data_4ZU7
#
_model_server_result.job_id            iRyb0T8R9WzGYOnzJRAQIQ 
_model_server_result.datetime_utc      '2024-10-12 17:20:42' 
_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          4zu7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":201}' 
#
_entry.id    4ZU7 
#
_exptl.entry_id    4ZU7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.5 
_cell.angle_gamma         90 
_cell.entry_id            4ZU7 
_cell.length_a            136.557 
_cell.length_b            96.174 
_cell.length_c            111.755 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZU7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,R,S 1 1 
C,D,K,L,M,T,U 2 1 
E,F,N,O,V,W 3 1 
G,H,P,Q,X,Y 4 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
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
#
_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 394 n n 
PA O2A TYD sing 395 n n 
PA O3A TYD sing 396 n n 
PA O5' TYD sing 397 n n 
O2A HOA2 TYD sing 398 n n 
O3A PB TYD sing 399 n n 
PB O1B TYD doub 400 n n 
PB O2B TYD sing 401 n n 
PB O3B TYD sing 402 n n 
O2B HOB2 TYD sing 403 n n 
O3B HOB3 TYD sing 404 n n 
O5' C5' TYD sing 405 n n 
C5' C4' TYD sing 406 n n 
C5' "H5'1" TYD sing 407 n n 
C5' "H5'2" TYD sing 408 n n 
C4' O4' TYD sing 409 n n 
C4' C3' TYD sing 410 n n 
C4' H4' TYD sing 411 n n 
O4' C1' TYD sing 412 n n 
C3' O3' TYD sing 413 n n 
C3' C2' TYD sing 414 n n 
C3' H3' TYD sing 415 n n 
O3' HO3' TYD sing 416 n n 
C2' C1' TYD sing 417 n n 
C2' "H2'1" TYD sing 418 n n 
C2' "H2'2" TYD sing 419 n n 
C1' N1 TYD sing 420 n n 
C1' H1' TYD sing 421 n n 
N1 C2 TYD sing 422 n y 
N1 C6 TYD sing 423 n y 
C2 O2 TYD doub 424 n n 
C2 N3 TYD sing 425 n y 
N3 C4 TYD sing 426 n y 
N3 HN3 TYD sing 427 n n 
C4 O4 TYD doub 428 n n 
C4 C5 TYD sing 429 n y 
C5 C5M TYD sing 430 n n 
C5 C6 TYD doub 431 n y 
C5M H51 TYD sing 432 n n 
C5M H52 TYD sing 433 n n 
C5M H53 TYD sing 434 n n 
C6 H6 TYD sing 435 n n 
#
_atom_sites.entry_id                     4ZU7 
_atom_sites.fract_transf_matrix[1][1]    0.007323 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003338 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010398 
_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]    0.009834 
_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
I 2 TYD A 1 201 2 TYD TYD . 
J 2 TYD B 1 201 1 TYD TYD . 
K 2 TYD C 1 201 4 TYD TYD . 
L 2 TYD D 1 201 3 TYD TYD . 
M 3 PXN D 1 202 1 PXN PXN . 
N 2 TYD E 1 201 6 TYD TYD . 
O 2 TYD F 1 201 5 TYD TYD . 
P 2 TYD G 1 201 8 TYD TYD . 
Q 2 TYD H 1 201 7 TYD TYD . 
R 4 HOH A 1 301 251 HOH HOH . 
R 4 HOH A 2 302 10 HOH HOH . 
R 4 HOH A 3 303 16 HOH HOH . 
R 4 HOH A 4 304 130 HOH HOH . 
R 4 HOH A 5 305 20 HOH HOH . 
R 4 HOH A 6 306 15 HOH HOH . 
R 4 HOH A 7 307 21 HOH HOH . 
R 4 HOH A 8 308 13 HOH HOH . 
R 4 HOH A 9 309 133 HOH HOH . 
R 4 HOH A 10 310 22 HOH HOH . 
R 4 HOH A 11 311 159 HOH HOH . 
R 4 HOH A 12 312 222 HOH HOH . 
R 4 HOH A 13 313 194 HOH HOH . 
R 4 HOH A 14 314 4 HOH HOH . 
R 4 HOH A 15 315 5 HOH HOH . 
R 4 HOH A 16 316 18 HOH HOH . 
R 4 HOH A 17 317 17 HOH HOH . 
R 4 HOH A 18 318 19 HOH HOH . 
R 4 HOH A 19 319 115 HOH HOH . 
R 4 HOH A 20 320 239 HOH HOH . 
R 4 HOH A 21 321 88 HOH HOH . 
R 4 HOH A 22 322 238 HOH HOH . 
R 4 HOH A 23 323 189 HOH HOH . 
R 4 HOH A 24 324 107 HOH HOH . 
R 4 HOH A 25 325 191 HOH HOH . 
R 4 HOH A 26 326 14 HOH HOH . 
R 4 HOH A 27 327 23 HOH HOH . 
R 4 HOH A 28 328 24 HOH HOH . 
R 4 HOH A 29 329 119 HOH HOH . 
R 4 HOH A 30 330 125 HOH HOH . 
R 4 HOH A 31 331 9 HOH HOH . 
R 4 HOH A 32 332 25 HOH HOH . 
R 4 HOH A 33 333 11 HOH HOH . 
R 4 HOH A 34 334 176 HOH HOH . 
R 4 HOH A 35 335 7 HOH HOH . 
R 4 HOH A 36 336 2 HOH HOH . 
S 4 HOH B 1 301 245 HOH HOH . 
S 4 HOH B 2 302 30 HOH HOH . 
S 4 HOH B 3 303 96 HOH HOH . 
S 4 HOH B 4 304 167 HOH HOH . 
S 4 HOH B 5 305 190 HOH HOH . 
S 4 HOH B 6 306 177 HOH HOH . 
S 4 HOH B 7 307 28 HOH HOH . 
S 4 HOH B 8 308 201 HOH HOH . 
S 4 HOH B 9 309 29 HOH HOH . 
S 4 HOH B 10 310 6 HOH HOH . 
S 4 HOH B 11 311 197 HOH HOH . 
S 4 HOH B 12 312 3 HOH HOH . 
S 4 HOH B 13 313 12 HOH HOH . 
S 4 HOH B 14 314 216 HOH HOH . 
S 4 HOH B 15 315 144 HOH HOH . 
S 4 HOH B 16 316 117 HOH HOH . 
S 4 HOH B 17 317 223 HOH HOH . 
S 4 HOH B 18 318 178 HOH HOH . 
S 4 HOH B 19 319 195 HOH HOH . 
S 4 HOH B 20 320 156 HOH HOH . 
S 4 HOH B 21 321 166 HOH HOH . 
S 4 HOH B 22 322 141 HOH HOH . 
S 4 HOH B 23 323 31 HOH HOH . 
S 4 HOH B 24 324 27 HOH HOH . 
S 4 HOH B 25 325 32 HOH HOH . 
S 4 HOH B 26 326 208 HOH HOH . 
S 4 HOH B 27 327 198 HOH HOH . 
T 4 HOH C 1 301 252 HOH HOH . 
T 4 HOH C 2 302 43 HOH HOH . 
T 4 HOH C 3 303 165 HOH HOH . 
T 4 HOH C 4 304 8 HOH HOH . 
T 4 HOH C 5 305 184 HOH HOH . 
T 4 HOH C 6 306 37 HOH HOH . 
T 4 HOH C 7 307 44 HOH HOH . 
T 4 HOH C 8 308 219 HOH HOH . 
T 4 HOH C 9 309 202 HOH HOH . 
T 4 HOH C 10 310 45 HOH HOH . 
T 4 HOH C 11 311 103 HOH HOH . 
T 4 HOH C 12 312 154 HOH HOH . 
T 4 HOH C 13 313 199 HOH HOH . 
T 4 HOH C 14 314 196 HOH HOH . 
T 4 HOH C 15 315 33 HOH HOH . 
T 4 HOH C 16 316 41 HOH HOH . 
T 4 HOH C 17 317 46 HOH HOH . 
T 4 HOH C 18 318 147 HOH HOH . 
T 4 HOH C 19 319 214 HOH HOH . 
T 4 HOH C 20 320 34 HOH HOH . 
T 4 HOH C 21 321 203 HOH HOH . 
T 4 HOH C 22 322 192 HOH HOH . 
T 4 HOH C 23 323 109 HOH HOH . 
T 4 HOH C 24 324 92 HOH HOH . 
T 4 HOH C 25 325 104 HOH HOH . 
T 4 HOH C 26 326 241 HOH HOH . 
T 4 HOH C 27 327 128 HOH HOH . 
T 4 HOH C 28 328 42 HOH HOH . 
T 4 HOH C 29 329 39 HOH HOH . 
T 4 HOH C 30 330 47 HOH HOH . 
T 4 HOH C 31 331 1 HOH HOH . 
U 4 HOH D 1 301 61 HOH HOH . 
U 4 HOH D 2 302 246 HOH HOH . 
U 4 HOH D 3 303 53 HOH HOH . 
U 4 HOH D 4 304 51 HOH HOH . 
U 4 HOH D 5 305 200 HOH HOH . 
U 4 HOH D 6 306 249 HOH HOH . 
U 4 HOH D 7 307 157 HOH HOH . 
U 4 HOH D 8 308 49 HOH HOH . 
U 4 HOH D 9 309 63 HOH HOH . 
U 4 HOH D 10 310 97 HOH HOH . 
U 4 HOH D 11 311 247 HOH HOH . 
U 4 HOH D 12 312 248 HOH HOH . 
U 4 HOH D 13 313 35 HOH HOH . 
U 4 HOH D 14 314 59 HOH HOH . 
U 4 HOH D 15 315 114 HOH HOH . 
U 4 HOH D 16 316 36 HOH HOH . 
U 4 HOH D 17 317 118 HOH HOH . 
U 4 HOH D 18 318 220 HOH HOH . 
U 4 HOH D 19 319 40 HOH HOH . 
U 4 HOH D 20 320 54 HOH HOH . 
U 4 HOH D 21 321 38 HOH HOH . 
U 4 HOH D 22 322 60 HOH HOH . 
U 4 HOH D 23 323 50 HOH HOH . 
U 4 HOH D 24 324 148 HOH HOH . 
U 4 HOH D 25 325 57 HOH HOH . 
U 4 HOH D 26 326 122 HOH HOH . 
U 4 HOH D 27 327 62 HOH HOH . 
U 4 HOH D 28 328 64 HOH HOH . 
U 4 HOH D 29 329 205 HOH HOH . 
U 4 HOH D 30 330 230 HOH HOH . 
U 4 HOH D 31 331 56 HOH HOH . 
U 4 HOH D 32 332 52 HOH HOH . 
U 4 HOH D 33 333 55 HOH HOH . 
V 4 HOH E 1 301 68 HOH HOH . 
V 4 HOH E 2 302 70 HOH HOH . 
V 4 HOH E 3 303 111 HOH HOH . 
V 4 HOH E 4 304 142 HOH HOH . 
V 4 HOH E 5 305 162 HOH HOH . 
V 4 HOH E 6 306 67 HOH HOH . 
V 4 HOH E 7 307 160 HOH HOH . 
V 4 HOH E 8 308 232 HOH HOH . 
V 4 HOH E 9 309 207 HOH HOH . 
V 4 HOH E 10 310 71 HOH HOH . 
V 4 HOH E 11 311 250 HOH HOH . 
V 4 HOH E 12 312 66 HOH HOH . 
W 4 HOH F 1 301 174 HOH HOH . 
W 4 HOH F 2 302 72 HOH HOH . 
W 4 HOH F 3 303 65 HOH HOH . 
W 4 HOH F 4 304 152 HOH HOH . 
W 4 HOH F 5 305 217 HOH HOH . 
W 4 HOH F 6 306 149 HOH HOH . 
W 4 HOH F 7 307 58 HOH HOH . 
W 4 HOH F 8 308 76 HOH HOH . 
W 4 HOH F 9 309 89 HOH HOH . 
W 4 HOH F 10 310 74 HOH HOH . 
W 4 HOH F 11 311 140 HOH HOH . 
W 4 HOH F 12 312 135 HOH HOH . 
W 4 HOH F 13 313 227 HOH HOH . 
W 4 HOH F 14 314 170 HOH HOH . 
W 4 HOH F 15 315 77 HOH HOH . 
W 4 HOH F 16 316 237 HOH HOH . 
W 4 HOH F 17 317 75 HOH HOH . 
W 4 HOH F 18 318 73 HOH HOH . 
W 4 HOH F 19 319 69 HOH HOH . 
X 4 HOH G 1 301 79 HOH HOH . 
X 4 HOH G 2 302 187 HOH HOH . 
X 4 HOH G 3 303 132 HOH HOH . 
X 4 HOH G 4 304 150 HOH HOH . 
X 4 HOH G 5 305 81 HOH HOH . 
X 4 HOH G 6 306 116 HOH HOH . 
X 4 HOH G 7 307 206 HOH HOH . 
X 4 HOH G 8 308 113 HOH HOH . 
X 4 HOH G 9 309 82 HOH HOH . 
X 4 HOH G 10 310 78 HOH HOH . 
Y 4 HOH H 1 301 84 HOH HOH . 
Y 4 HOH H 2 302 101 HOH HOH . 
Y 4 HOH H 3 303 169 HOH HOH . 
Y 4 HOH H 4 304 80 HOH HOH . 
Y 4 HOH H 5 305 85 HOH HOH . 
Y 4 HOH H 6 306 83 HOH HOH . 
Y 4 HOH H 7 307 228 HOH HOH . 
Y 4 HOH H 8 308 145 HOH HOH . 
Y 4 HOH H 9 309 182 HOH HOH . 
Y 4 HOH H 10 310 86 HOH HOH . 
Y 4 HOH H 11 311 87 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 . . . I 2 -19.661 25.802 8.325 1 43.91 ? PA TYD 201 A 1 
HETATM 2 O O1A TYD . . . I 2 -19.736 25.924 6.824 1 50.29 ? O1A TYD 201 A 1 
HETATM 3 O O2A TYD . . . I 2 -20.13 24.505 8.976 1 53.49 ? O2A TYD 201 A 1 
HETATM 4 O O3A TYD . . . I 2 -20.269 27.148 9.047 1 44.7 ? O3A TYD 201 A 1 
HETATM 5 P PB TYD . . . I 2 -21.628 27.583 9.887 1 41.59 ? PB TYD 201 A 1 
HETATM 6 O O1B TYD . . . I 2 -22.511 28.124 8.813 1 49.08 ? O1B TYD 201 A 1 
HETATM 7 O O2B TYD . . . I 2 -22.175 26.458 10.811 1 41.02 ? O2B TYD 201 A 1 
HETATM 8 O O3B TYD . . . I 2 -21.144 28.716 10.716 1 46.42 ? O3B TYD 201 A 1 
HETATM 9 O O5' TYD . . . I 2 -18.1 26.009 8.727 1 46.12 ? O5' TYD 201 A 1 
HETATM 10 C C5' TYD . . . I 2 -17.093 26.719 7.995 1 41.67 ? C5' TYD 201 A 1 
HETATM 11 C C4' TYD . . . I 2 -15.763 25.945 7.929 1 46.04 ? C4' TYD 201 A 1 
HETATM 12 O O4' TYD . . . I 2 -15.247 25.669 9.24 1 45.96 ? O4' TYD 201 A 1 
HETATM 13 C C3' TYD . . . I 2 -15.814 24.596 7.205 1 46.26 ? C3' TYD 201 A 1 
HETATM 14 O O3' TYD . . . I 2 -14.757 24.445 6.247 1 49.74 ? O3' TYD 201 A 1 
HETATM 15 C C2' TYD . . . I 2 -15.548 23.543 8.238 1 47.07 ? C2' TYD 201 A 1 
HETATM 16 C C1' TYD . . . I 2 -14.801 24.31 9.317 1 46.4 ? C1' TYD 201 A 1 
HETATM 17 N N1 TYD . . . I 2 -15.108 23.67 10.601 1 42.71 ? N1 TYD 201 A 1 
HETATM 18 C C2 TYD . . . I 2 -14.136 22.842 11.245 1 41.59 ? C2 TYD 201 A 1 
HETATM 19 O O2 TYD . . . I 2 -12.97 22.641 10.79 1 39.93 ? O2 TYD 201 A 1 
HETATM 20 N N3 TYD . . . I 2 -14.462 22.268 12.414 1 42.9 ? N3 TYD 201 A 1 
HETATM 21 C C4 TYD . . . I 2 -15.68 22.423 12.968 1 37.27 ? C4 TYD 201 A 1 
HETATM 22 O O4 TYD . . . I 2 -15.905 21.833 14.031 1 32.73 ? O4 TYD 201 A 1 
HETATM 23 C C5 TYD . . . I 2 -16.705 23.272 12.288 1 34.28 ? C5 TYD 201 A 1 
HETATM 24 C C5M TYD . . . I 2 -18.075 23.501 12.833 1 34.32 ? C5M TYD 201 A 1 
HETATM 25 C C6 TYD . . . I 2 -16.351 23.853 11.101 1 38.29 ? C6 TYD 201 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#