data_3DDI
#
_model_server_result.job_id            '_BDSmrGcOJc4JQTQJp4L0g' 
_model_server_result.datetime_utc      '2024-10-19 15:36:26' 
_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          3ddi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":201}' 
#
_entry.id    3DDI 
#
_exptl.entry_id    3DDI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-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          90 
_cell.angle_gamma         120 
_cell.entry_id            3DDI 
_cell.length_a            70.084 
_cell.length_b            70.084 
_cell.length_c            103.313 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DDI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? hexameric 6 author_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1,2,3 
A,C,D,G 2 1 
B,E,F,H 2 3 
#
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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.084 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 35.042 60.694524 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 E MG MG . B MG 142 1_555 F O1A TYD . B TYD 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc2 E MG MG . B MG 142 1_555 H O HOH . B HOH 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc3 E MG MG . B MG 142 1_555 H O HOH . B HOH 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                TYD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-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
PA O1A TYD doub 334 n n 
PA O2A TYD sing 335 n n 
PA O3A TYD sing 336 n n 
PA O5' TYD sing 337 n n 
O2A HOA2 TYD sing 338 n n 
O3A PB TYD sing 339 n n 
PB O1B TYD doub 340 n n 
PB O2B TYD sing 341 n n 
PB O3B TYD sing 342 n n 
O2B HOB2 TYD sing 343 n n 
O3B HOB3 TYD sing 344 n n 
O5' C5' TYD sing 345 n n 
C5' C4' TYD sing 346 n n 
C5' "H5'1" TYD sing 347 n n 
C5' "H5'2" TYD sing 348 n n 
C4' O4' TYD sing 349 n n 
C4' C3' TYD sing 350 n n 
C4' H4' TYD sing 351 n n 
O4' C1' TYD sing 352 n n 
C3' O3' TYD sing 353 n n 
C3' C2' TYD sing 354 n n 
C3' H3' TYD sing 355 n n 
O3' HO3' TYD sing 356 n n 
C2' C1' TYD sing 357 n n 
C2' "H2'1" TYD sing 358 n n 
C2' "H2'2" TYD sing 359 n n 
C1' N1 TYD sing 360 n n 
C1' H1' TYD sing 361 n n 
N1 C2 TYD sing 362 n y 
N1 C6 TYD sing 363 n y 
C2 O2 TYD doub 364 n n 
C2 N3 TYD sing 365 n y 
N3 C4 TYD sing 366 n y 
N3 HN3 TYD sing 367 n n 
C4 O4 TYD doub 368 n n 
C4 C5 TYD sing 369 n y 
C5 C5M TYD sing 370 n n 
C5 C6 TYD doub 371 n y 
C5M H51 TYD sing 372 n n 
C5M H52 TYD sing 373 n n 
C5M H53 TYD sing 374 n n 
C6 H6 TYD sing 375 n n 
#
_atom_sites.entry_id                     3DDI 
_atom_sites.fract_transf_matrix[1][1]    0.014269 
_atom_sites.fract_transf_matrix[1][2]    0.008238 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016476 
_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]    0.009679 
_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 MG A 1 142 1 MG MG . 
D 3 TYD A 1 201 201 TYD TYD . 
E 2 MG B 1 142 1 MG MG . 
F 3 TYD B 1 201 201 TYD TYD . 
G 4 HOH A 1 202 2 HOH HOH . 
G 4 HOH A 2 203 3 HOH HOH . 
G 4 HOH A 3 204 4 HOH HOH . 
G 4 HOH A 4 205 6 HOH HOH . 
G 4 HOH A 5 206 7 HOH HOH . 
G 4 HOH A 6 207 8 HOH HOH . 
G 4 HOH A 7 208 10 HOH HOH . 
G 4 HOH A 8 209 12 HOH HOH . 
G 4 HOH A 9 210 13 HOH HOH . 
G 4 HOH A 10 211 15 HOH HOH . 
G 4 HOH A 11 212 16 HOH HOH . 
G 4 HOH A 12 213 19 HOH HOH . 
G 4 HOH A 13 214 20 HOH HOH . 
G 4 HOH A 14 215 21 HOH HOH . 
G 4 HOH A 15 216 22 HOH HOH . 
G 4 HOH A 16 217 23 HOH HOH . 
G 4 HOH A 17 218 24 HOH HOH . 
G 4 HOH A 18 219 27 HOH HOH . 
G 4 HOH A 19 220 28 HOH HOH . 
G 4 HOH A 20 221 33 HOH HOH . 
G 4 HOH A 21 222 34 HOH HOH . 
G 4 HOH A 22 223 39 HOH HOH . 
G 4 HOH A 23 224 44 HOH HOH . 
G 4 HOH A 24 225 45 HOH HOH . 
G 4 HOH A 25 226 50 HOH HOH . 
G 4 HOH A 26 227 51 HOH HOH . 
G 4 HOH A 27 228 53 HOH HOH . 
G 4 HOH A 28 229 54 HOH HOH . 
G 4 HOH A 29 230 57 HOH HOH . 
G 4 HOH A 30 231 58 HOH HOH . 
G 4 HOH A 31 232 61 HOH HOH . 
G 4 HOH A 32 233 65 HOH HOH . 
G 4 HOH A 33 234 66 HOH HOH . 
G 4 HOH A 34 235 68 HOH HOH . 
G 4 HOH A 35 236 69 HOH HOH . 
G 4 HOH A 36 237 70 HOH HOH . 
G 4 HOH A 37 238 73 HOH HOH . 
G 4 HOH A 38 239 74 HOH HOH . 
G 4 HOH A 39 240 76 HOH HOH . 
G 4 HOH A 40 241 77 HOH HOH . 
G 4 HOH A 41 242 78 HOH HOH . 
G 4 HOH A 42 243 80 HOH HOH . 
G 4 HOH A 43 244 81 HOH HOH . 
G 4 HOH A 44 245 84 HOH HOH . 
G 4 HOH A 45 246 87 HOH HOH . 
G 4 HOH A 46 247 91 HOH HOH . 
G 4 HOH A 47 248 94 HOH HOH . 
G 4 HOH A 48 249 95 HOH HOH . 
G 4 HOH A 49 250 97 HOH HOH . 
G 4 HOH A 50 251 99 HOH HOH . 
G 4 HOH A 51 252 100 HOH HOH . 
G 4 HOH A 52 253 101 HOH HOH . 
G 4 HOH A 53 254 102 HOH HOH . 
G 4 HOH A 54 255 108 HOH HOH . 
G 4 HOH A 55 256 111 HOH HOH . 
G 4 HOH A 56 257 112 HOH HOH . 
G 4 HOH A 57 258 113 HOH HOH . 
G 4 HOH A 58 259 117 HOH HOH . 
G 4 HOH A 59 260 119 HOH HOH . 
G 4 HOH A 60 261 120 HOH HOH . 
G 4 HOH A 61 262 121 HOH HOH . 
G 4 HOH A 62 263 122 HOH HOH . 
G 4 HOH A 63 264 124 HOH HOH . 
G 4 HOH A 64 265 129 HOH HOH . 
G 4 HOH A 65 266 130 HOH HOH . 
G 4 HOH A 66 267 131 HOH HOH . 
G 4 HOH A 67 268 132 HOH HOH . 
G 4 HOH A 68 269 137 HOH HOH . 
G 4 HOH A 69 270 139 HOH HOH . 
G 4 HOH A 70 271 140 HOH HOH . 
G 4 HOH A 71 272 142 HOH HOH . 
G 4 HOH A 72 273 144 HOH HOH . 
G 4 HOH A 73 274 145 HOH HOH . 
G 4 HOH A 74 275 150 HOH HOH . 
G 4 HOH A 75 276 151 HOH HOH . 
G 4 HOH A 76 277 153 HOH HOH . 
G 4 HOH A 77 278 154 HOH HOH . 
G 4 HOH A 78 279 156 HOH HOH . 
G 4 HOH A 79 280 158 HOH HOH . 
G 4 HOH A 80 281 159 HOH HOH . 
G 4 HOH A 81 282 42 HOH HOH . 
G 4 HOH A 82 283 160 HOH HOH . 
H 4 HOH B 1 202 1 HOH HOH . 
H 4 HOH B 2 203 5 HOH HOH . 
H 4 HOH B 3 204 9 HOH HOH . 
H 4 HOH B 4 205 11 HOH HOH . 
H 4 HOH B 5 206 14 HOH HOH . 
H 4 HOH B 6 207 17 HOH HOH . 
H 4 HOH B 7 208 18 HOH HOH . 
H 4 HOH B 8 209 25 HOH HOH . 
H 4 HOH B 9 210 26 HOH HOH . 
H 4 HOH B 10 211 29 HOH HOH . 
H 4 HOH B 11 212 30 HOH HOH . 
H 4 HOH B 12 213 31 HOH HOH . 
H 4 HOH B 13 214 32 HOH HOH . 
H 4 HOH B 14 215 35 HOH HOH . 
H 4 HOH B 15 216 36 HOH HOH . 
H 4 HOH B 16 217 37 HOH HOH . 
H 4 HOH B 17 218 38 HOH HOH . 
H 4 HOH B 18 219 40 HOH HOH . 
H 4 HOH B 19 220 41 HOH HOH . 
H 4 HOH B 20 222 43 HOH HOH . 
H 4 HOH B 21 223 46 HOH HOH . 
H 4 HOH B 22 224 47 HOH HOH . 
H 4 HOH B 23 225 48 HOH HOH . 
H 4 HOH B 24 226 49 HOH HOH . 
H 4 HOH B 25 227 52 HOH HOH . 
H 4 HOH B 26 228 55 HOH HOH . 
H 4 HOH B 27 229 56 HOH HOH . 
H 4 HOH B 28 230 59 HOH HOH . 
H 4 HOH B 29 231 60 HOH HOH . 
H 4 HOH B 30 232 62 HOH HOH . 
H 4 HOH B 31 233 64 HOH HOH . 
H 4 HOH B 32 234 71 HOH HOH . 
H 4 HOH B 33 235 72 HOH HOH . 
H 4 HOH B 34 236 75 HOH HOH . 
H 4 HOH B 35 237 79 HOH HOH . 
H 4 HOH B 36 238 82 HOH HOH . 
H 4 HOH B 37 239 83 HOH HOH . 
H 4 HOH B 38 240 85 HOH HOH . 
H 4 HOH B 39 241 86 HOH HOH . 
H 4 HOH B 40 242 88 HOH HOH . 
H 4 HOH B 41 243 89 HOH HOH . 
H 4 HOH B 42 244 90 HOH HOH . 
H 4 HOH B 43 245 92 HOH HOH . 
H 4 HOH B 44 246 93 HOH HOH . 
H 4 HOH B 45 247 96 HOH HOH . 
H 4 HOH B 46 248 98 HOH HOH . 
H 4 HOH B 47 249 103 HOH HOH . 
H 4 HOH B 48 250 104 HOH HOH . 
H 4 HOH B 49 251 105 HOH HOH . 
H 4 HOH B 50 252 106 HOH HOH . 
H 4 HOH B 51 253 107 HOH HOH . 
H 4 HOH B 52 254 109 HOH HOH . 
H 4 HOH B 53 255 110 HOH HOH . 
H 4 HOH B 54 256 114 HOH HOH . 
H 4 HOH B 55 257 115 HOH HOH . 
H 4 HOH B 56 258 116 HOH HOH . 
H 4 HOH B 57 259 118 HOH HOH . 
H 4 HOH B 58 260 123 HOH HOH . 
H 4 HOH B 59 261 125 HOH HOH . 
H 4 HOH B 60 262 126 HOH HOH . 
H 4 HOH B 61 263 127 HOH HOH . 
H 4 HOH B 62 264 128 HOH HOH . 
H 4 HOH B 63 265 133 HOH HOH . 
H 4 HOH B 64 266 134 HOH HOH . 
H 4 HOH B 65 267 135 HOH HOH . 
H 4 HOH B 66 268 136 HOH HOH . 
H 4 HOH B 67 269 146 HOH HOH . 
H 4 HOH B 68 270 147 HOH HOH . 
H 4 HOH B 69 271 149 HOH HOH . 
H 4 HOH B 70 272 152 HOH HOH . 
H 4 HOH B 71 273 155 HOH HOH . 
H 4 HOH B 72 274 157 HOH HOH . 
H 4 HOH B 73 276 161 HOH HOH . 
H 4 HOH B 74 277 162 HOH HOH . 
H 4 HOH B 75 278 163 HOH HOH . 
H 4 HOH B 76 279 164 HOH HOH . 
H 4 HOH B 77 280 165 HOH HOH . 
H 4 HOH B 78 281 166 HOH HOH . 
H 4 HOH B 79 282 167 HOH HOH . 
H 4 HOH B 80 283 168 HOH HOH . 
H 4 HOH B 81 284 169 HOH HOH . 
H 4 HOH B 82 285 170 HOH HOH . 
H 4 HOH B 83 286 171 HOH HOH . 
H 4 HOH B 84 287 172 HOH HOH . 
H 4 HOH B 85 288 173 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 PA TYD . . . F 3 51.697 32.281 34.197 1 26.4 ? PA TYD 201 B 1 
HETATM 2 O O1A TYD . . . F 3 51.253 33.712 34.108 1 25.06 ? O1A TYD 201 B 1 
HETATM 3 O O2A TYD . . . F 3 51.862 31.639 35.559 1 28.33 ? O2A TYD 201 B 1 
HETATM 4 O O3A TYD . . . F 3 50.729 31.309 33.333 1 28.07 ? O3A TYD 201 B 1 
HETATM 5 P PB TYD . . . F 3 49.494 31.7 32.352 1 24.4 ? PB TYD 201 B 1 
HETATM 6 O O1B TYD . . . F 3 50.112 31.841 30.981 1 20.38 ? O1B TYD 201 B 1 
HETATM 7 O O2B TYD . . . F 3 48.854 32.962 32.884 1 22.56 ? O2B TYD 201 B 1 
HETATM 8 O O3B TYD . . . F 3 48.605 30.484 32.492 1 18.77 ? O3B TYD 201 B 1 
HETATM 9 O O5' TYD . . . F 3 53.111 32.075 33.459 1 27.04 ? O5' TYD 201 B 1 
HETATM 10 C C5' TYD . . . F 3 53.472 32.869 32.335 1 24.69 ? C5' TYD 201 B 1 
HETATM 11 C C4' TYD . . . F 3 54.166 31.957 31.337 1 23.53 ? C4' TYD 201 B 1 
HETATM 12 O O4' TYD . . . F 3 55.403 31.5 31.889 1 25.58 ? O4' TYD 201 B 1 
HETATM 13 C C3' TYD . . . F 3 53.359 30.693 31.053 1 24.45 ? C3' TYD 201 B 1 
HETATM 14 O O3' TYD . . . F 3 52.464 30.843 29.946 1 20.93 ? O3' TYD 201 B 1 
HETATM 15 C C2' TYD . . . F 3 54.417 29.658 30.737 1 22.93 ? C2' TYD 201 B 1 
HETATM 16 C C1' TYD . . . F 3 55.641 30.149 31.494 1 25.43 ? C1' TYD 201 B 1 
HETATM 17 N N1 TYD . . . F 3 55.831 29.299 32.671 1 27.99 ? N1 TYD 201 B 1 
HETATM 18 C C2 TYD . . . F 3 56.76 28.24 32.602 1 28.02 ? C2 TYD 201 B 1 
HETATM 19 O O2 TYD . . . F 3 57.383 28.067 31.535 1 23.96 ? O2 TYD 201 B 1 
HETATM 20 N N3 TYD . . . F 3 56.973 27.427 33.65 1 28.53 ? N3 TYD 201 B 1 
HETATM 21 C C4 TYD . . . F 3 56.301 27.616 34.792 1 27.99 ? C4 TYD 201 B 1 
HETATM 22 O O4 TYD . . . F 3 56.482 26.876 35.779 1 33.87 ? O4 TYD 201 B 1 
HETATM 23 C C5 TYD . . . F 3 55.323 28.719 34.888 1 26.41 ? C5 TYD 201 B 1 
HETATM 24 C C5M TYD . . . F 3 54.56 28.941 36.17 1 31.47 ? C5M TYD 201 B 1 
HETATM 25 C C6 TYD . . . F 3 55.133 29.538 33.787 1 26.3 ? C6 TYD 201 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#