data_3H9K
#
_model_server_result.job_id            MMbW-4-D1q35bzmC8QlRWA 
_model_server_result.datetime_utc      '2024-11-23 21:51:11' 
_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          3h9k 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":400}' 
#
_entry.id    3H9K 
#
_exptl.entry_id    3H9K 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              326.172 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          115.18 
_cell.angle_gamma         90 
_cell.entry_id            3H9K 
_cell.length_a            200.284 
_cell.length_b            122.19 
_cell.length_c            99.828 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 3H9K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,H,I,M,N 1 1 
C,J,O 2 1,2 
D,E,K,L,P,Q 3 1 
#
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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -42.473162 0 90.341906 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 F N N 
? 2 H N N 
? 2 K N 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 371 n n 
N1 C6 UFP sing 372 n n 
N1 C1' UFP sing 373 n n 
C2 N3 UFP sing 374 n n 
C2 O2 UFP doub 375 n n 
N3 C4 UFP sing 376 n n 
N3 HN3 UFP sing 377 n n 
C4 C5 UFP sing 378 n n 
C4 O4 UFP doub 379 n n 
C5 C6 UFP doub 380 n n 
C5 F5 UFP sing 381 n n 
C6 H6 UFP sing 382 n n 
C1' C2' UFP sing 383 n n 
C1' O4' UFP sing 384 n n 
C1' H1' UFP sing 385 n n 
C2' C3' UFP sing 386 n n 
C2' "H2'1" UFP sing 387 n n 
C2' "H2'2" UFP sing 388 n n 
C3' C4' UFP sing 389 n n 
C3' O3' UFP sing 390 n n 
C3' H3' UFP sing 391 n n 
C4' O4' UFP sing 392 n n 
C4' C5' UFP sing 393 n n 
C4' H4' UFP sing 394 n n 
O3' HO3' UFP sing 395 n n 
C5' O5' UFP sing 396 n n 
C5' "H5'1" UFP sing 397 n n 
C5' "H5'2" UFP sing 398 n n 
O5' P UFP sing 399 n n 
P O1P UFP doub 400 n n 
P O2P UFP sing 401 n n 
P O3P UFP sing 402 n n 
O2P HOP2 UFP sing 403 n n 
O3P HOP3 UFP sing 404 n n 
#
_atom_sites.entry_id                     3H9K 
_atom_sites.fract_transf_matrix[1][1]    0.004993 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002347 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008184 
_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]    0.011069 
_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
F 2 UFP A 1 400 400 UFP UFP . 
G 3 EDO A 1 401 401 EDO EDO . 
H 2 UFP B 1 400 400 UFP UFP . 
I 3 EDO B 1 401 401 EDO EDO . 
J 4 PO4 C 1 365 365 PO4 PO4 . 
K 2 UFP D 1 565 565 UFP UFP . 
L 4 PO4 D 1 616 616 PO4 PO4 . 
M 5 HOH A 1 314 2 HOH HOH . 
M 5 HOH A 2 315 6 HOH HOH . 
M 5 HOH A 3 316 13 HOH HOH . 
M 5 HOH A 4 317 15 HOH HOH . 
M 5 HOH A 5 318 17 HOH HOH . 
M 5 HOH A 6 319 20 HOH HOH . 
M 5 HOH A 7 320 21 HOH HOH . 
M 5 HOH A 8 321 23 HOH HOH . 
M 5 HOH A 9 322 24 HOH HOH . 
M 5 HOH A 10 323 39 HOH HOH . 
M 5 HOH A 11 324 47 HOH HOH . 
M 5 HOH A 12 325 55 HOH HOH . 
N 5 HOH B 1 314 3 HOH HOH . 
N 5 HOH B 2 315 4 HOH HOH . 
N 5 HOH B 3 316 7 HOH HOH . 
N 5 HOH B 4 317 12 HOH HOH . 
N 5 HOH B 5 318 14 HOH HOH . 
N 5 HOH B 6 319 18 HOH HOH . 
N 5 HOH B 7 320 22 HOH HOH . 
N 5 HOH B 8 321 25 HOH HOH . 
N 5 HOH B 9 322 27 HOH HOH . 
N 5 HOH B 10 323 34 HOH HOH . 
O 5 HOH C 1 314 5 HOH HOH . 
O 5 HOH C 2 315 9 HOH HOH . 
O 5 HOH C 3 316 10 HOH HOH . 
O 5 HOH C 4 317 28 HOH HOH . 
O 5 HOH C 5 318 31 HOH HOH . 
O 5 HOH C 6 319 33 HOH HOH . 
O 5 HOH C 7 320 35 HOH HOH . 
O 5 HOH C 8 321 36 HOH HOH . 
O 5 HOH C 9 322 41 HOH HOH . 
O 5 HOH C 10 323 42 HOH HOH . 
O 5 HOH C 11 324 54 HOH HOH . 
O 5 HOH C 12 325 57 HOH HOH . 
P 5 HOH D 1 314 8 HOH HOH . 
P 5 HOH D 2 315 16 HOH HOH . 
P 5 HOH D 3 316 43 HOH HOH . 
P 5 HOH D 4 317 58 HOH HOH . 
P 5 HOH D 5 318 59 HOH HOH . 
P 5 HOH D 6 319 60 HOH HOH . 
Q 5 HOH E 1 314 1 HOH HOH . 
Q 5 HOH E 2 315 11 HOH HOH . 
Q 5 HOH E 3 316 19 HOH HOH . 
Q 5 HOH E 4 317 26 HOH HOH . 
Q 5 HOH E 5 318 29 HOH HOH . 
Q 5 HOH E 6 319 40 HOH HOH . 
Q 5 HOH E 7 320 44 HOH HOH . 
Q 5 HOH E 8 321 45 HOH HOH . 
Q 5 HOH E 9 322 48 HOH HOH . 
Q 5 HOH E 10 323 51 HOH HOH . 
Q 5 HOH E 11 324 61 HOH HOH . 
Q 5 HOH E 12 325 62 HOH HOH . 
Q 5 HOH E 13 326 63 HOH HOH . 
Q 5 HOH E 14 327 64 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 . . . F 2 25.553 -11.003 100.859 0.9 100.59 ? N1 UFP 400 A 1 
HETATM 2 C C2 UFP . . . F 2 25.887 -10.255 99.736 0.9 101.07 ? C2 UFP 400 A 1 
HETATM 3 N N3 UFP . . . F 2 26.031 -10.867 98.531 0.9 102.86 ? N3 UFP 400 A 1 
HETATM 4 C C4 UFP . . . F 2 25.871 -12.222 98.397 0.9 106.45 ? C4 UFP 400 A 1 
HETATM 5 C C5 UFP . . . F 2 25.532 -13.015 99.552 0.9 106.79 ? C5 UFP 400 A 1 
HETATM 6 C C6 UFP . . . F 2 25.387 -12.382 100.753 0.9 104.39 ? C6 UFP 400 A 1 
HETATM 7 O O2 UFP . . . F 2 26.035 -9.049 99.809 0.9 98.5 ? O2 UFP 400 A 1 
HETATM 8 O O4 UFP . . . F 2 26.002 -12.764 97.314 0.9 106.76 ? O4 UFP 400 A 1 
HETATM 9 F F5 UFP . . . F 2 25.364 -14.36 99.449 0.9 111.14 ? F5 UFP 400 A 1 
HETATM 10 C C1' UFP . . . F 2 25.37 -10.402 102.215 0.9 95.93 ? C1' UFP 400 A 1 
HETATM 11 C C2' UFP . . . F 2 26.521 -9.49 102.71 0.9 94.19 ? C2' UFP 400 A 1 
HETATM 12 C C3' UFP . . . F 2 25.786 -8.599 103.766 0.9 89.94 ? C3' UFP 400 A 1 
HETATM 13 C C4' UFP . . . F 2 24.348 -9.163 103.716 0.9 86.6 ? C4' UFP 400 A 1 
HETATM 14 O O3' UFP . . . F 2 26.354 -8.792 105.069 0.9 89.89 ? O3' UFP 400 A 1 
HETATM 15 O O4' UFP . . . F 2 24.217 -9.553 102.328 0.9 90.76 ? O4' UFP 400 A 1 
HETATM 16 C C5' UFP . . . F 2 23.298 -8.125 104.154 0.9 78.12 ? C5' UFP 400 A 1 
HETATM 17 O O5' UFP . . . F 2 21.973 -8.685 104.103 0.9 65.48 ? O5' UFP 400 A 1 
HETATM 18 P P UFP . . . F 2 20.882 -7.628 104.613 1 52.93 ? P UFP 400 A 1 
HETATM 19 O O1P UFP . . . F 2 20.909 -6.314 103.718 1 62.41 ? O1P UFP 400 A 1 
HETATM 20 O O2P UFP . . . F 2 19.426 -8.266 104.527 1 63.02 ? O2P UFP 400 A 1 
HETATM 21 O O3P UFP . . . F 2 21.195 -7.234 106.118 1 61.72 ? O3P UFP 400 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           21 
#