data_1BP0
#
_model_server_result.job_id            Xr85HDIUGPlYiP6C_owiKA 
_model_server_result.datetime_utc      '2025-02-05 07:49:06' 
_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          1bp0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":317}' 
#
_entry.id    1BP0 
#
_exptl.entry_id    1BP0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  syn 
_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            1BP0 
_cell.length_a            79.1 
_cell.length_b            79.1 
_cell.length_c            243.3 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BP0 
_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,PQS 
_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 -121.65 
#
_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 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? 
metalc ? metalc2 A OG SER 183 A SER 183 11_554 B K K . A K 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? 
metalc ? metalc3 A O TRP 185 A TRP 185 1_555 B K K . A K 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc4 A O TRP 185 A TRP 185 11_554 B K K . A K 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? 
#
_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 358 n n 
N1 C6 UMP sing 359 n n 
N1 C1' UMP sing 360 n n 
C2 N3 UMP sing 361 n n 
C2 O2 UMP doub 362 n n 
N3 C4 UMP sing 363 n n 
N3 HN3 UMP sing 364 n n 
C4 C5 UMP sing 365 n n 
C4 O4 UMP doub 366 n n 
C5 C6 UMP doub 367 n n 
C5 H5 UMP sing 368 n n 
C6 H6 UMP sing 369 n n 
C1' C2' UMP sing 370 n n 
C1' O4' UMP sing 371 n n 
C1' H1' UMP sing 372 n n 
C2' C3' UMP sing 373 n n 
C2' H2' UMP sing 374 n n 
C2' "H2''" UMP sing 375 n n 
C3' C4' UMP sing 376 n n 
C3' O3' UMP sing 377 n n 
C3' H3' UMP sing 378 n n 
C4' O4' UMP sing 379 n n 
C4' C5' UMP sing 380 n n 
C4' H4' UMP sing 381 n n 
O3' HO3' UMP sing 382 n n 
C5' O5' UMP sing 383 n n 
C5' H5' UMP sing 384 n n 
C5' "H5''" UMP sing 385 n n 
O5' P UMP sing 386 n n 
P OP1 UMP doub 387 n n 
P OP2 UMP sing 388 n n 
P OP3 UMP sing 389 n n 
OP2 HOP2 UMP sing 390 n n 
OP3 HOP3 UMP sing 391 n n 
#
_atom_sites.entry_id                     1BP0 
_atom_sites.fract_transf_matrix[1][1]    0.012642 
_atom_sites.fract_transf_matrix[1][2]    0.007299 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014598 
_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]    0.00411 
_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 1 318 52 K POT . 
C 3 UMP A 1 317 317 UMP DUM . 
D 4 HOH A 1 319 1 HOH HOH . 
D 4 HOH A 2 320 2 HOH HOH . 
D 4 HOH A 3 321 3 HOH HOH . 
D 4 HOH A 4 322 4 HOH HOH . 
D 4 HOH A 5 323 5 HOH HOH . 
D 4 HOH A 6 324 6 HOH HOH . 
D 4 HOH A 7 325 7 HOH HOH . 
D 4 HOH A 8 326 8 HOH HOH . 
D 4 HOH A 9 327 9 HOH HOH . 
D 4 HOH A 10 328 10 HOH HOH . 
D 4 HOH A 11 329 11 HOH HOH . 
D 4 HOH A 12 330 12 HOH HOH . 
D 4 HOH A 13 331 13 HOH HOH . 
D 4 HOH A 14 332 14 HOH HOH . 
D 4 HOH A 15 333 15 HOH HOH . 
D 4 HOH A 16 334 16 HOH HOH . 
D 4 HOH A 17 335 17 HOH HOH . 
D 4 HOH A 18 336 18 HOH HOH . 
D 4 HOH A 19 337 19 HOH HOH . 
D 4 HOH A 20 338 20 HOH HOH . 
D 4 HOH A 21 339 21 HOH HOH . 
D 4 HOH A 22 340 22 HOH HOH . 
D 4 HOH A 23 341 23 HOH HOH . 
D 4 HOH A 24 342 24 HOH HOH . 
D 4 HOH A 25 343 25 HOH HOH . 
D 4 HOH A 26 344 26 HOH HOH . 
D 4 HOH A 27 345 27 HOH HOH . 
D 4 HOH A 28 346 28 HOH HOH . 
D 4 HOH A 29 347 29 HOH HOH . 
D 4 HOH A 30 348 30 HOH HOH . 
D 4 HOH A 31 349 31 HOH HOH . 
D 4 HOH A 32 350 32 HOH HOH . 
D 4 HOH A 33 351 33 HOH HOH . 
D 4 HOH A 34 352 34 HOH HOH . 
D 4 HOH A 35 353 35 HOH HOH . 
D 4 HOH A 36 354 36 HOH HOH . 
D 4 HOH A 37 355 37 HOH HOH . 
D 4 HOH A 38 356 38 HOH HOH . 
D 4 HOH A 39 357 39 HOH HOH . 
D 4 HOH A 40 358 40 HOH HOH . 
D 4 HOH A 41 359 41 HOH HOH . 
D 4 HOH A 42 360 42 HOH HOH . 
D 4 HOH A 43 361 43 HOH HOH . 
D 4 HOH A 44 362 44 HOH HOH . 
D 4 HOH A 45 363 45 HOH HOH . 
D 4 HOH A 46 364 46 HOH HOH . 
D 4 HOH A 47 365 47 HOH HOH . 
D 4 HOH A 48 366 48 HOH HOH . 
D 4 HOH A 49 367 49 HOH HOH . 
D 4 HOH A 50 368 50 HOH HOH . 
D 4 HOH A 51 369 51 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 14.632 49.369 -54.067 0.6 22.58 ? N1 UMP 317 A 1 
HETATM 2 C C2 UMP . . . C 3 13.759 48.36 -53.613 0.6 23.53 ? C2 UMP 317 A 1 
HETATM 3 N N3 UMP . . . C 3 12.908 48.772 -52.601 0.6 27.38 ? N3 UMP 317 A 1 
HETATM 4 C C4 UMP . . . C 3 12.872 50.053 -52.034 0.6 29.21 ? C4 UMP 317 A 1 
HETATM 5 C C5 UMP . . . C 3 13.818 51.008 -52.578 0.6 30.52 ? C5 UMP 317 A 1 
HETATM 6 C C6 UMP . . . C 3 14.671 50.596 -53.594 0.6 26.9 ? C6 UMP 317 A 1 
HETATM 7 O O2 UMP . . . C 3 13.683 47.193 -54.004 0.6 16.83 ? O2 UMP 317 A 1 
HETATM 8 O O4 UMP . . . C 3 12.082 50.312 -51.131 0.6 30.1 ? O4 UMP 317 A 1 
HETATM 9 C C1' UMP . . . C 3 15.586 49.178 -55.15 0.6 25.34 ? C1' UMP 317 A 1 
HETATM 10 C C2' UMP . . . C 3 14.998 48.878 -56.528 0.6 24.35 ? C2' UMP 317 A 1 
HETATM 11 C C3' UMP . . . C 3 16.231 49.011 -57.408 0.6 26.03 ? C3' UMP 317 A 1 
HETATM 12 C C4' UMP . . . C 3 16.93 50.302 -56.963 0.6 27.54 ? C4' UMP 317 A 1 
HETATM 13 O O3' UMP . . . C 3 17.086 47.897 -57.073 0.6 21.87 ? O3' UMP 317 A 1 
HETATM 14 O O4' UMP . . . C 3 16.522 50.302 -55.503 0.6 27.2 ? O4' UMP 317 A 1 
HETATM 15 C C5' UMP . . . C 3 16.333 51.521 -57.679 0.6 24.92 ? C5' UMP 317 A 1 
HETATM 16 O O5' UMP . . . C 3 16.783 51.582 -59.09 0.6 21.27 ? O5' UMP 317 A 1 
HETATM 17 P P UMP . . . C 3 15.834 52.212 -60.167 1 21.52 ? P UMP 317 A 1 
HETATM 18 O OP1 UMP . . . C 3 14.785 51.209 -60.29 1 33.36 ? OP1 UMP 317 A 1 
HETATM 19 O OP2 UMP . . . C 3 15.274 53.49 -59.674 1 22.67 ? OP2 UMP 317 A 1 
HETATM 20 O OP3 UMP . . . C 3 16.37 52.467 -61.51 1 20 ? OP3 UMP 317 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#