data_1BP6
#
_model_server_result.job_id            lrI9G9BdZkSqFBrfmHJQdw 
_model_server_result.datetime_utc      '2024-11-22 07:08:35' 
_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          1bp6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":318}' 
#
_entry.id    1BP6 
#
_exptl.entry_id    1BP6 
_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            1BP6 
_cell.length_a            78.5 
_cell.length_b            78.5 
_cell.length_c            243.4 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1BP6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA,PQS dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D 1 1,2 
A,B,C,D 2 1,3 
#
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' 9_654 -x+1,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 78.5 0 -81.133333 
3 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -121.7 
#
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc2 A OG SER 183 A SER 183 11_554 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? 
metalc ? metalc3 A O TRP 185 A TRP 185 1_555 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc4 A O TRP 185 A TRP 185 11_554 B K K . A K 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
#
_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                     1BP6 
_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]    0.004108 
_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 39 K POT . 
C 3 UMP A 1 318 317 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 40 HOH HOH . 
D 4 HOH A 40 358 43 HOH HOH . 
D 4 HOH A 41 359 45 HOH HOH . 
D 4 HOH A 42 360 46 HOH HOH . 
D 4 HOH A 43 361 47 HOH HOH . 
D 4 HOH A 44 362 50 HOH HOH . 
D 4 HOH A 45 363 52 HOH HOH . 
D 4 HOH A 46 364 53 HOH HOH . 
D 4 HOH A 47 365 54 HOH HOH . 
D 4 HOH A 48 366 55 HOH HOH . 
D 4 HOH A 49 367 56 HOH HOH . 
D 4 HOH A 50 368 57 HOH HOH . 
D 4 HOH A 51 369 58 HOH HOH . 
D 4 HOH A 52 370 59 HOH HOH . 
D 4 HOH A 53 371 60 HOH HOH . 
D 4 HOH A 54 372 61 HOH HOH . 
D 4 HOH A 55 373 62 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 14.245 49.035 -53.916 0.66 46.77 ? N1 UMP 318 A 1 
HETATM 2 C C2 UMP . . . C 3 13.574 47.949 -53.302 0.66 43.28 ? C2 UMP 318 A 1 
HETATM 3 N N3 UMP . . . C 3 12.903 48.211 -52.115 0.66 43.19 ? N3 UMP 318 A 1 
HETATM 4 C C4 UMP . . . C 3 12.846 49.459 -51.504 0.66 43.47 ? C4 UMP 318 A 1 
HETATM 5 C C5 UMP . . . C 3 13.532 50.53 -52.218 0.66 45.82 ? C5 UMP 318 A 1 
HETATM 6 C C6 UMP . . . C 3 14.209 50.265 -53.416 0.66 46.18 ? C6 UMP 318 A 1 
HETATM 7 O O2 UMP . . . C 3 13.48 46.811 -53.742 0.66 32.87 ? O2 UMP 318 A 1 
HETATM 8 O O4 UMP . . . C 3 12.294 49.611 -50.416 0.66 41.56 ? O4 UMP 318 A 1 
HETATM 9 C C1' UMP . . . C 3 15.278 48.869 -54.973 0.66 50.08 ? C1' UMP 318 A 1 
HETATM 10 C C2' UMP . . . C 3 14.823 48.573 -56.402 0.66 51 ? C2' UMP 318 A 1 
HETATM 11 C C3' UMP . . . C 3 16.119 48.752 -57.182 0.66 52.39 ? C3' UMP 318 A 1 
HETATM 12 C C4' UMP . . . C 3 16.726 50.07 -56.698 0.66 53.05 ? C4' UMP 318 A 1 
HETATM 13 O O3' UMP . . . C 3 17.038 47.701 -56.797 0.66 48.21 ? O3' UMP 318 A 1 
HETATM 14 O O4' UMP . . . C 3 16.241 50.015 -55.264 0.66 54.58 ? O4' UMP 318 A 1 
HETATM 15 C C5' UMP . . . C 3 16.098 51.258 -57.436 0.66 53.07 ? C5' UMP 318 A 1 
HETATM 16 O O5' UMP . . . C 3 16.554 51.306 -58.845 0.66 52.15 ? O5' UMP 318 A 1 
HETATM 17 P P UMP . . . C 3 15.753 52.143 -59.959 1 48.13 ? P UMP 318 A 1 
HETATM 18 O OP1 UMP . . . C 3 14.52 51.4 -60.182 1 58.06 ? OP1 UMP 318 A 1 
HETATM 19 O OP2 UMP . . . C 3 15.429 53.489 -59.464 1 55.36 ? OP2 UMP 318 A 1 
HETATM 20 O OP3 UMP . . . C 3 16.453 52.29 -61.277 1 53.64 ? OP3 UMP 318 A 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#