data_2TDD
#
_model_server_result.job_id            q-4Uxa2D-KQ8mcRzZ599eA 
_model_server_result.datetime_utc      '2025-04-25 20:27:40' 
_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          2tdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":529}' 
#
_entry.id    2TDD 
#
_exptl.entry_id    2TDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              326.172 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-FLUORO-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            2TDD 
_cell.length_a            78.4 
_cell.length_b            78.4 
_cell.length_c            242.2 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2TDD 
_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 -121.1 
#
_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 H12 F N2 O8 P' 
_chem_comp.formula_weight    326.172 
_chem_comp.id                UFP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'dna linking' 
_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 UFP sing 417 n n 
N1 C6 UFP sing 418 n n 
N1 C1' UFP sing 419 n n 
C2 N3 UFP sing 420 n n 
C2 O2 UFP doub 421 n n 
N3 C4 UFP sing 422 n n 
N3 HN3 UFP sing 423 n n 
C4 C5 UFP sing 424 n n 
C4 O4 UFP doub 425 n n 
C5 C6 UFP doub 426 n n 
C5 F5 UFP sing 427 n n 
C6 H6 UFP sing 428 n n 
C1' C2' UFP sing 429 n n 
C1' O4' UFP sing 430 n n 
C1' H1' UFP sing 431 n n 
C2' C3' UFP sing 432 n n 
C2' "H2'1" UFP sing 433 n n 
C2' "H2'2" UFP sing 434 n n 
C3' C4' UFP sing 435 n n 
C3' O3' UFP sing 436 n n 
C3' H3' UFP sing 437 n n 
C4' O4' UFP sing 438 n n 
C4' C5' UFP sing 439 n n 
C4' H4' UFP sing 440 n n 
O3' HO3' UFP sing 441 n n 
C5' O5' UFP sing 442 n n 
C5' "H5'1" UFP sing 443 n n 
C5' "H5'2" UFP sing 444 n n 
O5' P UFP sing 445 n n 
P O1P UFP doub 446 n n 
P O2P UFP sing 447 n n 
P O3P UFP sing 448 n n 
O2P HOP2 UFP sing 449 n n 
O3P HOP3 UFP sing 450 n n 
#
_atom_sites.entry_id                     2TDD 
_atom_sites.fract_transf_matrix[1][1]    0.012755 
_atom_sites.fract_transf_matrix[1][2]    0.007364 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014728 
_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]    0.004129 
_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 THF A 1 568 568 THF THF . 
C 3 UFP A 1 529 529 UFP UFP . 
D 4 HOH A 1 377 377 HOH HOH . 
D 4 HOH A 2 378 378 HOH HOH . 
D 4 HOH A 3 379 379 HOH HOH . 
D 4 HOH A 4 380 380 HOH HOH . 
D 4 HOH A 5 382 382 HOH HOH . 
D 4 HOH A 6 383 383 HOH HOH . 
D 4 HOH A 7 384 384 HOH HOH . 
D 4 HOH A 8 385 385 HOH HOH . 
D 4 HOH A 9 386 386 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 UFP . . . C 3 15.272 48.793 -53.828 1 21.66 ? N1 UFP 529 A 1 
HETATM 2 C C2 UFP . . . C 3 13.874 48.882 -53.498 1 22.65 ? C2 UFP 529 A 1 
HETATM 3 N N3 UFP . . . C 3 13.478 48.819 -52.148 1 23.75 ? N3 UFP 529 A 1 
HETATM 4 C C4 UFP . . . C 3 14.371 48.743 -51.069 1 25.38 ? C4 UFP 529 A 1 
HETATM 5 C C5 UFP . . . C 3 15.819 48.63 -51.484 1 22.87 ? C5 UFP 529 A 1 
HETATM 6 C C6 UFP . . . C 3 16.23 48.709 -52.854 1 21.41 ? C6 UFP 529 A 1 
HETATM 7 O O2 UFP . . . C 3 12.981 49.03 -54.327 1 19.67 ? O2 UFP 529 A 1 
HETATM 8 O O4 UFP . . . C 3 13.913 48.812 -49.91 1 27.33 ? O4 UFP 529 A 1 
HETATM 9 F F5 UFP . . . C 3 16.678 48.276 -50.556 1 17.02 ? F5 UFP 529 A 1 
HETATM 10 C C1' UFP . . . C 3 15.838 48.78 -55.185 1 19.42 ? C1' UFP 529 A 1 
HETATM 11 C C2' UFP . . . C 3 15.657 47.761 -56.176 1 20.8 ? C2' UFP 529 A 1 
HETATM 12 C C3' UFP . . . C 3 16.586 48.193 -57.253 1 18.82 ? C3' UFP 529 A 1 
HETATM 13 C C4' UFP . . . C 3 16.757 49.72 -56.926 1 20.36 ? C4' UFP 529 A 1 
HETATM 14 O O3' UFP . . . C 3 17.87 47.525 -57.098 1 17.38 ? O3' UFP 529 A 1 
HETATM 15 O O4' UFP . . . C 3 16.618 49.826 -55.428 1 19.02 ? O4' UFP 529 A 1 
HETATM 16 C C5' UFP . . . C 3 15.981 50.737 -57.713 1 18.24 ? C5' UFP 529 A 1 
HETATM 17 O O5' UFP . . . C 3 16.504 50.84 -59.094 1 15.3 ? O5' UFP 529 A 1 
HETATM 18 P P UFP . . . C 3 15.789 51.877 -60.201 1 12.26 ? P UFP 529 A 1 
HETATM 19 O O1P UFP . . . C 3 16.38 51.683 -61.617 1 16.43 ? O1P UFP 529 A 1 
HETATM 20 O O2P UFP . . . C 3 14.38 51.349 -60.005 1 15.5 ? O2P UFP 529 A 1 
HETATM 21 O O3P UFP . . . C 3 16.092 53.258 -59.675 1 12.04 ? O3P UFP 529 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           374 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#