data_1TDC
#
_model_server_result.job_id            2s6nM0kY7_BlF6vccdAeZA 
_model_server_result.datetime_utc      '2025-08-29 07:30:35' 
_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          1tdc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":529}' 
#
_entry.id    1TDC 
#
_exptl.entry_id    1TDC 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          2 
_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            1TDC 
_cell.length_a            78.8 
_cell.length_b            78.8 
_cell.length_c            243.2 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1TDC 
_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 
_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 -121.6 
#
_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 
#
_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 356 n n 
N1 C6 UMP sing 357 n n 
N1 C1' UMP sing 358 n n 
C2 N3 UMP sing 359 n n 
C2 O2 UMP doub 360 n n 
N3 C4 UMP sing 361 n n 
N3 HN3 UMP sing 362 n n 
C4 C5 UMP sing 363 n n 
C4 O4 UMP doub 364 n n 
C5 C6 UMP doub 365 n n 
C5 H5 UMP sing 366 n n 
C6 H6 UMP sing 367 n n 
C1' C2' UMP sing 368 n n 
C1' O4' UMP sing 369 n n 
C1' H1' UMP sing 370 n n 
C2' C3' UMP sing 371 n n 
C2' H2' UMP sing 372 n n 
C2' "H2''" UMP sing 373 n n 
C3' C4' UMP sing 374 n n 
C3' O3' UMP sing 375 n n 
C3' H3' UMP sing 376 n n 
C4' O4' UMP sing 377 n n 
C4' C5' UMP sing 378 n n 
C4' H4' UMP sing 379 n n 
O3' HO3' UMP sing 380 n n 
C5' O5' UMP sing 381 n n 
C5' H5' UMP sing 382 n n 
C5' "H5''" UMP sing 383 n n 
O5' P UMP sing 384 n n 
P OP1 UMP doub 385 n n 
P OP2 UMP sing 386 n n 
P OP3 UMP sing 387 n n 
OP2 HOP2 UMP sing 388 n n 
OP3 HOP3 UMP sing 389 n n 
#
_atom_sites.entry_id                     1TDC 
_atom_sites.fract_transf_matrix[1][1]    0.01269 
_atom_sites.fract_transf_matrix[1][2]    0.007327 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014654 
_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]    0.004112 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           UMP 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      529 
_pdbx_nonpoly_scheme.auth_seq_num     529 
_pdbx_nonpoly_scheme.pdb_mon_id       UMP 
_pdbx_nonpoly_scheme.auth_mon_id      UMP 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 . . . B 2 14.821 48.495 -54.234 1 18.6 ? N1 UMP 529 A 1 
HETATM 2 C C2 UMP . . . B 2 13.781 47.717 -53.857 1 19.25 ? C2 UMP 529 A 1 
HETATM 3 N N3 UMP . . . B 2 13.529 47.606 -52.559 1 19.71 ? N3 UMP 529 A 1 
HETATM 4 C C4 UMP . . . B 2 14.248 48.208 -51.566 1 21.6 ? C4 UMP 529 A 1 
HETATM 5 C C5 UMP . . . B 2 15.316 49.018 -52.066 1 19.46 ? C5 UMP 529 A 1 
HETATM 6 C C6 UMP . . . B 2 15.548 49.132 -53.401 1 16.87 ? C6 UMP 529 A 1 
HETATM 7 O O2 UMP . . . B 2 13.1 47.058 -54.603 1 16.81 ? O2 UMP 529 A 1 
HETATM 8 O O4 UMP . . . B 2 14.053 47.978 -50.351 1 19.54 ? O4 UMP 529 A 1 
HETATM 9 C C1' UMP . . . B 2 15.398 48.616 -55.564 1 19.01 ? C1' UMP 529 A 1 
HETATM 10 C C2' UMP . . . B 2 15.116 47.958 -56.857 1 18.21 ? C2' UMP 529 A 1 
HETATM 11 C C3' UMP . . . B 2 16.389 48.175 -57.649 1 18.86 ? C3' UMP 529 A 1 
HETATM 12 C C4' UMP . . . B 2 16.805 49.543 -57.146 1 18.43 ? C4' UMP 529 A 1 
HETATM 13 O O3' UMP . . . B 2 17.361 47.244 -57.217 1 17.04 ? O3' UMP 529 A 1 
HETATM 14 O O4' UMP . . . B 2 16.45 49.574 -55.777 1 18.63 ? O4' UMP 529 A 1 
HETATM 15 C C5' UMP . . . B 2 16.106 50.701 -57.765 1 17.18 ? C5' UMP 529 A 1 
HETATM 16 O O5' UMP . . . B 2 16.65 50.808 -59.091 1 12.72 ? O5' UMP 529 A 1 
HETATM 17 P P UMP . . . B 2 15.769 51.206 -60.243 1 9.69 ? P UMP 529 A 1 
HETATM 18 O OP1 UMP . . . B 2 16.739 51.372 -61.326 1 9 ? OP1 UMP 529 A 1 
HETATM 19 O OP2 UMP . . . B 2 14.945 50.033 -60.367 1 9.91 ? OP2 UMP 529 A 1 
HETATM 20 O OP3 UMP . . . B 2 15.06 52.404 -59.711 1 8.72 ? OP3 UMP 529 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#