data_3AKC
#
_model_server_result.job_id            co8YFd9duZzxzkF90r7u5g 
_model_server_result.datetime_utc      '2024-10-19 08:28:15' 
_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          3akc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":209}' 
#
_entry.id    3AKC 
#
_exptl.entry_id    3AKC 
_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         120 
_cell.entry_id            3AKC 
_cell.length_a            62.206 
_cell.length_b            62.206 
_cell.length_c            110.951 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AKC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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                      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 A OG SER 16 A SER 16 1_555 D GD GD . A GD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc2 B O2B CDP . A CDP 209 1_555 D GD GD . A GD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc3 C O3B ADP . A ADP 210 1_555 D GD GD . A GD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc4 C O2A ADP . A ADP 210 1_555 D GD GD . A GD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc5 C O2B ADP . A ADP 210 1_555 D GD GD . A GD 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? 
metalc ? metalc6 D GD GD . A GD 211 1_555 E O HOH . A HOH 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? 
metalc ? metalc7 D GD GD . A GD 211 1_555 E O HOH . A HOH 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc8 D GD GD . A GD 211 1_555 E O HOH . A HOH 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc9 D GD GD . A GD 211 1_555 E O HOH . A HOH 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
#
_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 114 n n 
PB O1B CDP doub 115 n n 
PB O2B CDP sing 116 n n 
PB O3A CDP sing 117 n n 
O3A PA CDP sing 118 n n 
PA O1A CDP doub 119 n n 
PA O2A CDP sing 120 n n 
PA O5' CDP sing 121 n n 
O5' C5' CDP sing 122 n n 
C5' C4' CDP sing 123 n n 
C5' "H5'1" CDP sing 124 n n 
C5' "H5'2" CDP sing 125 n n 
C4' O4' CDP sing 126 n n 
C4' C3' CDP sing 127 n n 
C4' H4' CDP sing 128 n n 
O4' C1' CDP sing 129 n n 
C3' O3' CDP sing 130 n n 
C3' C2' CDP sing 131 n n 
C3' H3' CDP sing 132 n n 
O3' HA CDP sing 133 n n 
C2' O2' CDP sing 134 n n 
C2' C1' CDP sing 135 n n 
C2' H2' CDP sing 136 n n 
O2' HB CDP sing 137 n n 
C1' N1 CDP sing 138 n n 
C1' H1' CDP sing 139 n n 
N1 C2 CDP sing 140 n n 
N1 C6 CDP sing 141 n n 
C2 O2 CDP doub 142 n n 
C2 N3 CDP sing 143 n n 
N3 C4 CDP doub 144 n n 
C4 N4 CDP sing 145 n n 
C4 C5 CDP sing 146 n n 
N4 H4N1 CDP sing 147 n n 
N4 H4N2 CDP sing 148 n n 
C5 C6 CDP doub 149 n n 
C5 H5 CDP sing 150 n n 
C6 H6 CDP sing 151 n n 
HO1 O2A CDP sing 152 n n 
HO2 O2B CDP sing 153 n n 
HO3 O3B CDP sing 154 n n 
#
_atom_sites.entry_id                     3AKC 
_atom_sites.fract_transf_matrix[1][1]    0.016076 
_atom_sites.fract_transf_matrix[1][2]    0.009281 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018563 
_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]    0.009013 
_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 1 209 209 CDP CDP . 
C 3 ADP A 1 210 210 ADP ADP . 
D 4 GD A 1 211 211 GD GD . 
E 5 HOH A 1 212 1 HOH TIP . 
E 5 HOH A 2 213 2 HOH TIP . 
E 5 HOH A 3 214 3 HOH TIP . 
E 5 HOH A 4 215 4 HOH TIP . 
E 5 HOH A 5 216 5 HOH TIP . 
E 5 HOH A 6 217 6 HOH TIP . 
E 5 HOH A 7 218 7 HOH TIP . 
E 5 HOH A 8 219 8 HOH TIP . 
E 5 HOH A 9 220 10 HOH TIP . 
E 5 HOH A 10 221 11 HOH TIP . 
E 5 HOH A 11 222 12 HOH TIP . 
E 5 HOH A 12 223 13 HOH TIP . 
E 5 HOH A 13 224 14 HOH TIP . 
E 5 HOH A 14 225 15 HOH TIP . 
E 5 HOH A 15 226 16 HOH TIP . 
E 5 HOH A 16 227 17 HOH TIP . 
E 5 HOH A 17 228 18 HOH TIP . 
E 5 HOH A 18 229 19 HOH TIP . 
E 5 HOH A 19 230 20 HOH TIP . 
E 5 HOH A 20 231 21 HOH TIP . 
E 5 HOH A 21 232 22 HOH TIP . 
E 5 HOH A 22 233 23 HOH TIP . 
E 5 HOH A 23 234 24 HOH TIP . 
E 5 HOH A 24 235 25 HOH TIP . 
E 5 HOH A 25 236 26 HOH TIP . 
E 5 HOH A 26 237 27 HOH TIP . 
E 5 HOH A 27 238 28 HOH TIP . 
E 5 HOH A 28 239 29 HOH TIP . 
E 5 HOH A 29 240 30 HOH TIP . 
E 5 HOH A 30 241 31 HOH TIP . 
E 5 HOH A 31 242 32 HOH TIP . 
E 5 HOH A 32 243 33 HOH TIP . 
E 5 HOH A 33 244 34 HOH TIP . 
E 5 HOH A 34 245 35 HOH TIP . 
E 5 HOH A 35 246 36 HOH TIP . 
E 5 HOH A 36 247 37 HOH TIP . 
E 5 HOH A 37 248 38 HOH TIP . 
E 5 HOH A 38 249 39 HOH TIP . 
E 5 HOH A 39 250 40 HOH TIP . 
E 5 HOH A 40 251 41 HOH TIP . 
E 5 HOH A 41 252 42 HOH TIP . 
E 5 HOH A 42 253 43 HOH TIP . 
E 5 HOH A 43 254 44 HOH TIP . 
E 5 HOH A 44 255 45 HOH TIP . 
E 5 HOH A 45 256 46 HOH TIP . 
E 5 HOH A 46 257 47 HOH TIP . 
E 5 HOH A 47 258 48 HOH TIP . 
E 5 HOH A 48 259 49 HOH TIP . 
E 5 HOH A 49 260 50 HOH TIP . 
E 5 HOH A 50 261 51 HOH TIP . 
E 5 HOH A 51 262 52 HOH TIP . 
E 5 HOH A 52 263 53 HOH TIP . 
E 5 HOH A 53 264 54 HOH TIP . 
E 5 HOH A 54 265 55 HOH TIP . 
E 5 HOH A 55 266 56 HOH TIP . 
E 5 HOH A 56 267 57 HOH TIP . 
E 5 HOH A 57 268 58 HOH TIP . 
E 5 HOH A 58 269 59 HOH TIP . 
E 5 HOH A 59 270 60 HOH TIP . 
E 5 HOH A 60 271 61 HOH TIP . 
E 5 HOH A 61 272 62 HOH TIP . 
E 5 HOH A 62 273 63 HOH TIP . 
E 5 HOH A 63 274 64 HOH TIP . 
E 5 HOH A 64 275 65 HOH TIP . 
E 5 HOH A 65 276 66 HOH TIP . 
E 5 HOH A 66 277 67 HOH TIP . 
E 5 HOH A 67 278 68 HOH TIP . 
E 5 HOH A 68 279 69 HOH TIP . 
E 5 HOH A 69 280 70 HOH TIP . 
E 5 HOH A 70 281 71 HOH TIP . 
E 5 HOH A 71 282 72 HOH TIP . 
E 5 HOH A 72 283 73 HOH TIP . 
E 5 HOH A 73 284 74 HOH TIP . 
E 5 HOH A 74 285 75 HOH TIP . 
E 5 HOH A 75 286 76 HOH TIP . 
E 5 HOH A 76 287 77 HOH TIP . 
E 5 HOH A 77 288 78 HOH TIP . 
E 5 HOH A 78 289 79 HOH TIP . 
E 5 HOH A 79 290 80 HOH TIP . 
E 5 HOH A 80 291 81 HOH TIP . 
E 5 HOH A 81 292 82 HOH TIP . 
E 5 HOH A 82 293 83 HOH TIP . 
E 5 HOH A 83 294 84 HOH TIP . 
E 5 HOH A 84 295 85 HOH TIP . 
E 5 HOH A 85 296 86 HOH TIP . 
E 5 HOH A 86 297 87 HOH TIP . 
E 5 HOH A 87 298 88 HOH TIP . 
E 5 HOH A 88 299 89 HOH TIP . 
E 5 HOH A 89 300 90 HOH TIP . 
E 5 HOH A 90 301 91 HOH TIP . 
E 5 HOH A 91 302 92 HOH TIP . 
E 5 HOH A 92 303 93 HOH TIP . 
E 5 HOH A 93 304 94 HOH TIP . 
E 5 HOH A 94 305 95 HOH TIP . 
E 5 HOH A 95 306 96 HOH TIP . 
E 5 HOH A 96 307 97 HOH TIP . 
E 5 HOH A 97 308 98 HOH TIP . 
E 5 HOH A 98 309 99 HOH TIP . 
E 5 HOH A 99 310 100 HOH TIP . 
E 5 HOH A 100 311 101 HOH TIP . 
E 5 HOH A 101 312 102 HOH TIP . 
E 5 HOH A 102 313 103 HOH TIP . 
E 5 HOH A 103 314 104 HOH TIP . 
E 5 HOH A 104 315 105 HOH TIP . 
E 5 HOH A 105 316 106 HOH TIP . 
E 5 HOH A 106 317 107 HOH TIP . 
E 5 HOH A 107 318 108 HOH TIP . 
E 5 HOH A 108 319 109 HOH TIP . 
E 5 HOH A 109 320 110 HOH TIP . 
E 5 HOH A 110 321 111 HOH TIP . 
E 5 HOH A 111 322 112 HOH TIP . 
E 5 HOH A 112 323 113 HOH TIP . 
E 5 HOH A 113 324 114 HOH TIP . 
E 5 HOH A 114 325 115 HOH TIP . 
E 5 HOH A 115 326 116 HOH TIP . 
E 5 HOH A 116 327 117 HOH TIP . 
#
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 -3.507 34.197 16.635 1 28.29 ? O3B CDP 209 A 1 
HETATM 2 P PB CDP . . . B 2 -4.752 35.017 16.973 1 28.23 ? PB CDP 209 A 1 
HETATM 3 O O1B CDP . . . B 2 -4.357 36.339 17.422 1 28.53 ? O1B CDP 209 A 1 
HETATM 4 O O2B CDP . . . B 2 -5.582 34.344 17.936 1 28.22 ? O2B CDP 209 A 1 
HETATM 5 O O3A CDP . . . B 2 -5.728 35.155 15.718 1 28.28 ? O3A CDP 209 A 1 
HETATM 6 P PA CDP . . . B 2 -7.214 35.574 15.946 1 26.18 ? PA CDP 209 A 1 
HETATM 7 O O1A CDP . . . B 2 -7.368 36.535 17.066 1 27.82 ? O1A CDP 209 A 1 
HETATM 8 O O2A CDP . . . B 2 -8.004 34.294 16.157 1 28.52 ? O2A CDP 209 A 1 
HETATM 9 O O5' CDP . . . B 2 -7.64 36.335 14.676 1 28.17 ? O5' CDP 209 A 1 
HETATM 10 C C5' CDP . . . B 2 -7.51 35.631 13.492 1 28.8 ? C5' CDP 209 A 1 
HETATM 11 C C4' CDP . . . B 2 -7.594 36.407 12.305 1 28.85 ? C4' CDP 209 A 1 
HETATM 12 O O4' CDP . . . B 2 -8.792 37.089 12.292 1 28.15 ? O4' CDP 209 A 1 
HETATM 13 C C3' CDP . . . B 2 -6.591 37.402 12.387 1 29.06 ? C3' CDP 209 A 1 
HETATM 14 O O3' CDP . . . B 2 -5.189 37.535 11.922 1 29.71 ? O3' CDP 209 A 1 
HETATM 15 C C2' CDP . . . B 2 -7.165 38.771 11.905 1 29.48 ? C2' CDP 209 A 1 
HETATM 16 O O2' CDP . . . B 2 -6.864 38.782 10.451 1 29.32 ? O2' CDP 209 A 1 
HETATM 17 C C1' CDP . . . B 2 -8.556 38.342 11.93 1 28.55 ? C1' CDP 209 A 1 
HETATM 18 N N1 CDP . . . B 2 -9.076 39.264 12.964 1 28.48 ? N1 CDP 209 A 1 
HETATM 19 C C2 CDP . . . B 2 -9.339 40.431 12.558 1 28.94 ? C2 CDP 209 A 1 
HETATM 20 O O2 CDP . . . B 2 -9.215 41.146 11.345 1 29.27 ? O2 CDP 209 A 1 
HETATM 21 N N3 CDP . . . B 2 -9.9 41.361 13.326 1 28.72 ? N3 CDP 209 A 1 
HETATM 22 C C4 CDP . . . B 2 -10.228 41.061 14.583 1 28.82 ? C4 CDP 209 A 1 
HETATM 23 N N4 CDP . . . B 2 -11.116 41.679 15.344 1 29.2 ? N4 CDP 209 A 1 
HETATM 24 C C5 CDP . . . B 2 -9.991 39.805 15.037 1 28.51 ? C5 CDP 209 A 1 
HETATM 25 C C6 CDP . . . B 2 -9.401 38.885 14.211 1 28.81 ? C6 CDP 209 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#