data_3VA5
#
_model_server_result.job_id            l3qPAenYmAmsdUvdwvUw8Q 
_model_server_result.datetime_utc      '2024-10-11 10:18:50' 
_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          3va5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    3VA5 
#
_exptl.entry_id    3VA5 
_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          94.78 
_cell.angle_gamma         90 
_cell.entry_id            3VA5 
_cell.length_a            31.179 
_cell.length_b            60.266 
_cell.length_c            38.1 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VA5 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.032 ? 
metalc ? metalc5 B CA CA . A CA 201 1_555 C O4P THP . A THP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.164 ? 
metalc ? metalc6 B CA CA . A CA 201 1_555 D O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? 
metalc ? metalc7 B CA CA . A CA 201 1_555 D O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? 
#
_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                     3VA5 
_atom_sites.fract_transf_matrix[1][1]    0.032073 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002682 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016593 
_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]    0.026338 
_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 44 HOH HOH . 
D 4 HOH A 2 302 45 HOH HOH . 
D 4 HOH A 3 303 46 HOH HOH . 
D 4 HOH A 4 304 47 HOH HOH . 
D 4 HOH A 5 305 48 HOH HOH . 
D 4 HOH A 6 306 49 HOH HOH . 
D 4 HOH A 7 307 1 HOH HOH . 
D 4 HOH A 8 308 2 HOH HOH . 
D 4 HOH A 9 309 3 HOH HOH . 
D 4 HOH A 10 310 4 HOH HOH . 
D 4 HOH A 11 311 5 HOH HOH . 
D 4 HOH A 12 312 6 HOH HOH . 
D 4 HOH A 13 313 7 HOH HOH . 
D 4 HOH A 14 314 8 HOH HOH . 
D 4 HOH A 15 315 9 HOH HOH . 
D 4 HOH A 16 316 10 HOH HOH . 
D 4 HOH A 17 317 11 HOH HOH . 
D 4 HOH A 18 318 12 HOH HOH . 
D 4 HOH A 19 319 13 HOH HOH . 
D 4 HOH A 20 320 14 HOH HOH . 
D 4 HOH A 21 321 15 HOH HOH . 
D 4 HOH A 22 322 16 HOH HOH . 
D 4 HOH A 23 323 17 HOH HOH . 
D 4 HOH A 24 324 18 HOH HOH . 
D 4 HOH A 25 325 19 HOH HOH . 
D 4 HOH A 26 326 20 HOH HOH . 
D 4 HOH A 27 327 21 HOH HOH . 
D 4 HOH A 28 328 22 HOH HOH . 
D 4 HOH A 29 329 23 HOH HOH . 
D 4 HOH A 30 330 24 HOH HOH . 
D 4 HOH A 31 331 25 HOH HOH . 
D 4 HOH A 32 332 26 HOH HOH . 
D 4 HOH A 33 333 27 HOH HOH . 
D 4 HOH A 34 334 28 HOH HOH . 
D 4 HOH A 35 335 29 HOH HOH . 
D 4 HOH A 36 336 30 HOH HOH . 
D 4 HOH A 37 337 31 HOH HOH . 
D 4 HOH A 38 338 32 HOH HOH . 
D 4 HOH A 39 339 33 HOH HOH . 
D 4 HOH A 40 340 34 HOH HOH . 
D 4 HOH A 41 341 35 HOH HOH . 
D 4 HOH A 42 342 36 HOH HOH . 
D 4 HOH A 43 343 37 HOH HOH . 
D 4 HOH A 44 344 38 HOH HOH . 
D 4 HOH A 45 345 39 HOH HOH . 
D 4 HOH A 46 346 40 HOH HOH . 
D 4 HOH A 47 347 41 HOH HOH . 
D 4 HOH A 48 348 42 HOH HOH . 
D 4 HOH A 49 349 43 HOH HOH . 
D 4 HOH A 50 350 51 HOH HOH . 
D 4 HOH A 51 351 52 HOH HOH . 
D 4 HOH A 52 352 53 HOH HOH . 
D 4 HOH A 53 353 54 HOH HOH . 
D 4 HOH A 54 354 55 HOH HOH . 
D 4 HOH A 55 355 56 HOH HOH . 
D 4 HOH A 56 356 57 HOH HOH . 
D 4 HOH A 57 357 58 HOH HOH . 
D 4 HOH A 58 358 59 HOH HOH . 
D 4 HOH A 59 359 60 HOH HOH . 
D 4 HOH A 60 360 61 HOH HOH . 
D 4 HOH A 61 361 62 HOH HOH . 
D 4 HOH A 62 362 63 HOH HOH . 
D 4 HOH A 63 363 64 HOH HOH . 
D 4 HOH A 64 364 65 HOH HOH . 
D 4 HOH A 65 365 66 HOH HOH . 
D 4 HOH A 66 366 67 HOH HOH . 
D 4 HOH A 67 367 68 HOH HOH . 
D 4 HOH A 68 368 69 HOH HOH . 
D 4 HOH A 69 369 70 HOH HOH . 
D 4 HOH A 70 370 71 HOH HOH . 
D 4 HOH A 71 371 72 HOH HOH . 
D 4 HOH A 72 372 73 HOH HOH . 
D 4 HOH A 73 373 74 HOH HOH . 
D 4 HOH A 74 374 75 HOH HOH . 
D 4 HOH A 75 375 76 HOH HOH . 
D 4 HOH A 76 376 77 HOH HOH . 
D 4 HOH A 77 377 78 HOH HOH . 
D 4 HOH A 78 378 79 HOH HOH . 
D 4 HOH A 79 379 80 HOH HOH . 
D 4 HOH A 80 380 81 HOH HOH . 
D 4 HOH A 81 381 82 HOH HOH . 
D 4 HOH A 82 382 83 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 . 
D 4 HOH A 96 396 98 HOH HOH . 
D 4 HOH A 97 397 99 HOH HOH . 
D 4 HOH A 98 398 100 HOH HOH . 
D 4 HOH A 99 399 101 HOH HOH . 
D 4 HOH A 100 400 102 HOH HOH . 
D 4 HOH A 101 401 103 HOH HOH . 
D 4 HOH A 102 402 104 HOH HOH . 
D 4 HOH A 103 403 105 HOH HOH . 
D 4 HOH A 104 404 106 HOH HOH . 
D 4 HOH A 105 405 107 HOH HOH . 
D 4 HOH A 106 406 108 HOH HOH . 
D 4 HOH A 107 407 109 HOH HOH . 
D 4 HOH A 108 408 110 HOH HOH . 
D 4 HOH A 109 409 111 HOH HOH . 
D 4 HOH A 110 410 112 HOH HOH . 
D 4 HOH A 111 411 113 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 17.878 44.596 4.955 1 20.43 ? P2 THP 202 A 1 
HETATM 2 O O4P THP . . . C 3 16.659 45.333 5.489 1 20.42 ? O4P THP 202 A 1 
HETATM 3 O O5P THP . . . C 3 17.874 43.062 5.276 1 21.12 ? O5P THP 202 A 1 
HETATM 4 O O6P THP . . . C 3 19.166 45.272 5.591 1 23.9 ? O6P THP 202 A 1 
HETATM 5 P P1 THP . . . C 3 21.14 48.136 1.209 1 22.28 ? P1 THP 202 A 1 
HETATM 6 O O1P THP . . . C 3 21.792 47.056 2.05 1 25.09 ? O1P THP 202 A 1 
HETATM 7 O O2P THP . . . C 3 22.261 48.762 0.284 1 24.14 ? O2P THP 202 A 1 
HETATM 8 O O3P THP . . . C 3 20.471 49.149 2.233 1 24.77 ? O3P THP 202 A 1 
HETATM 9 O O5' THP . . . C 3 17.838 44.623 3.369 1 19.35 ? O5' THP 202 A 1 
HETATM 10 C C5' THP . . . C 3 17.978 45.936 2.819 1 21.1 ? C5' THP 202 A 1 
HETATM 11 C C4' THP . . . C 3 18.855 45.9 1.568 1 18.7 ? C4' THP 202 A 1 
HETATM 12 O O4' THP . . . C 3 18.454 44.819 0.717 1 18.17 ? O4' THP 202 A 1 
HETATM 13 C C3' THP . . . C 3 18.773 47.19 0.716 1 21.27 ? C3' THP 202 A 1 
HETATM 14 O O3' THP . . . C 3 20.096 47.46 0.154 1 20.84 ? O3' THP 202 A 1 
HETATM 15 C C2' THP . . . C 3 17.879 46.702 -0.442 1 18.06 ? C2' THP 202 A 1 
HETATM 16 C C1' THP . . . C 3 18.151 45.178 -0.624 1 16.35 ? C1' THP 202 A 1 
HETATM 17 N N1 THP . . . C 3 16.822 44.535 -0.992 1 18.33 ? N1 THP 202 A 1 
HETATM 18 C C2 THP . . . C 3 16.553 44.349 -2.316 1 20.93 ? C2 THP 202 A 1 
HETATM 19 O O2 THP . . . C 3 17.376 44.737 -3.215 1 22.63 ? O2 THP 202 A 1 
HETATM 20 N N3 THP . . . C 3 15.363 43.884 -2.781 1 20.44 ? N3 THP 202 A 1 
HETATM 21 C C4 THP . . . C 3 14.412 43.533 -1.831 1 19.59 ? C4 THP 202 A 1 
HETATM 22 O O4 THP . . . C 3 13.331 43.171 -2.258 1 18.63 ? O4 THP 202 A 1 
HETATM 23 C C5 THP . . . C 3 14.669 43.727 -0.441 1 20.78 ? C5 THP 202 A 1 
HETATM 24 C C5M THP . . . C 3 13.635 43.332 0.621 1 22.36 ? C5M THP 202 A 1 
HETATM 25 C C6 THP . . . C 3 15.892 44.163 -0.029 1 19.44 ? C6 THP 202 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#