data_4DU9
#
_model_server_result.job_id            1QVG6nI5RN8K_TkekuGouQ 
_model_server_result.datetime_utc      '2024-10-11 10:20:21' 
_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          4du9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    4DU9 
#
_exptl.entry_id    4DU9 
_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-3',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          93.85 
_cell.angle_gamma         90 
_cell.entry_id            4DU9 
_cell.length_a            31.05 
_cell.length_b            60.517 
_cell.length_c            38.601 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DU9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_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 
_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                      3 
_struct_asym.id                             C 
_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 OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? 
metalc ? metalc5 B CA CA . A CA 201 1_555 D O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc6 B CA CA . A CA 201 1_555 D O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.751 ? 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                THP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-3',5'-DIPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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
P2 O4P THP doub 277 n n 
P2 O5P THP sing 278 n n 
P2 O6P THP sing 279 n n 
P2 O5' THP sing 280 n n 
O5P HOP5 THP sing 281 n n 
O6P HOP6 THP sing 282 n n 
P1 O1P THP doub 283 n n 
P1 O2P THP sing 284 n n 
P1 O3P THP sing 285 n n 
P1 O3' THP sing 286 n n 
O2P HOP2 THP sing 287 n n 
O3P HOP3 THP sing 288 n n 
O5' C5' THP sing 289 n n 
C5' C4' THP sing 290 n n 
C5' "H5'1" THP sing 291 n n 
C5' "H5'2" THP sing 292 n n 
C4' O4' THP sing 293 n n 
C4' C3' THP sing 294 n n 
C4' H4' THP sing 295 n n 
O4' C1' THP sing 296 n n 
C3' O3' THP sing 297 n n 
C3' C2' THP sing 298 n n 
C3' H3' THP sing 299 n n 
C2' C1' THP sing 300 n n 
C2' "H2'1" THP sing 301 n n 
C2' "H2'2" THP sing 302 n n 
C1' N1 THP sing 303 n n 
C1' H1' THP sing 304 n n 
N1 C2 THP sing 305 n n 
N1 C6 THP sing 306 n n 
C2 O2 THP doub 307 n n 
C2 N3 THP sing 308 n n 
N3 C4 THP sing 309 n n 
N3 H3 THP sing 310 n n 
C4 O4 THP doub 311 n n 
C4 C5 THP sing 312 n n 
C5 C5M THP sing 313 n n 
C5 C6 THP doub 314 n n 
C5M H51 THP sing 315 n n 
C5M H52 THP sing 316 n n 
C5M H53 THP sing 317 n n 
C6 H6 THP sing 318 n n 
#
_atom_sites.entry_id                     4DU9 
_atom_sites.fract_transf_matrix[1][1]    0.032206 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002168 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016524 
_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]    0.025965 
_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 CA A 1 201 1 CA CA . 
C 3 THP A 1 202 1 THP THP . 
D 4 HOH A 1 301 1 HOH HOH . 
D 4 HOH A 2 302 2 HOH HOH . 
D 4 HOH A 3 303 3 HOH HOH . 
D 4 HOH A 4 304 4 HOH HOH . 
D 4 HOH A 5 305 5 HOH HOH . 
D 4 HOH A 6 306 6 HOH HOH . 
D 4 HOH A 7 307 7 HOH HOH . 
D 4 HOH A 8 308 8 HOH HOH . 
D 4 HOH A 9 309 9 HOH HOH . 
D 4 HOH A 10 310 10 HOH HOH . 
D 4 HOH A 11 311 11 HOH HOH . 
D 4 HOH A 12 312 12 HOH HOH . 
D 4 HOH A 13 313 13 HOH HOH . 
D 4 HOH A 14 314 14 HOH HOH . 
D 4 HOH A 15 315 15 HOH HOH . 
D 4 HOH A 16 316 16 HOH HOH . 
D 4 HOH A 17 317 17 HOH HOH . 
D 4 HOH A 18 318 18 HOH HOH . 
D 4 HOH A 19 319 19 HOH HOH . 
D 4 HOH A 20 320 20 HOH HOH . 
D 4 HOH A 21 321 21 HOH HOH . 
D 4 HOH A 22 322 22 HOH HOH . 
D 4 HOH A 23 323 23 HOH HOH . 
D 4 HOH A 24 324 24 HOH HOH . 
D 4 HOH A 25 325 25 HOH HOH . 
D 4 HOH A 26 326 26 HOH HOH . 
D 4 HOH A 27 327 27 HOH HOH . 
D 4 HOH A 28 328 28 HOH HOH . 
D 4 HOH A 29 329 29 HOH HOH . 
D 4 HOH A 30 330 30 HOH HOH . 
D 4 HOH A 31 331 31 HOH HOH . 
D 4 HOH A 32 332 33 HOH HOH . 
D 4 HOH A 33 333 34 HOH HOH . 
D 4 HOH A 34 334 35 HOH HOH . 
D 4 HOH A 35 335 36 HOH HOH . 
D 4 HOH A 36 336 37 HOH HOH . 
D 4 HOH A 37 337 38 HOH HOH . 
D 4 HOH A 38 338 39 HOH HOH . 
D 4 HOH A 39 339 40 HOH HOH . 
D 4 HOH A 40 340 41 HOH HOH . 
D 4 HOH A 41 341 42 HOH HOH . 
D 4 HOH A 42 342 43 HOH HOH . 
D 4 HOH A 43 343 44 HOH HOH . 
D 4 HOH A 44 344 45 HOH HOH . 
D 4 HOH A 45 345 46 HOH HOH . 
D 4 HOH A 46 346 47 HOH HOH . 
D 4 HOH A 47 347 48 HOH HOH . 
D 4 HOH A 48 348 49 HOH HOH . 
D 4 HOH A 49 349 50 HOH HOH . 
D 4 HOH A 50 350 52 HOH HOH . 
D 4 HOH A 51 351 53 HOH HOH . 
D 4 HOH A 52 352 54 HOH HOH . 
D 4 HOH A 53 353 55 HOH HOH . 
D 4 HOH A 54 354 56 HOH HOH . 
D 4 HOH A 55 355 57 HOH HOH . 
D 4 HOH A 56 356 58 HOH HOH . 
D 4 HOH A 57 357 59 HOH HOH . 
D 4 HOH A 58 358 60 HOH HOH . 
D 4 HOH A 59 359 61 HOH HOH . 
D 4 HOH A 60 360 62 HOH HOH . 
D 4 HOH A 61 361 63 HOH HOH . 
D 4 HOH A 62 362 64 HOH HOH . 
D 4 HOH A 63 363 65 HOH HOH . 
D 4 HOH A 64 364 66 HOH HOH . 
D 4 HOH A 65 365 67 HOH HOH . 
D 4 HOH A 66 366 68 HOH HOH . 
D 4 HOH A 67 367 69 HOH HOH . 
D 4 HOH A 68 368 70 HOH HOH . 
D 4 HOH A 69 369 71 HOH HOH . 
D 4 HOH A 70 370 72 HOH HOH . 
D 4 HOH A 71 371 73 HOH HOH . 
D 4 HOH A 72 372 74 HOH HOH . 
D 4 HOH A 73 373 75 HOH HOH . 
D 4 HOH A 74 374 76 HOH HOH . 
D 4 HOH A 75 375 77 HOH HOH . 
D 4 HOH A 76 376 78 HOH HOH . 
D 4 HOH A 77 377 79 HOH HOH . 
D 4 HOH A 78 378 80 HOH HOH . 
D 4 HOH A 79 379 81 HOH HOH . 
D 4 HOH A 80 380 82 HOH HOH . 
D 4 HOH A 81 381 83 HOH HOH . 
D 4 HOH A 82 382 84 HOH HOH . 
D 4 HOH A 83 383 85 HOH HOH . 
D 4 HOH A 84 384 86 HOH HOH . 
D 4 HOH A 85 385 87 HOH HOH . 
D 4 HOH A 86 386 88 HOH HOH . 
D 4 HOH A 87 387 89 HOH HOH . 
D 4 HOH A 88 388 90 HOH HOH . 
D 4 HOH A 89 389 91 HOH HOH . 
D 4 HOH A 90 390 92 HOH HOH . 
D 4 HOH A 91 391 93 HOH HOH . 
D 4 HOH A 92 392 94 HOH HOH . 
D 4 HOH A 93 393 95 HOH HOH . 
D 4 HOH A 94 394 96 HOH HOH . 
D 4 HOH A 95 395 97 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 P2 THP . . . C 3 17.925 11.127 4.82 1 22.92 ? P2 THP 202 A 1 
HETATM 2 O O4P THP . . . C 3 17.951 9.632 5.043 1 22.11 ? O4P THP 202 A 1 
HETATM 3 O O5P THP . . . C 3 16.694 11.872 5.243 1 25.36 ? O5P THP 202 A 1 
HETATM 4 O O6P THP . . . C 3 19.201 11.871 5.281 1 28.28 ? O6P THP 202 A 1 
HETATM 5 P P1 THP . . . C 3 21.162 14.698 0.984 1 29.66 ? P1 THP 202 A 1 
HETATM 6 O O1P THP . . . C 3 22.079 15.189 -0.122 1 34 ? O1P THP 202 A 1 
HETATM 7 O O2P THP . . . C 3 21.796 13.519 1.759 1 34.92 ? O2P THP 202 A 1 
HETATM 8 O O3P THP . . . C 3 20.556 15.629 1.895 1 30.73 ? O3P THP 202 A 1 
HETATM 9 O O5' THP . . . C 3 17.92 11.118 3.288 1 20.89 ? O5' THP 202 A 1 
HETATM 10 C C5' THP . . . C 3 17.977 12.45 2.65 1 31.61 ? C5' THP 202 A 1 
HETATM 11 C C4' THP . . . C 3 18.838 12.412 1.419 1 27.52 ? C4' THP 202 A 1 
HETATM 12 O O4' THP . . . C 3 18.529 11.351 0.568 1 26.06 ? O4' THP 202 A 1 
HETATM 13 C C3' THP . . . C 3 18.799 13.695 0.56 1 28.31 ? C3' THP 202 A 1 
HETATM 14 O O3' THP . . . C 3 20.126 13.938 0.01 1 31.12 ? O3' THP 202 A 1 
HETATM 15 C C2' THP . . . C 3 17.925 13.22 -0.581 1 26.45 ? C2' THP 202 A 1 
HETATM 16 C C1' THP . . . C 3 18.204 11.69 -0.726 1 23.42 ? C1' THP 202 A 1 
HETATM 17 N N1 THP . . . C 3 16.872 11.043 -1.074 1 24.68 ? N1 THP 202 A 1 
HETATM 18 C C2 THP . . . C 3 16.595 10.781 -2.415 1 27.75 ? C2 THP 202 A 1 
HETATM 19 O O2 THP . . . C 3 17.411 11.095 -3.304 1 30.86 ? O2 THP 202 A 1 
HETATM 20 N N3 THP . . . C 3 15.398 10.274 -2.872 1 25.69 ? N3 THP 202 A 1 
HETATM 21 C C4 THP . . . C 3 14.469 10.014 -1.922 1 26.01 ? C4 THP 202 A 1 
HETATM 22 O O4 THP . . . C 3 13.418 9.579 -2.418 1 26.98 ? O4 THP 202 A 1 
HETATM 23 C C5 THP . . . C 3 14.73 10.254 -0.505 1 21.99 ? C5 THP 202 A 1 
HETATM 24 C C5M THP . . . C 3 13.658 9.871 0.542 1 21.7 ? C5M THP 202 A 1 
HETATM 25 C C6 THP . . . C 3 15.999 10.733 -0.1 1 23.81 ? C6 THP 202 A 1 
#
_model_server_stats.io_time_ms              40 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           25 
#