data_3IEW
#
_model_server_result.job_id            '_fj54gU2BylXZcSU0r4tgw' 
_model_server_result.datetime_utc      '2024-11-23 07:43:10' 
_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          3iew 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":901}' 
#
_entry.id    3IEW 
#
_exptl.entry_id    3IEW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              403.176 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-5'-DIPHOSPHATE" 
_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          95.85 
_cell.angle_gamma         90 
_cell.entry_id            3IEW 
_cell.length_a            117.703 
_cell.length_b            67.548 
_cell.length_c            60.152 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3IEW 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,I,J,K,L,M 
_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
? 3 E N N 
? 3 I 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
metalc ? metalc1 A OD2 ASP 31 A ASP 10 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc2 A NE2 HIS 33 A HIS 12 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc3 A ND1 HIS 65 A HIS 44 1_555 D ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc4 D ZN ZN . A ZN 801 1_555 F O2B CTP . B CTP 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc5 B OD2 ASP 31 B ASP 10 1_555 G ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc6 B NE2 HIS 33 B HIS 12 1_555 G ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc7 B ND1 HIS 65 B HIS 44 1_555 G ZN ZN . B ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc8 G ZN ZN . B ZN 801 1_555 I O2B CDP . C CDP 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc9 C OD2 ASP 31 C ASP 10 1_555 J ZN ZN . C ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc10 C NE2 HIS 33 C HIS 12 1_555 J ZN ZN . C ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc11 C ND1 HIS 65 C HIS 44 1_555 J ZN ZN . C ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
#
_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 70 n n 
PB O1B CDP doub 71 n n 
PB O2B CDP sing 72 n n 
PB O3A CDP sing 73 n n 
O3A PA CDP sing 74 n n 
PA O1A CDP doub 75 n n 
PA O2A CDP sing 76 n n 
PA O5' CDP sing 77 n n 
O5' C5' CDP sing 78 n n 
C5' C4' CDP sing 79 n n 
C5' "H5'1" CDP sing 80 n n 
C5' "H5'2" CDP sing 81 n n 
C4' O4' CDP sing 82 n n 
C4' C3' CDP sing 83 n n 
C4' H4' CDP sing 84 n n 
O4' C1' CDP sing 85 n n 
C3' O3' CDP sing 86 n n 
C3' C2' CDP sing 87 n n 
C3' H3' CDP sing 88 n n 
O3' HA CDP sing 89 n n 
C2' O2' CDP sing 90 n n 
C2' C1' CDP sing 91 n n 
C2' H2' CDP sing 92 n n 
O2' HB CDP sing 93 n n 
C1' N1 CDP sing 94 n n 
C1' H1' CDP sing 95 n n 
N1 C2 CDP sing 96 n n 
N1 C6 CDP sing 97 n n 
C2 O2 CDP doub 98 n n 
C2 N3 CDP sing 99 n n 
N3 C4 CDP doub 100 n n 
C4 N4 CDP sing 101 n n 
C4 C5 CDP sing 102 n n 
N4 H4N1 CDP sing 103 n n 
N4 H4N2 CDP sing 104 n n 
C5 C6 CDP doub 105 n n 
C5 H5 CDP sing 106 n n 
C6 H6 CDP sing 107 n n 
HO1 O2A CDP sing 108 n n 
HO2 O2B CDP sing 109 n n 
HO3 O3B CDP sing 110 n n 
#
_atom_sites.entry_id                     3IEW 
_atom_sites.fract_transf_matrix[1][1]    0.008496 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000871 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014804 
_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]    0.016712 
_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
D 2 ZN A 1 801 801 ZN ZN . 
E 3 CDP A 1 901 901 CDP CDP . 
F 4 CTP B 1 901 901 CTP CTP . 
G 2 ZN B 1 801 801 ZN ZN . 
H 5 GOL B 1 163 1 GOL GOL . 
I 3 CDP C 1 901 901 CDP CDP . 
J 2 ZN C 1 801 801 ZN ZN . 
K 6 HOH A 1 163 1 HOH HOH . 
K 6 HOH A 2 164 2 HOH HOH . 
K 6 HOH A 3 165 7 HOH HOH . 
K 6 HOH A 4 166 8 HOH HOH . 
K 6 HOH A 5 167 9 HOH HOH . 
K 6 HOH A 6 168 13 HOH HOH . 
K 6 HOH A 7 169 15 HOH HOH . 
K 6 HOH A 8 170 16 HOH HOH . 
K 6 HOH A 9 171 17 HOH HOH . 
K 6 HOH A 10 172 18 HOH HOH . 
K 6 HOH A 11 173 22 HOH HOH . 
K 6 HOH A 12 174 24 HOH HOH . 
K 6 HOH A 13 175 25 HOH HOH . 
K 6 HOH A 14 176 26 HOH HOH . 
K 6 HOH A 15 177 30 HOH HOH . 
K 6 HOH A 16 178 31 HOH HOH . 
K 6 HOH A 17 179 32 HOH HOH . 
K 6 HOH A 18 180 34 HOH HOH . 
K 6 HOH A 19 181 36 HOH HOH . 
K 6 HOH A 20 182 42 HOH HOH . 
K 6 HOH A 21 183 45 HOH HOH . 
K 6 HOH A 22 184 48 HOH HOH . 
K 6 HOH A 23 185 51 HOH HOH . 
K 6 HOH A 24 186 55 HOH HOH . 
K 6 HOH A 25 187 56 HOH HOH . 
K 6 HOH A 26 188 58 HOH HOH . 
K 6 HOH A 27 189 61 HOH HOH . 
K 6 HOH A 28 190 62 HOH HOH . 
K 6 HOH A 29 191 64 HOH HOH . 
K 6 HOH A 30 192 65 HOH HOH . 
K 6 HOH A 31 193 67 HOH HOH . 
K 6 HOH A 32 194 70 HOH HOH . 
K 6 HOH A 33 195 71 HOH HOH . 
K 6 HOH A 34 196 72 HOH HOH . 
K 6 HOH A 35 197 76 HOH HOH . 
K 6 HOH A 36 198 80 HOH HOH . 
K 6 HOH A 37 199 83 HOH HOH . 
K 6 HOH A 38 200 84 HOH HOH . 
K 6 HOH A 39 201 85 HOH HOH . 
K 6 HOH A 40 202 87 HOH HOH . 
K 6 HOH A 41 203 91 HOH HOH . 
K 6 HOH A 42 204 93 HOH HOH . 
K 6 HOH A 43 205 94 HOH HOH . 
K 6 HOH A 44 206 98 HOH HOH . 
K 6 HOH A 45 207 100 HOH HOH . 
K 6 HOH A 46 208 101 HOH HOH . 
K 6 HOH A 47 209 104 HOH HOH . 
K 6 HOH A 48 210 105 HOH HOH . 
K 6 HOH A 49 211 107 HOH HOH . 
K 6 HOH A 50 212 109 HOH HOH . 
K 6 HOH A 51 213 112 HOH HOH . 
K 6 HOH A 52 214 113 HOH HOH . 
K 6 HOH A 53 215 120 HOH HOH . 
K 6 HOH A 54 216 124 HOH HOH . 
K 6 HOH A 55 217 126 HOH HOH . 
K 6 HOH A 56 218 129 HOH HOH . 
K 6 HOH A 57 219 130 HOH HOH . 
K 6 HOH A 58 220 131 HOH HOH . 
K 6 HOH A 59 221 133 HOH HOH . 
K 6 HOH A 60 222 134 HOH HOH . 
K 6 HOH A 61 223 135 HOH HOH . 
K 6 HOH A 62 224 90 HOH HOH . 
L 6 HOH B 1 164 3 HOH HOH . 
L 6 HOH B 2 165 4 HOH HOH . 
L 6 HOH B 3 166 5 HOH HOH . 
L 6 HOH B 4 167 10 HOH HOH . 
L 6 HOH B 5 168 11 HOH HOH . 
L 6 HOH B 6 169 12 HOH HOH . 
L 6 HOH B 7 170 21 HOH HOH . 
L 6 HOH B 8 171 23 HOH HOH . 
L 6 HOH B 9 172 28 HOH HOH . 
L 6 HOH B 10 173 33 HOH HOH . 
L 6 HOH B 11 174 43 HOH HOH . 
L 6 HOH B 12 175 44 HOH HOH . 
L 6 HOH B 13 176 46 HOH HOH . 
L 6 HOH B 14 177 47 HOH HOH . 
L 6 HOH B 15 178 49 HOH HOH . 
L 6 HOH B 16 179 54 HOH HOH . 
L 6 HOH B 17 180 57 HOH HOH . 
L 6 HOH B 18 181 60 HOH HOH . 
L 6 HOH B 19 182 66 HOH HOH . 
L 6 HOH B 20 183 74 HOH HOH . 
L 6 HOH B 21 184 75 HOH HOH . 
L 6 HOH B 22 185 77 HOH HOH . 
L 6 HOH B 23 186 88 HOH HOH . 
L 6 HOH B 24 187 89 HOH HOH . 
L 6 HOH B 25 188 95 HOH HOH . 
L 6 HOH B 26 189 96 HOH HOH . 
L 6 HOH B 27 190 97 HOH HOH . 
L 6 HOH B 28 191 99 HOH HOH . 
L 6 HOH B 29 192 102 HOH HOH . 
L 6 HOH B 30 194 110 HOH HOH . 
L 6 HOH B 31 195 111 HOH HOH . 
L 6 HOH B 32 196 115 HOH HOH . 
L 6 HOH B 33 197 117 HOH HOH . 
L 6 HOH B 34 198 118 HOH HOH . 
L 6 HOH B 35 199 119 HOH HOH . 
L 6 HOH B 36 200 123 HOH HOH . 
L 6 HOH B 37 201 125 HOH HOH . 
L 6 HOH B 38 202 127 HOH HOH . 
M 6 HOH C 1 163 6 HOH HOH . 
M 6 HOH C 2 164 14 HOH HOH . 
M 6 HOH C 3 165 19 HOH HOH . 
M 6 HOH C 4 166 20 HOH HOH . 
M 6 HOH C 5 167 27 HOH HOH . 
M 6 HOH C 6 168 29 HOH HOH . 
M 6 HOH C 7 169 35 HOH HOH . 
M 6 HOH C 8 170 37 HOH HOH . 
M 6 HOH C 9 171 38 HOH HOH . 
M 6 HOH C 10 172 39 HOH HOH . 
M 6 HOH C 11 173 41 HOH HOH . 
M 6 HOH C 12 174 50 HOH HOH . 
M 6 HOH C 13 175 52 HOH HOH . 
M 6 HOH C 14 176 53 HOH HOH . 
M 6 HOH C 15 177 59 HOH HOH . 
M 6 HOH C 16 178 63 HOH HOH . 
M 6 HOH C 17 179 68 HOH HOH . 
M 6 HOH C 18 180 69 HOH HOH . 
M 6 HOH C 19 181 73 HOH HOH . 
M 6 HOH C 20 182 78 HOH HOH . 
M 6 HOH C 21 183 79 HOH HOH . 
M 6 HOH C 22 184 81 HOH HOH . 
M 6 HOH C 23 185 82 HOH HOH . 
M 6 HOH C 24 186 86 HOH HOH . 
M 6 HOH C 25 188 92 HOH HOH . 
M 6 HOH C 26 189 103 HOH HOH . 
M 6 HOH C 27 190 108 HOH HOH . 
M 6 HOH C 28 191 114 HOH HOH . 
M 6 HOH C 29 192 116 HOH HOH . 
M 6 HOH C 30 193 106 HOH HOH . 
M 6 HOH C 31 194 122 HOH HOH . 
M 6 HOH C 32 195 128 HOH HOH . 
M 6 HOH C 33 196 132 HOH HOH . 
M 6 HOH C 34 197 136 HOH HOH . 
M 6 HOH C 35 198 137 HOH HOH . 
M 6 HOH C 36 199 121 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 . . . E 3 28.99 -37.597 0.958 1 72.4 ? O3B CDP 901 A 1 
HETATM 2 P PB CDP . . . E 3 28.513 -36.196 0.634 1 72.36 ? PB CDP 901 A 1 
HETATM 3 O O1B CDP . . . E 3 29.08 -35.154 1.571 1 72.66 ? O1B CDP 901 A 1 
HETATM 4 O O2B CDP . . . E 3 28.651 -35.881 -0.837 1 71.19 ? O2B CDP 901 A 1 
HETATM 5 O O3A CDP . . . E 3 26.906 -36.185 0.919 1 69.33 ? O3A CDP 901 A 1 
HETATM 6 P PA CDP . . . E 3 25.953 -34.864 0.981 1 65.55 ? PA CDP 901 A 1 
HETATM 7 O O1A CDP . . . E 3 26.662 -33.775 1.759 1 66.36 ? O1A CDP 901 A 1 
HETATM 8 O O2A CDP . . . E 3 25.447 -34.548 -0.406 1 65.84 ? O2A CDP 901 A 1 
HETATM 9 O O5' CDP . . . E 3 24.686 -35.321 1.886 1 63.87 ? O5' CDP 901 A 1 
HETATM 10 C C5' CDP . . . E 3 23.997 -36.571 1.741 1 61.29 ? C5' CDP 901 A 1 
HETATM 11 C C4' CDP . . . E 3 22.994 -36.845 2.878 1 59.29 ? C4' CDP 901 A 1 
HETATM 12 O O4' CDP . . . E 3 22.426 -35.644 3.417 1 58.3 ? O4' CDP 901 A 1 
HETATM 13 C C3' CDP . . . E 3 21.811 -37.69 2.407 1 58.56 ? C3' CDP 901 A 1 
HETATM 14 O O3' CDP . . . E 3 21.43 -38.692 3.36 1 58.26 ? O3' CDP 901 A 1 
HETATM 15 C C2' CDP . . . E 3 20.656 -36.729 2.267 1 57.4 ? C2' CDP 901 A 1 
HETATM 16 O O2' CDP . . . E 3 19.401 -37.393 2.517 1 57.68 ? O2' CDP 901 A 1 
HETATM 17 C C1' CDP . . . E 3 21 -35.604 3.238 1 56.16 ? C1' CDP 901 A 1 
HETATM 18 N N1 CDP . . . E 3 20.556 -34.308 2.696 1 52.63 ? N1 CDP 901 A 1 
HETATM 19 C C2 CDP . . . E 3 19.457 -33.628 3.255 1 51.54 ? C2 CDP 901 A 1 
HETATM 20 O O2 CDP . . . E 3 18.843 -34.104 4.231 1 51.72 ? O2 CDP 901 A 1 
HETATM 21 N N3 CDP . . . E 3 19.047 -32.439 2.744 1 50.13 ? N3 CDP 901 A 1 
HETATM 22 C C4 CDP . . . E 3 19.679 -31.873 1.701 1 48.86 ? C4 CDP 901 A 1 
HETATM 23 N N4 CDP . . . E 3 19.26 -30.687 1.206 1 47.81 ? N4 CDP 901 A 1 
HETATM 24 C C5 CDP . . . E 3 20.764 -32.527 1.136 1 50.51 ? C5 CDP 901 A 1 
HETATM 25 C C6 CDP . . . E 3 21.187 -33.752 1.652 1 51.35 ? C6 CDP 901 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#