data_4KY7
#
_model_server_result.job_id            UWHUSGXs6_O8xf10ntuJYA 
_model_server_result.datetime_utc      '2024-10-11 10:21:06' 
_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          4ky7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    4KY7 
#
_exptl.entry_id    4KY7 
_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-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          90 
_cell.angle_gamma         90 
_cell.entry_id            4KY7 
_cell.length_a            30.895 
_cell.length_b            60.521 
_cell.length_c            75.061 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KY7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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                      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 OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? 
metalc ? metalc4 B O4P THP . A THP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.121 ? 
metalc ? metalc5 C CA CA . A CA 202 1_555 D O HOH . A HOH 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? 
metalc ? metalc6 C CA CA . A CA 202 1_555 D O HOH . A HOH 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? 
metalc ? metalc7 C CA CA . A CA 202 1_555 D O HOH . A HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.105 ? 
#
_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                     4KY7 
_atom_sites.fract_transf_matrix[1][1]    0.032368 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016523 
_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]    0.013322 
_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 THP A 1 201 142 THP THP . 
C 3 CA A 1 202 1 CA CA . 
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 1 HOH HOH . 
D 4 HOH A 29 329 2 HOH HOH . 
D 4 HOH A 30 330 3 HOH HOH . 
D 4 HOH A 31 331 4 HOH HOH . 
D 4 HOH A 32 332 5 HOH HOH . 
D 4 HOH A 33 333 6 HOH HOH . 
D 4 HOH A 34 334 7 HOH HOH . 
D 4 HOH A 35 335 8 HOH HOH . 
D 4 HOH A 36 336 9 HOH HOH . 
D 4 HOH A 37 337 10 HOH HOH . 
D 4 HOH A 38 338 11 HOH HOH . 
D 4 HOH A 39 339 12 HOH HOH . 
D 4 HOH A 40 340 13 HOH HOH . 
D 4 HOH A 41 341 14 HOH HOH . 
D 4 HOH A 42 342 15 HOH HOH . 
D 4 HOH A 43 343 16 HOH HOH . 
D 4 HOH A 44 344 17 HOH HOH . 
D 4 HOH A 45 345 18 HOH HOH . 
D 4 HOH A 46 346 19 HOH HOH . 
D 4 HOH A 47 347 20 HOH HOH . 
D 4 HOH A 48 348 21 HOH HOH . 
D 4 HOH A 49 349 22 HOH HOH . 
D 4 HOH A 50 350 23 HOH HOH . 
D 4 HOH A 51 351 25 HOH HOH . 
D 4 HOH A 52 352 26 HOH HOH . 
D 4 HOH A 53 353 27 HOH HOH . 
D 4 HOH A 54 354 28 HOH HOH . 
D 4 HOH A 55 355 29 HOH HOH . 
D 4 HOH A 56 356 30 HOH HOH . 
D 4 HOH A 57 357 31 HOH HOH . 
D 4 HOH A 58 358 32 HOH HOH . 
D 4 HOH A 59 359 33 HOH HOH . 
D 4 HOH A 60 360 34 HOH HOH . 
D 4 HOH A 61 361 35 HOH HOH . 
D 4 HOH A 62 362 36 HOH HOH . 
D 4 HOH A 63 363 37 HOH HOH . 
D 4 HOH A 64 364 38 HOH HOH . 
D 4 HOH A 65 365 39 HOH HOH . 
D 4 HOH A 66 366 42 HOH HOH . 
D 4 HOH A 67 367 43 HOH HOH . 
D 4 HOH A 68 368 44 HOH HOH . 
D 4 HOH A 69 369 45 HOH HOH . 
D 4 HOH A 70 370 46 HOH HOH . 
D 4 HOH A 71 371 47 HOH HOH . 
D 4 HOH A 72 372 48 HOH HOH . 
D 4 HOH A 73 373 49 HOH HOH . 
D 4 HOH A 74 374 50 HOH HOH . 
D 4 HOH A 75 375 52 HOH HOH . 
D 4 HOH A 76 376 53 HOH HOH . 
D 4 HOH A 77 377 54 HOH HOH . 
D 4 HOH A 78 378 56 HOH HOH . 
D 4 HOH A 79 379 57 HOH HOH . 
D 4 HOH A 80 380 61 HOH HOH . 
D 4 HOH A 81 381 62 HOH HOH . 
D 4 HOH A 82 382 63 HOH HOH . 
D 4 HOH A 83 383 65 HOH HOH . 
D 4 HOH A 84 384 66 HOH HOH . 
D 4 HOH A 85 385 68 HOH HOH . 
D 4 HOH A 86 386 70 HOH HOH . 
D 4 HOH A 87 387 71 HOH HOH . 
D 4 HOH A 88 388 72 HOH HOH . 
D 4 HOH A 89 389 73 HOH HOH . 
D 4 HOH A 90 390 74 HOH HOH . 
D 4 HOH A 91 391 75 HOH HOH . 
D 4 HOH A 92 392 76 HOH HOH . 
D 4 HOH A 93 393 78 HOH HOH . 
D 4 HOH A 94 394 81 HOH HOH . 
D 4 HOH A 95 395 83 HOH HOH . 
D 4 HOH A 96 396 88 HOH HOH . 
D 4 HOH A 97 397 91 HOH HOH . 
D 4 HOH A 98 398 92 HOH HOH . 
D 4 HOH A 99 399 94 HOH HOH . 
D 4 HOH A 100 400 95 HOH HOH . 
D 4 HOH A 101 401 97 HOH HOH . 
D 4 HOH A 102 402 99 HOH HOH . 
D 4 HOH A 103 403 100 HOH HOH . 
D 4 HOH A 104 404 104 HOH HOH . 
D 4 HOH A 105 405 109 HOH HOH . 
D 4 HOH A 106 406 110 HOH HOH . 
D 4 HOH A 107 407 111 HOH HOH . 
D 4 HOH A 108 408 115 HOH HOH . 
D 4 HOH A 109 409 117 HOH HOH . 
D 4 HOH A 110 410 118 HOH HOH . 
D 4 HOH A 111 411 122 HOH HOH . 
D 4 HOH A 112 412 133 HOH HOH . 
D 4 HOH A 113 413 137 HOH HOH . 
D 4 HOH A 114 414 140 HOH HOH . 
D 4 HOH A 115 415 161 HOH HOH . 
D 4 HOH A 116 416 1 HOH HOH . 
D 4 HOH A 117 417 2 HOH HOH . 
D 4 HOH A 118 418 3 HOH HOH . 
D 4 HOH A 119 419 4 HOH HOH . 
D 4 HOH A 120 420 5 HOH HOH . 
D 4 HOH A 121 421 6 HOH HOH . 
D 4 HOH A 122 422 1 HOH HOH . 
D 4 HOH A 123 423 2 HOH HOH . 
D 4 HOH A 124 424 3 HOH HOH . 
D 4 HOH A 125 425 4 HOH HOH . 
D 4 HOH A 126 426 5 HOH HOH . 
D 4 HOH A 127 427 9 HOH HOH . 
D 4 HOH A 128 428 1 HOH HOH . 
D 4 HOH A 129 429 2 HOH HOH . 
D 4 HOH A 130 430 3 HOH HOH . 
D 4 HOH A 131 431 4 HOH HOH . 
D 4 HOH A 132 432 5 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 . . . B 2 -1.951 -17.231 -15.091 1 10.25 ? P2 THP 201 A 1 
HETATM 2 O O4P THP . . . B 2 -0.749 -18.117 -14.776 1 10.79 ? O4P THP 201 A 1 
HETATM 3 O O5P THP . . . B 2 -1.758 -15.782 -14.745 1 9.52 ? O5P THP 201 A 1 
HETATM 4 O O6P THP . . . B 2 -3.17 -17.99 -14.488 1 13.65 ? O6P THP 201 A 1 
HETATM 5 P P1 THP . . . B 2 -4.893 -20.589 -20.133 1 21.36 ? P1 THP 201 A 1 
HETATM 6 O O1P THP . . . B 2 -4.536 -21.224 -21.45 1 26.36 ? O1P THP 201 A 1 
HETATM 7 O O2P THP . . . B 2 -4.479 -21.69 -19.248 1 18.13 ? O2P THP 201 A 1 
HETATM 8 O O3P THP . . . B 2 -6.244 -19.986 -19.874 1 28.3 ? O3P THP 201 A 1 
HETATM 9 O O5' THP . . . B 2 -1.989 -17.239 -16.584 1 10.29 ? O5' THP 201 A 1 
HETATM 10 C C5' THP . . . B 2 -2.063 -18.36 -17.485 1 10.54 ? C5' THP 201 A 1 
HETATM 11 C C4' THP . . . B 2 -2.754 -18.003 -18.751 1 10.41 ? C4' THP 201 A 1 
HETATM 12 O O4' THP . . . B 2 -2.139 -16.86 -19.341 1 10.7 ? O4' THP 201 A 1 
HETATM 13 C C3' THP . . . B 2 -2.679 -19.195 -19.665 1 13.02 ? C3' THP 201 A 1 
HETATM 14 O O3' THP . . . B 2 -4.029 -19.225 -20.239 1 16.18 ? O3' THP 201 A 1 
HETATM 15 C C2' THP . . . B 2 -1.757 -18.681 -20.723 1 10.1 ? C2' THP 201 A 1 
HETATM 16 C C1' THP . . . B 2 -1.758 -17.162 -20.635 1 9.31 ? C1' THP 201 A 1 
HETATM 17 N N1 THP . . . B 2 -0.46 -16.609 -20.977 1 7.99 ? N1 THP 201 A 1 
HETATM 18 C C2 THP . . . B 2 -0.247 -16.263 -22.271 1 8.21 ? C2 THP 201 A 1 
HETATM 19 O O2 THP . . . B 2 -1.2 -16.401 -23.155 1 11.09 ? O2 THP 201 A 1 
HETATM 20 N N3 THP . . . B 2 0.899 -15.714 -22.684 1 8.25 ? N3 THP 201 A 1 
HETATM 21 C C4 THP . . . B 2 1.915 -15.592 -21.748 1 7.22 ? C4 THP 201 A 1 
HETATM 22 O O4 THP . . . B 2 2.988 -15.195 -22.168 1 7.76 ? O4 THP 201 A 1 
HETATM 23 C C5 THP . . . B 2 1.71 -15.932 -20.384 1 7.15 ? C5 THP 201 A 1 
HETATM 24 C C5M THP . . . B 2 2.805 -15.767 -19.378 1 8.18 ? C5M THP 201 A 1 
HETATM 25 C C6 THP . . . B 2 0.516 -16.453 -20.004 1 7.5 ? C6 THP 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#