 125 2126 125 HOH HOH . 
E 5 HOH A 126 2127 126 HOH HOH . 
E 5 HOH A 127 2128 127 HOH HOH . 
E 5 HOH A 128 2129 128 HOH HOH . 
E 5 HOH A 129 2130 129 HOH HOH . 
E 5 HOH A 130 2131 130 HOH HOH . 
E 5 HOH A 131 2132 131 HOH HOH . 
E 5 HOH A 132 2133 132 HOH HOH . 
E 5 HOH A 133 2134 133 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 . . . D 4 26.594 53.224 18.014 1 51.33 ? O3B CDP 1002 A 1 
HETATM 2 P PB CDP . . . D 4 26.975 52.819 16.6 1 50.93 ? PB CDP 1002 A 1 
HETATM 3 O O1B CDP . . . D 4 28.433 52.893 16.272 1 52.1 ? O1B CDP 1002 A 1 
HETATM 4 O O2B CDP . . . D 4 26.201 53.428 15.445 1 51.37 ? O2B CDP 1002 A 1 
HETATM 5 O O3A CDP . . . D 4 26.731 51.215 16.677 1 50.8 ? O3A CDP 1002 A 1 
HETATM 6 P PA CDP . . . D 4 25.618 50.321 15.905 1 50.37 ? PA CDP 1002 A 1 
HETATM 7 O O1A CDP . . . D 4 26.141 48.911 16.012 1 50.35 ? O1A CDP 1002 A 1 
HETATM 8 O O2A CDP . . . D 4 25.218 50.856 14.523 1 50.37 ? O2A CDP 1002 A 1 
HETATM 9 O O5' CDP . . . D 4 24.39 50.501 16.923 1 50.11 ? O5' CDP 1002 A 1 
HETATM 10 C C5' CDP . . . D 4 23.719 49.399 17.532 1 50.7 ? C5' CDP 1002 A 1 
HETATM 11 C C4' CDP . . . D 4 22.593 49.9 18.434 1 51.09 ? C4' CDP 1002 A 1 
HETATM 12 O O4' CDP . . . D 4 22.398 51.325 18.353 1 51.29 ? O4' CDP 1002 A 1 
HETATM 13 C C3' CDP . . . D 4 21.292 49.238 18.03 1 50.43 ? C3' CDP 1002 A 1 
HETATM 14 O O3' CDP . . . D 4 20.919 48.306 19.045 1 53.05 ? O3' CDP 1002 A 1 
HETATM 15 C C2' CDP . . . D 4 20.28 50.358 17.885 1 49.47 ? C2' CDP 1002 A 1 
HETATM 16 O O2' CDP . . . D 4 19.376 50.344 18.99 1 47.47 ? O2' CDP 1002 A 1 
HETATM 17 C C1' CDP . . . D 4 21.085 51.654 17.857 1 50.69 ? C1' CDP 1002 A 1 
HETATM 18 N N1 CDP . . . D 4 21.123 52.238 16.49 1 51.4 ? N1 CDP 1002 A 1 
HETATM 19 C C2 CDP . . . D 4 20.14 53.164 16.046 1 51.3 ? C2 CDP 1002 A 1 
HETATM 20 O O2 CDP . . . D 4 19.208 53.535 16.808 1 52.12 ? O2 CDP 1002 A 1 
HETATM 21 N N3 CDP . . . D 4 20.214 53.656 14.782 1 50.93 ? N3 CDP 1002 A 1 
HETATM 22 C C4 CDP . . . D 4 21.209 53.295 13.929 1 51.28 ? C4 CDP 1002 A 1 
HETATM 23 N N4 CDP . . . D 4 21.286 53.797 12.673 1 50.93 ? N4 CDP 1002 A 1 
HETATM 24 C C5 CDP . . . D 4 22.178 52.394 14.341 1 52.09 ? C5 CDP 1002 A 1 
HETATM 25 C C6 CDP . . . D 4 22.101 51.885 15.631 1 51.87 ? C6 CDP 1002 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#