data_3BFI
#
_model_server_result.job_id            sa9a5cqXsoswgUzRxUAhcw 
_model_server_result.datetime_utc      '2024-10-11 13:27:25' 
_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          3bfi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":266}' 
#
_entry.id    3BFI 
#
_exptl.entry_id    3BFI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              355.195 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXY-5-NITROURIDINE 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         90 
_cell.entry_id            3BFI 
_cell.length_a            133.02 
_cell.length_b            133.02 
_cell.length_c            133.02 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BFI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_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' 16_555 x,-y,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 0 66.51 
#
_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 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            C 
_struct_conn.ptnr1_label_comp_id            CXM 
_struct_conn.ptnr1_label_seq_id             1 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             CXM 
_struct_conn.ptnr1_auth_seq_id              1 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            A 
_struct_conn.ptnr2_label_atom_id            N 
_struct_conn.ptnr2_label_comp_id            LYS 
_struct_conn.ptnr2_label_seq_id             2 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             LYS 
_struct_conn.ptnr2_auth_seq_id              2 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.306 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C9 H14 N3 O10 P' 
_chem_comp.formula_weight    355.195 
_chem_comp.id                NDU 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "2'-DEOXY-5-NITROURIDINE 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
P OP1 NDU doub 259 n n 
P OP2 NDU sing 260 n n 
P OP3 NDU sing 261 n n 
P O5' NDU sing 262 n n 
O5' C5' NDU sing 263 n n 
C5' C4' NDU sing 264 n n 
C4' C3' NDU sing 265 n n 
C4' O4' NDU sing 266 n n 
C3' O3' NDU sing 267 n n 
C3' C2' NDU sing 268 n n 
C2' C1' NDU sing 269 n n 
C1' O4' NDU sing 270 n n 
C1' N1 NDU sing 271 n n 
N1 C2 NDU sing 272 n n 
N1 C6 NDU sing 273 n n 
C2 O2 NDU doub 274 n n 
C2 N3 NDU sing 275 n n 
N3 C4 NDU sing 276 n n 
C4 O4 NDU doub 277 n n 
C4 C5 NDU sing 278 n n 
C5 C6 NDU sing 279 n n 
C5 N5 NDU sing 280 n n 
N5 O51 NDU sing 281 n n 
N5 O52 NDU doub 282 n n 
OP2 HP2 NDU sing 283 n n 
OP3 HP3 NDU sing 284 n n 
C5' H51' NDU sing 285 n n 
C5' H52' NDU sing 286 n n 
C4' H4' NDU sing 287 n n 
C3' H3' NDU sing 288 n n 
O3' HA NDU sing 289 n n 
C2' H21' NDU sing 290 n n 
C2' H22' NDU sing 291 n n 
C1' H1' NDU sing 292 n n 
C6 H611 NDU sing 293 n n 
C6 H612 NDU sing 294 n n 
N3 H3 NDU sing 295 n n 
C5 H5 NDU sing 296 n n 
#
_atom_sites.entry_id                     3BFI 
_atom_sites.fract_transf_matrix[1][1]    0.007518 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007518 
_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]    0.007518 
_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 SO4 A 1 265 1 SO4 SO4 . 
C 3 NDU A 1 266 265 NDU NDU . 
D 4 HOH A 1 301 301 HOH HOH . 
D 4 HOH A 2 302 302 HOH HOH . 
D 4 HOH A 3 303 303 HOH HOH . 
D 4 HOH A 4 304 304 HOH HOH . 
D 4 HOH A 5 305 305 HOH HOH . 
D 4 HOH A 6 306 306 HOH HOH . 
D 4 HOH A 7 307 307 HOH HOH . 
D 4 HOH A 8 308 308 HOH HOH . 
D 4 HOH A 9 309 309 HOH HOH . 
D 4 HOH A 10 310 310 HOH HOH . 
D 4 HOH A 11 311 311 HOH HOH . 
D 4 HOH A 12 312 312 HOH HOH . 
D 4 HOH A 13 313 313 HOH HOH . 
D 4 HOH A 14 314 314 HOH HOH . 
D 4 HOH A 15 315 315 HOH HOH . 
D 4 HOH A 16 316 316 HOH HOH . 
D 4 HOH A 17 317 317 HOH HOH . 
D 4 HOH A 18 318 318 HOH HOH . 
D 4 HOH A 19 319 319 HOH HOH . 
D 4 HOH A 20 320 320 HOH HOH . 
D 4 HOH A 21 321 321 HOH HOH . 
D 4 HOH A 22 322 322 HOH HOH . 
D 4 HOH A 23 323 323 HOH HOH . 
D 4 HOH A 24 324 324 HOH HOH . 
D 4 HOH A 25 325 325 HOH HOH . 
D 4 HOH A 26 326 326 HOH HOH . 
D 4 HOH A 27 327 327 HOH HOH . 
D 4 HOH A 28 328 328 HOH HOH . 
D 4 HOH A 29 329 329 HOH HOH . 
D 4 HOH A 30 330 330 HOH HOH . 
D 4 HOH A 31 331 331 HOH HOH . 
D 4 HOH A 32 332 332 HOH HOH . 
D 4 HOH A 33 333 333 HOH HOH . 
D 4 HOH A 34 334 334 HOH HOH . 
D 4 HOH A 35 335 335 HOH HOH . 
D 4 HOH A 36 336 336 HOH HOH . 
D 4 HOH A 37 337 337 HOH HOH . 
D 4 HOH A 38 338 338 HOH HOH . 
D 4 HOH A 39 339 339 HOH HOH . 
D 4 HOH A 40 340 340 HOH HOH . 
D 4 HOH A 41 341 341 HOH HOH . 
D 4 HOH A 42 342 342 HOH HOH . 
D 4 HOH A 43 343 343 HOH HOH . 
D 4 HOH A 44 344 344 HOH HOH . 
D 4 HOH A 45 345 345 HOH HOH . 
D 4 HOH A 46 346 346 HOH HOH . 
D 4 HOH A 47 347 347 HOH HOH . 
D 4 HOH A 48 348 348 HOH HOH . 
D 4 HOH A 49 349 349 HOH HOH . 
D 4 HOH A 50 350 350 HOH HOH . 
D 4 HOH A 51 351 351 HOH HOH . 
D 4 HOH A 52 352 352 HOH HOH . 
D 4 HOH A 53 353 353 HOH HOH . 
D 4 HOH A 54 354 354 HOH HOH . 
D 4 HOH A 55 355 355 HOH HOH . 
D 4 HOH A 56 356 356 HOH HOH . 
D 4 HOH A 57 357 357 HOH HOH . 
D 4 HOH A 58 358 358 HOH HOH . 
D 4 HOH A 59 359 359 HOH HOH . 
D 4 HOH A 60 360 360 HOH HOH . 
D 4 HOH A 61 361 361 HOH HOH . 
D 4 HOH A 62 362 362 HOH HOH . 
D 4 HOH A 63 363 363 HOH HOH . 
D 4 HOH A 64 364 364 HOH HOH . 
D 4 HOH A 65 365 365 HOH HOH . 
D 4 HOH A 66 366 366 HOH HOH . 
D 4 HOH A 67 367 367 HOH HOH . 
D 4 HOH A 68 368 368 HOH HOH . 
D 4 HOH A 69 369 369 HOH HOH . 
D 4 HOH A 70 370 370 HOH HOH . 
D 4 HOH A 71 371 371 HOH HOH . 
D 4 HOH A 72 372 372 HOH HOH . 
D 4 HOH A 73 373 373 HOH HOH . 
D 4 HOH A 74 374 374 HOH HOH . 
D 4 HOH A 75 375 375 HOH HOH . 
D 4 HOH A 76 376 376 HOH HOH . 
D 4 HOH A 77 377 377 HOH HOH . 
D 4 HOH A 78 378 378 HOH HOH . 
D 4 HOH A 79 379 379 HOH HOH . 
D 4 HOH A 80 380 380 HOH HOH . 
D 4 HOH A 81 381 381 HOH HOH . 
D 4 HOH A 82 382 382 HOH HOH . 
D 4 HOH A 83 383 383 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 P P NDU . . . C 3 -31.589 -13.12 24.471 1 24.11 ? P NDU 266 A 1 
HETATM 2 O OP1 NDU . . . C 3 -31.606 -14.556 24.869 1 26.54 ? OP1 NDU 266 A 1 
HETATM 3 O OP2 NDU . . . C 3 -30.527 -12.34 25.222 1 21.57 ? OP2 NDU 266 A 1 
HETATM 4 O OP3 NDU . . . C 3 -32.883 -12.429 24.466 1 23.61 ? OP3 NDU 266 A 1 
HETATM 5 O O5' NDU . . . C 3 -31.151 -13.138 22.915 1 22.6 ? O5' NDU 266 A 1 
HETATM 6 C C5' NDU . . . C 3 -30.928 -11.933 22.18 1 21.86 ? C5' NDU 266 A 1 
HETATM 7 C C4' NDU . . . C 3 -29.642 -12.122 21.376 1 24.09 ? C4' NDU 266 A 1 
HETATM 8 C C3' NDU . . . C 3 -28.326 -12.033 22.166 1 22.86 ? C3' NDU 266 A 1 
HETATM 9 O O3' NDU . . . C 3 -27.274 -12.728 21.464 1 23.43 ? O3' NDU 266 A 1 
HETATM 10 C C2' NDU . . . C 3 -28.008 -10.538 22.205 1 21.55 ? C2' NDU 266 A 1 
HETATM 11 C C1' NDU . . . C 3 -28.463 -10.168 20.824 1 22.55 ? C1' NDU 266 A 1 
HETATM 12 O O4' NDU . . . C 3 -29.546 -11.047 20.463 1 22.56 ? O4' NDU 266 A 1 
HETATM 13 N N1 NDU . . . C 3 -28.874 -8.793 20.515 1 23.33 ? N1 NDU 266 A 1 
HETATM 14 C C2 NDU . . . C 3 -27.913 -7.781 20.396 1 21.73 ? C2 NDU 266 A 1 
HETATM 15 O O2 NDU . . . C 3 -26.719 -7.99 20.656 1 22.17 ? O2 NDU 266 A 1 
HETATM 16 N N3 NDU . . . C 3 -28.314 -6.582 20.007 1 23.1 ? N3 NDU 266 A 1 
HETATM 17 C C4 NDU . . . C 3 -29.574 -6.301 19.644 1 23.85 ? C4 NDU 266 A 1 
HETATM 18 O O4 NDU . . . C 3 -29.888 -5.144 19.261 1 24.02 ? O4 NDU 266 A 1 
HETATM 19 C C5 NDU . . . C 3 -30.578 -7.394 19.742 1 25.98 ? C5 NDU 266 A 1 
HETATM 20 C C6 NDU . . . C 3 -30.193 -8.449 20.614 1 23.01 ? C6 NDU 266 A 1 
HETATM 21 N N5 NDU . . . C 3 -31.942 -7.191 19.386 1 25.68 ? N5 NDU 266 A 1 
HETATM 22 O O51 NDU . . . C 3 -32.372 -6.145 18.904 1 28.08 ? O51 NDU 266 A 1 
HETATM 23 O O52 NDU . . . C 3 -32.833 -8.224 19.611 1 29.73 ? O52 NDU 266 A 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           23 
#