data_8Y1W
#
_model_server_result.job_id            -JENOgLoJTm1tvwbQz3p7g 
_model_server_result.datetime_utc      '2024-11-30 15:52:52' 
_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          8y1w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    8Y1W 
#
_exptl.entry_id    8Y1W 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_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         120 
_cell.entry_id            8Y1W 
_cell.length_a            52.616 
_cell.length_b            52.616 
_cell.length_c            87.519 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Y1W 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    'P 6c' 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        ? 
_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,E,F 
_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 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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
N1 C2 UMP sing 362 n n 
N1 C6 UMP sing 363 n n 
N1 C1' UMP sing 364 n n 
C2 N3 UMP sing 365 n n 
C2 O2 UMP doub 366 n n 
N3 C4 UMP sing 367 n n 
N3 HN3 UMP sing 368 n n 
C4 C5 UMP sing 369 n n 
C4 O4 UMP doub 370 n n 
C5 C6 UMP doub 371 n n 
C5 H5 UMP sing 372 n n 
C6 H6 UMP sing 373 n n 
C1' C2' UMP sing 374 n n 
C1' O4' UMP sing 375 n n 
C1' H1' UMP sing 376 n n 
C2' C3' UMP sing 377 n n 
C2' H2' UMP sing 378 n n 
C2' "H2''" UMP sing 379 n n 
C3' C4' UMP sing 380 n n 
C3' O3' UMP sing 381 n n 
C3' H3' UMP sing 382 n n 
C4' O4' UMP sing 383 n n 
C4' C5' UMP sing 384 n n 
C4' H4' UMP sing 385 n n 
O3' HO3' UMP sing 386 n n 
C5' O5' UMP sing 387 n n 
C5' H5' UMP sing 388 n n 
C5' "H5''" UMP sing 389 n n 
O5' P UMP sing 390 n n 
P OP1 UMP doub 391 n n 
P OP2 UMP sing 392 n n 
P OP3 UMP sing 393 n n 
OP2 HOP2 UMP sing 394 n n 
OP3 HOP3 UMP sing 395 n n 
#
_atom_sites.entry_id                     8Y1W 
_atom_sites.fract_transf_matrix[1][1]    0.019006 
_atom_sites.fract_transf_matrix[1][2]    0.010973 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021946 
_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]    0.011426 
_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 GOL A 1 201 202 GOL GOL . 
C 3 UMP A 1 202 1 UMP DU . 
D 4 PO4 A 1 203 1 PO4 PO4 . 
E 4 PO4 A 1 204 2 PO4 PO4 . 
F 5 HOH A 1 301 25 HOH HOH . 
F 5 HOH A 2 302 58 HOH HOH . 
F 5 HOH A 3 303 83 HOH HOH . 
F 5 HOH A 4 304 32 HOH HOH . 
F 5 HOH A 5 305 57 HOH HOH . 
F 5 HOH A 6 306 67 HOH HOH . 
F 5 HOH A 7 307 87 HOH HOH . 
F 5 HOH A 8 308 47 HOH HOH . 
F 5 HOH A 9 309 59 HOH HOH . 
F 5 HOH A 10 310 41 HOH HOH . 
F 5 HOH A 11 311 91 HOH HOH . 
F 5 HOH A 12 312 65 HOH HOH . 
F 5 HOH A 13 313 29 HOH HOH . 
F 5 HOH A 14 314 86 HOH HOH . 
F 5 HOH A 15 315 88 HOH HOH . 
F 5 HOH A 16 316 72 HOH HOH . 
F 5 HOH A 17 317 28 HOH HOH . 
F 5 HOH A 18 318 99 HOH HOH . 
F 5 HOH A 19 319 19 HOH HOH . 
F 5 HOH A 20 320 22 HOH HOH . 
F 5 HOH A 21 321 42 HOH HOH . 
F 5 HOH A 22 322 33 HOH HOH . 
F 5 HOH A 23 323 11 HOH HOH . 
F 5 HOH A 24 324 36 HOH HOH . 
F 5 HOH A 25 325 4 HOH HOH . 
F 5 HOH A 26 326 23 HOH HOH . 
F 5 HOH A 27 327 95 HOH HOH . 
F 5 HOH A 28 328 5 HOH HOH . 
F 5 HOH A 29 329 17 HOH HOH . 
F 5 HOH A 30 330 79 HOH HOH . 
F 5 HOH A 31 331 55 HOH HOH . 
F 5 HOH A 32 332 89 HOH HOH . 
F 5 HOH A 33 333 24 HOH HOH . 
F 5 HOH A 34 334 35 HOH HOH . 
F 5 HOH A 35 335 66 HOH HOH . 
F 5 HOH A 36 336 8 HOH HOH . 
F 5 HOH A 37 337 7 HOH HOH . 
F 5 HOH A 38 338 81 HOH HOH . 
F 5 HOH A 39 339 2 HOH HOH . 
F 5 HOH A 40 340 37 HOH HOH . 
F 5 HOH A 41 341 20 HOH HOH . 
F 5 HOH A 42 342 50 HOH HOH . 
F 5 HOH A 43 343 85 HOH HOH . 
F 5 HOH A 44 344 64 HOH HOH . 
F 5 HOH A 45 345 31 HOH HOH . 
F 5 HOH A 46 346 54 HOH HOH . 
F 5 HOH A 47 347 78 HOH HOH . 
F 5 HOH A 48 348 48 HOH HOH . 
F 5 HOH A 49 349 16 HOH HOH . 
F 5 HOH A 50 350 102 HOH HOH . 
F 5 HOH A 51 351 53 HOH HOH . 
F 5 HOH A 52 352 82 HOH HOH . 
F 5 HOH A 53 353 63 HOH HOH . 
F 5 HOH A 54 354 56 HOH HOH . 
F 5 HOH A 55 355 21 HOH HOH . 
F 5 HOH A 56 356 90 HOH HOH . 
F 5 HOH A 57 357 27 HOH HOH . 
F 5 HOH A 58 358 93 HOH HOH . 
F 5 HOH A 59 359 98 HOH HOH . 
F 5 HOH A 60 360 100 HOH HOH . 
F 5 HOH A 61 361 101 HOH HOH . 
F 5 HOH A 62 362 77 HOH HOH . 
F 5 HOH A 63 363 69 HOH HOH . 
F 5 HOH A 64 364 3 HOH HOH . 
F 5 HOH A 65 365 14 HOH HOH . 
F 5 HOH A 66 366 40 HOH HOH . 
F 5 HOH A 67 367 6 HOH HOH . 
F 5 HOH A 68 368 80 HOH HOH . 
F 5 HOH A 69 369 39 HOH HOH . 
F 5 HOH A 70 370 76 HOH HOH . 
F 5 HOH A 71 371 1 HOH HOH . 
F 5 HOH A 72 372 51 HOH HOH . 
F 5 HOH A 73 373 49 HOH HOH . 
F 5 HOH A 74 374 10 HOH HOH . 
F 5 HOH A 75 375 92 HOH HOH . 
F 5 HOH A 76 376 9 HOH HOH . 
F 5 HOH A 77 377 18 HOH HOH . 
F 5 HOH A 78 378 30 HOH HOH . 
F 5 HOH A 79 379 34 HOH HOH . 
F 5 HOH A 80 380 26 HOH HOH . 
F 5 HOH A 81 381 84 HOH HOH . 
F 5 HOH A 82 382 70 HOH HOH . 
F 5 HOH A 83 383 45 HOH HOH . 
F 5 HOH A 84 384 52 HOH HOH . 
F 5 HOH A 85 385 60 HOH HOH . 
F 5 HOH A 86 386 15 HOH HOH . 
F 5 HOH A 87 387 12 HOH HOH . 
F 5 HOH A 88 388 73 HOH HOH . 
F 5 HOH A 89 389 94 HOH HOH . 
F 5 HOH A 90 390 62 HOH HOH . 
F 5 HOH A 91 391 44 HOH HOH . 
F 5 HOH A 92 392 97 HOH HOH . 
F 5 HOH A 93 393 38 HOH HOH . 
F 5 HOH A 94 394 13 HOH HOH . 
F 5 HOH A 95 395 75 HOH HOH . 
F 5 HOH A 96 396 61 HOH HOH . 
F 5 HOH A 97 397 46 HOH HOH . 
F 5 HOH A 98 398 74 HOH HOH . 
F 5 HOH A 99 399 96 HOH HOH . 
F 5 HOH A 100 400 68 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 N N1 UMP . . . C 3 -3.596 17.275 9.296 1 21.85 ? N1 UMP 202 A 1 
HETATM 2 C C2 UMP . . . C 3 -3.02 16.875 8.103 1 22.98 ? C2 UMP 202 A 1 
HETATM 3 N N3 UMP . . . C 3 -2.482 17.898 7.354 1 21.12 ? N3 UMP 202 A 1 
HETATM 4 C C4 UMP . . . C 3 -2.457 19.247 7.681 1 20.45 ? C4 UMP 202 A 1 
HETATM 5 C C5 UMP . . . C 3 -3.058 19.565 8.935 1 20.82 ? C5 UMP 202 A 1 
HETATM 6 C C6 UMP . . . C 3 -3.618 18.599 9.669 1 22.32 ? C6 UMP 202 A 1 
HETATM 7 O O2 UMP . . . C 3 -2.974 15.706 7.74 1 22.99 ? O2 UMP 202 A 1 
HETATM 8 O O4 UMP . . . C 3 -1.984 20.063 6.884 1 17.98 ? O4 UMP 202 A 1 
HETATM 9 C C1' UMP . . . C 3 -4.266 16.267 10.131 1 22.65 ? C1' UMP 202 A 1 
HETATM 10 C C2' UMP . . . C 3 -4.278 16.59 11.631 1 22.39 ? C2' UMP 202 A 1 
HETATM 11 C C3' UMP . . . C 3 -5.651 17.203 11.844 1 22.7 ? C3' UMP 202 A 1 
HETATM 12 C C4' UMP . . . C 3 -6.503 16.423 10.853 1 25.89 ? C4' UMP 202 A 1 
HETATM 13 O O3' UMP . . . C 3 -6.14 17.039 13.179 1 23.64 ? O3' UMP 202 A 1 
HETATM 14 O O4' UMP . . . C 3 -5.633 16.221 9.717 1 23.61 ? O4' UMP 202 A 1 
HETATM 15 C C5' UMP . . . C 3 -7.776 17.108 10.416 1 32.19 ? C5' UMP 202 A 1 
HETATM 16 O O5' UMP . . . C 3 -8.505 16.235 9.534 1 34.62 ? O5' UMP 202 A 1 
HETATM 17 P P UMP . . . C 3 -10.091 16.321 9.413 1 40.42 ? P UMP 202 A 1 
HETATM 18 O OP1 UMP . . . C 3 -10.493 15.417 8.152 1 42.68 ? OP1 UMP 202 A 1 
HETATM 19 O OP2 UMP . . . C 3 -10.737 16.012 10.846 1 44.3 ? OP2 UMP 202 A 1 
HETATM 20 O OP3 UMP . . . C 3 -10.367 17.855 9.035 1 41.96 ? OP3 UMP 202 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           375 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#