data_5KYI
#
_model_server_result.job_id            1q3ve7JMUU_qjTLdTUVR5g 
_model_server_result.datetime_utc      '2024-10-20 00:32:34' 
_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          5kyi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    5KYI 
#
_exptl.entry_id    5KYI 
_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          93.86 
_cell.angle_gamma         90 
_cell.entry_id            5KYI 
_cell.length_a            31.129 
_cell.length_b            60.426 
_cell.length_c            38.446 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KYI 
_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                      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 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.096 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? 
metalc ? metalc5 B O5P THP . A THP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.146 ? 
metalc ? metalc6 C CA CA . A CA 202 1_555 D O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc7 C CA CA . A CA 202 1_555 D O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.879 ? 
#
_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                     5KYI 
_atom_sites.fract_transf_matrix[1][1]    0.032124 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002167 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016549 
_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]    0.026069 
_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 1 201 143 THP THP . 
C 3 CA A 1 202 2 CA CA . 
D 4 HOH A 1 301 144 HOH HOH . 
D 4 HOH A 2 302 168 HOH HOH . 
D 4 HOH A 3 303 165 HOH HOH . 
D 4 HOH A 4 304 74 HOH HOH . 
D 4 HOH A 5 305 102 HOH HOH . 
D 4 HOH A 6 306 118 HOH HOH . 
D 4 HOH A 7 307 151 HOH HOH . 
D 4 HOH A 8 308 141 HOH HOH . 
D 4 HOH A 9 309 65 HOH HOH . 
D 4 HOH A 10 310 81 HOH HOH . 
D 4 HOH A 11 311 133 HOH HOH . 
D 4 HOH A 12 312 163 HOH HOH . 
D 4 HOH A 13 313 59 HOH HOH . 
D 4 HOH A 14 314 124 HOH HOH . 
D 4 HOH A 15 315 77 HOH HOH . 
D 4 HOH A 16 316 128 HOH HOH . 
D 4 HOH A 17 317 88 HOH HOH . 
D 4 HOH A 18 318 147 HOH HOH . 
D 4 HOH A 19 319 106 HOH HOH . 
D 4 HOH A 20 320 110 HOH HOH . 
D 4 HOH A 21 321 145 HOH HOH . 
D 4 HOH A 22 322 125 HOH HOH . 
D 4 HOH A 23 323 56 HOH HOH . 
D 4 HOH A 24 324 58 HOH HOH . 
D 4 HOH A 25 325 148 HOH HOH . 
D 4 HOH A 26 326 97 HOH HOH . 
D 4 HOH A 27 327 109 HOH HOH . 
D 4 HOH A 28 328 155 HOH HOH . 
D 4 HOH A 29 329 89 HOH HOH . 
D 4 HOH A 30 330 94 HOH HOH . 
D 4 HOH A 31 331 79 HOH HOH . 
D 4 HOH A 32 332 167 HOH HOH . 
D 4 HOH A 33 333 131 HOH HOH . 
D 4 HOH A 34 334 161 HOH HOH . 
D 4 HOH A 35 335 69 HOH HOH . 
D 4 HOH A 36 336 83 HOH HOH . 
D 4 HOH A 37 337 78 HOH HOH . 
D 4 HOH A 38 338 73 HOH HOH . 
D 4 HOH A 39 339 152 HOH HOH . 
D 4 HOH A 40 340 64 HOH HOH . 
D 4 HOH A 41 341 60 HOH HOH . 
D 4 HOH A 42 342 119 HOH HOH . 
D 4 HOH A 43 343 99 HOH HOH . 
D 4 HOH A 44 344 70 HOH HOH . 
D 4 HOH A 45 345 57 HOH HOH . 
D 4 HOH A 46 346 116 HOH HOH . 
D 4 HOH A 47 347 154 HOH HOH . 
D 4 HOH A 48 348 92 HOH HOH . 
D 4 HOH A 49 349 159 HOH HOH . 
D 4 HOH A 50 350 153 HOH HOH . 
D 4 HOH A 51 351 84 HOH HOH . 
D 4 HOH A 52 352 104 HOH HOH . 
D 4 HOH A 53 353 136 HOH HOH . 
D 4 HOH A 54 354 135 HOH HOH . 
D 4 HOH A 55 355 122 HOH HOH . 
D 4 HOH A 56 356 62 HOH HOH . 
D 4 HOH A 57 357 126 HOH HOH . 
D 4 HOH A 58 358 114 HOH HOH . 
D 4 HOH A 59 359 121 HOH HOH . 
D 4 HOH A 60 360 127 HOH HOH . 
D 4 HOH A 61 361 140 HOH HOH . 
D 4 HOH A 62 362 100 HOH HOH . 
D 4 HOH A 63 363 93 HOH HOH . 
D 4 HOH A 64 364 98 HOH HOH . 
D 4 HOH A 65 365 86 HOH HOH . 
D 4 HOH A 66 366 67 HOH HOH . 
D 4 HOH A 67 367 87 HOH HOH . 
D 4 HOH A 68 368 137 HOH HOH . 
D 4 HOH A 69 369 123 HOH HOH . 
D 4 HOH A 70 370 113 HOH HOH . 
D 4 HOH A 71 371 107 HOH HOH . 
D 4 HOH A 72 372 156 HOH HOH . 
D 4 HOH A 73 373 160 HOH HOH . 
D 4 HOH A 74 374 149 HOH HOH . 
D 4 HOH A 75 375 130 HOH HOH . 
D 4 HOH A 76 376 90 HOH HOH . 
D 4 HOH A 77 377 101 HOH HOH . 
D 4 HOH A 78 378 162 HOH HOH . 
D 4 HOH A 79 379 111 HOH HOH . 
D 4 HOH A 80 380 82 HOH HOH . 
D 4 HOH A 81 381 68 HOH HOH . 
D 4 HOH A 82 382 63 HOH HOH . 
D 4 HOH A 83 383 120 HOH HOH . 
D 4 HOH A 84 384 166 HOH HOH . 
D 4 HOH A 85 385 150 HOH HOH . 
D 4 HOH A 86 386 66 HOH HOH . 
D 4 HOH A 87 387 75 HOH HOH . 
D 4 HOH A 88 388 139 HOH HOH . 
D 4 HOH A 89 389 138 HOH HOH . 
D 4 HOH A 90 390 164 HOH HOH . 
D 4 HOH A 91 391 142 HOH HOH . 
D 4 HOH A 92 392 80 HOH HOH . 
D 4 HOH A 93 393 157 HOH HOH . 
D 4 HOH A 94 394 146 HOH HOH . 
D 4 HOH A 95 395 95 HOH HOH . 
D 4 HOH A 96 396 85 HOH HOH . 
D 4 HOH A 97 397 91 HOH HOH . 
D 4 HOH A 98 398 108 HOH HOH . 
D 4 HOH A 99 399 103 HOH HOH . 
D 4 HOH A 100 400 115 HOH HOH . 
D 4 HOH A 101 401 112 HOH HOH . 
D 4 HOH A 102 402 76 HOH HOH . 
D 4 HOH A 103 403 134 HOH HOH . 
D 4 HOH A 104 404 129 HOH HOH . 
D 4 HOH A 105 405 105 HOH HOH . 
D 4 HOH A 106 406 132 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 46.461 11.225 43.162 1 8.24 ? P2 THP 201 A 1 
HETATM 2 O O4P THP . . . B 2 46.456 9.767 43.466 1 8.03 ? O4P THP 201 A 1 
HETATM 3 O O5P THP . . . B 2 45.233 11.92 43.729 1 9.15 ? O5P THP 201 A 1 
HETATM 4 O O6P THP . . . B 2 47.724 11.953 43.641 1 9.42 ? O6P THP 201 A 1 
HETATM 5 P P1 THP . . . B 2 49.711 14.743 39.339 1 9.7 ? P1 THP 201 A 1 
HETATM 6 O O1P THP . . . B 2 50.662 15.333 38.382 1 10 ? O1P THP 201 A 1 
HETATM 7 O O2P THP . . . B 2 50.366 13.606 40.107 1 11.54 ? O2P THP 201 A 1 
HETATM 8 O O3P THP . . . B 2 49.033 15.672 40.239 1 10.62 ? O3P THP 201 A 1 
HETATM 9 O O5' THP . . . B 2 46.416 11.283 41.583 1 7.88 ? O5' THP 201 A 1 
HETATM 10 C C5' THP . . . B 2 46.402 12.524 40.861 1 8.76 ? C5' THP 201 A 1 
HETATM 11 C C4' THP . . . B 2 47.405 12.493 39.714 1 8.12 ? C4' THP 201 A 1 
HETATM 12 O O4' THP . . . B 2 47.012 11.399 38.901 1 8.1 ? O4' THP 201 A 1 
HETATM 13 C C3' THP . . . B 2 47.329 13.749 38.853 1 8.51 ? C3' THP 201 A 1 
HETATM 14 O O3' THP . . . B 2 48.622 14.037 38.315 1 8.19 ? O3' THP 201 A 1 
HETATM 15 C C2' THP . . . B 2 46.5 13.294 37.695 1 7.98 ? C2' THP 201 A 1 
HETATM 16 C C1' THP . . . B 2 46.745 11.785 37.592 1 8.01 ? C1' THP 201 A 1 
HETATM 17 N N1 THP . . . B 2 45.453 11.14 37.224 1 7.49 ? N1 THP 201 A 1 
HETATM 18 C C2 THP . . . B 2 45.174 10.917 35.857 1 8.29 ? C2 THP 201 A 1 
HETATM 19 O O2 THP . . . B 2 46.054 11.24 34.985 1 8.64 ? O2 THP 201 A 1 
HETATM 20 N N3 THP . . . B 2 44.007 10.367 35.477 1 7.15 ? N3 THP 201 A 1 
HETATM 21 C C4 THP . . . B 2 43.027 10.135 36.395 1 7.34 ? C4 THP 201 A 1 
HETATM 22 O O4 THP . . . B 2 41.94 9.697 35.966 1 7.03 ? O4 THP 201 A 1 
HETATM 23 C C5 THP . . . B 2 43.279 10.338 37.829 1 7.62 ? C5 THP 201 A 1 
HETATM 24 C C5M THP . . . B 2 42.249 9.946 38.895 1 8.41 ? C5M THP 201 A 1 
HETATM 25 C C6 THP . . . B 2 44.525 10.876 38.196 1 6.54 ? C6 THP 201 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#