data_1BO8
#
_model_server_result.job_id            X0fBlb9kh11Gc3zI4ZeLUQ 
_model_server_result.datetime_utc      '2024-12-26 15:25:50' 
_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          1bo8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":318}' 
#
_entry.id    1BO8 
#
_exptl.entry_id    1BO8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-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            1BO8 
_cell.length_a            78.5 
_cell.length_b            78.5 
_cell.length_c            241.7 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BO8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -120.85 
#
_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 OG SER 183 A SER 183 1_555 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? 
metalc ? metalc2 A O TRP 185 A TRP 185 1_555 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_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
N1 C2 U5P sing 358 n n 
N1 C6 U5P sing 359 n n 
N1 C1' U5P sing 360 n n 
C2 N3 U5P sing 361 n n 
C2 O2 U5P doub 362 n n 
N3 C4 U5P sing 363 n n 
N3 HN3 U5P sing 364 n n 
C4 C5 U5P sing 365 n n 
C4 O4 U5P doub 366 n n 
C5 C6 U5P doub 367 n n 
C5 H5 U5P sing 368 n n 
C6 H6 U5P sing 369 n n 
C1' C2' U5P sing 370 n n 
C1' O4' U5P sing 371 n n 
C1' H1' U5P sing 372 n n 
C2' O2' U5P sing 373 n n 
C2' C3' U5P sing 374 n n 
C2' H2' U5P sing 375 n n 
O2' HO2' U5P sing 376 n n 
C3' C4' U5P sing 377 n n 
C3' O3' U5P sing 378 n n 
C3' H3' U5P sing 379 n n 
C4' O4' U5P sing 380 n n 
C4' C5' U5P sing 381 n n 
C4' H4' U5P sing 382 n n 
O3' HO3' U5P sing 383 n n 
C5' O5' U5P sing 384 n n 
C5' "H5'1" U5P sing 385 n n 
C5' "H5'2" U5P sing 386 n n 
O5' P U5P sing 387 n n 
P O1P U5P doub 388 n n 
P O2P U5P sing 389 n n 
P O3P U5P sing 390 n n 
O2P HOP2 U5P sing 391 n n 
O3P HOP3 U5P sing 392 n n 
#
_atom_sites.entry_id                     1BO8 
_atom_sites.fract_transf_matrix[1][1]    0.012739 
_atom_sites.fract_transf_matrix[1][2]    0.007355 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014709 
_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]    0.004137 
_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 K A 1 317 1 K POT . 
C 3 U5P A 1 318 317 U5P DUM . 
D 4 HOH A 1 319 2 HOH HOH . 
D 4 HOH A 2 320 3 HOH HOH . 
D 4 HOH A 3 321 4 HOH HOH . 
D 4 HOH A 4 322 5 HOH HOH . 
D 4 HOH A 5 323 6 HOH HOH . 
D 4 HOH A 6 324 7 HOH HOH . 
D 4 HOH A 7 325 8 HOH HOH . 
D 4 HOH A 8 326 9 HOH HOH . 
D 4 HOH A 9 327 10 HOH HOH . 
D 4 HOH A 10 328 11 HOH HOH . 
D 4 HOH A 11 329 12 HOH HOH . 
D 4 HOH A 12 330 13 HOH HOH . 
D 4 HOH A 13 331 14 HOH HOH . 
D 4 HOH A 14 332 15 HOH HOH . 
D 4 HOH A 15 333 16 HOH HOH . 
D 4 HOH A 16 334 17 HOH HOH . 
D 4 HOH A 17 335 18 HOH HOH . 
D 4 HOH A 18 336 19 HOH HOH . 
D 4 HOH A 19 337 20 HOH HOH . 
D 4 HOH A 20 338 21 HOH HOH . 
D 4 HOH A 21 339 22 HOH HOH . 
D 4 HOH A 22 340 23 HOH HOH . 
D 4 HOH A 23 341 24 HOH HOH . 
D 4 HOH A 24 342 25 HOH HOH . 
D 4 HOH A 25 343 26 HOH HOH . 
D 4 HOH A 26 344 27 HOH HOH . 
D 4 HOH A 27 345 28 HOH HOH . 
D 4 HOH A 28 346 29 HOH HOH . 
D 4 HOH A 29 347 30 HOH HOH . 
D 4 HOH A 30 348 31 HOH HOH . 
D 4 HOH A 31 349 32 HOH HOH . 
D 4 HOH A 32 350 33 HOH HOH . 
D 4 HOH A 33 351 34 HOH HOH . 
D 4 HOH A 34 352 35 HOH HOH . 
D 4 HOH A 35 353 36 HOH HOH . 
D 4 HOH A 36 354 37 HOH HOH . 
D 4 HOH A 37 355 38 HOH HOH . 
D 4 HOH A 38 356 39 HOH HOH . 
D 4 HOH A 39 357 40 HOH HOH . 
D 4 HOH A 40 358 41 HOH HOH . 
D 4 HOH A 41 359 42 HOH HOH . 
D 4 HOH A 42 360 43 HOH HOH . 
D 4 HOH A 43 361 44 HOH HOH . 
D 4 HOH A 44 362 45 HOH HOH . 
D 4 HOH A 45 363 46 HOH HOH . 
D 4 HOH A 46 364 47 HOH HOH . 
D 4 HOH A 47 365 48 HOH HOH . 
D 4 HOH A 48 366 49 HOH HOH . 
D 4 HOH A 49 367 50 HOH HOH . 
D 4 HOH A 50 368 51 HOH HOH . 
D 4 HOH A 51 369 52 HOH HOH . 
D 4 HOH A 52 370 53 HOH HOH . 
D 4 HOH A 53 371 54 HOH HOH . 
D 4 HOH A 54 372 55 HOH HOH . 
D 4 HOH A 55 373 56 HOH HOH . 
D 4 HOH A 56 374 57 HOH HOH . 
D 4 HOH A 57 375 58 HOH HOH . 
D 4 HOH A 58 376 59 HOH HOH . 
D 4 HOH A 59 377 60 HOH HOH . 
D 4 HOH A 60 378 61 HOH HOH . 
D 4 HOH A 61 379 62 HOH HOH . 
D 4 HOH A 62 380 63 HOH HOH . 
D 4 HOH A 63 381 64 HOH HOH . 
D 4 HOH A 64 382 65 HOH HOH . 
D 4 HOH A 65 383 66 HOH HOH . 
D 4 HOH A 66 384 67 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 U5P . . . C 3 14.523 48.596 -53.502 0.64 46.54 ? N1 U5P 318 A 1 
HETATM 2 C C2 U5P . . . C 3 13.827 47.486 -52.984 0.64 45.05 ? C2 U5P 318 A 1 
HETATM 3 N N3 U5P . . . C 3 13.204 47.719 -51.769 0.64 51.8 ? N3 U5P 318 A 1 
HETATM 4 C C4 U5P . . . C 3 13.229 48.916 -51.044 0.64 51.17 ? C4 U5P 318 A 1 
HETATM 5 C C5 U5P . . . C 3 13.949 50.002 -51.666 0.64 52.43 ? C5 U5P 318 A 1 
HETATM 6 C C6 U5P . . . C 3 14.566 49.763 -52.893 0.64 51.65 ? C6 U5P 318 A 1 
HETATM 7 O O2 U5P . . . C 3 13.708 46.353 -53.437 0.64 32.7 ? O2 U5P 318 A 1 
HETATM 8 O O4 U5P . . . C 3 12.727 48.985 -49.926 0.64 47.94 ? O4 U5P 318 A 1 
HETATM 9 C C1' U5P . . . C 3 15.428 48.58 -54.643 0.64 46.84 ? C1' U5P 318 A 1 
HETATM 10 C C2' U5P . . . C 3 14.836 48.495 -56.044 0.64 45.1 ? C2' U5P 318 A 1 
HETATM 11 C C3' U5P . . . C 3 16.099 48.703 -56.871 0.64 48.49 ? C3' U5P 318 A 1 
HETATM 12 C C4' U5P . . . C 3 16.802 49.923 -56.255 0.64 48.65 ? C4' U5P 318 A 1 
HETATM 13 O O3' U5P . . . C 3 16.956 47.51 -56.761 0.64 37.12 ? O3' U5P 318 A 1 
HETATM 14 O O4' U5P . . . C 3 16.356 49.752 -54.843 0.64 46.77 ? O4' U5P 318 A 1 
HETATM 15 C C5' U5P . . . C 3 16.185 51.231 -56.755 0.64 53.82 ? C5' U5P 318 A 1 
HETATM 16 O O5' U5P . . . C 3 16.596 51.643 -58.148 0.64 59.56 ? O5' U5P 318 A 1 
HETATM 17 P P U5P . . . C 3 15.846 51.38 -59.574 1 56.1 ? P U5P 318 A 1 
HETATM 18 O O1P U5P . . . C 3 16.356 50.11 -60.194 1 54.35 ? O1P U5P 318 A 1 
HETATM 19 O O2P U5P . . . C 3 14.439 51.29 -59.175 1 63.35 ? O2P U5P 318 A 1 
HETATM 20 O O3P U5P . . . C 3 15.963 52.471 -60.535 1 54.13 ? O3P U5P 318 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           20 
#