data_8KBE
#
_model_server_result.job_id            eI658-yaek0OhFXmjHBoFg 
_model_server_result.datetime_utc      '2024-11-14 19:53:37' 
_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          8kbe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    8KBE 
#
_exptl.entry_id    8KBE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              541.3 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione 
_entity.pdbx_number_of_molecules    2 
_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            8KBE 
_cell.length_a            101.09 
_cell.length_b            101.09 
_cell.length_c            101.09 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8KBE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C15 H21 N5 O13 P2' 
_chem_comp.formula_weight    541.3 
_chem_comp.id                OJC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3R,3aS,5S,6R,7S,8R,11R,13S,15aR)-2-(6-amino-9H-purin-9-yl)-3,6,7,11,13-pentahydroxyoctahydro-2H,5H,11H,13H-5,8-epoxy-11lambda~5~,13lambda~5~-furo[2,3-g][1,3,5,9,2,4]tetraoxadiphosphacyclotetradecine-11,13-dione 
_chem_comp.type              non-polymer 
_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
N4 C1 OJC sing 237 n n 
C1 N OJC doub 238 n y 
C1 C2 OJC sing 239 n y 
N C OJC sing 240 n y 
C2 N3 OJC sing 241 n y 
C2 C3 OJC doub 242 n y 
C N1 OJC doub 243 n y 
N3 C4 OJC doub 244 n y 
C3 N1 OJC sing 245 n y 
C3 N2 OJC sing 246 n y 
C4 N2 OJC sing 247 n y 
N2 C5 OJC sing 248 n n 
O12 C6 OJC sing 249 n n 
C5 C6 OJC sing 250 n n 
C5 O OJC sing 251 n n 
C6 C7 OJC sing 252 n n 
O C8 OJC sing 253 n n 
O6 P1 OJC sing 254 n n 
C7 O9 OJC sing 255 n n 
C7 C8 OJC sing 256 n n 
O9 C14 OJC sing 257 n n 
C8 C9 OJC sing 258 n n 
O4 P1 OJC sing 259 n n 
O4 P OJC sing 260 n n 
O1 C9 OJC sing 261 n n 
O1 P OJC sing 262 n n 
P1 O7 OJC sing 263 n n 
P1 O5 OJC doub 264 n n 
C10 O7 OJC sing 265 n n 
C10 C11 OJC sing 266 n n 
C12 C13 OJC sing 267 n n 
C12 O11 OJC sing 268 n n 
C12 C11 OJC sing 269 n n 
O3 P OJC sing 270 n n 
C13 C14 OJC sing 271 n n 
C13 O10 OJC sing 272 n n 
C14 O8 OJC sing 273 n n 
P O2 OJC doub 274 n n 
C11 O8 OJC sing 275 n n 
C H8 OJC sing 276 n n 
C10 H14 OJC sing 277 n n 
C10 H15 OJC sing 278 n n 
C11 H4 OJC sing 279 n n 
C12 H5 OJC sing 280 n n 
C13 H6 OJC sing 281 n n 
C14 H7 OJC sing 282 n n 
C4 H9 OJC sing 283 n n 
C5 H OJC sing 284 n n 
C6 H1 OJC sing 285 n n 
C7 H2 OJC sing 286 n n 
C8 H3 OJC sing 287 n n 
C9 H10 OJC sing 288 n n 
C9 H11 OJC sing 289 n n 
N4 H20 OJC sing 290 n n 
N4 H19 OJC sing 291 n n 
O10 H16 OJC sing 292 n n 
O11 H17 OJC sing 293 n n 
O12 H18 OJC sing 294 n n 
O3 H12 OJC sing 295 n n 
O6 H13 OJC sing 296 n n 
#
_atom_sites.entry_id                     8KBE 
_atom_sites.fract_transf_matrix[1][1]    0.009892 
_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]    0.009892 
_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]    0.009892 
_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
C 2 OJC A 1 201 201 OJC 13C . 
D 2 OJC B 1 201 201 OJC 13C . 
E 3 HOH A 1 301 36 HOH HOH . 
E 3 HOH A 2 302 7 HOH HOH . 
E 3 HOH A 3 303 20 HOH HOH . 
E 3 HOH A 4 304 19 HOH HOH . 
E 3 HOH A 5 305 2 HOH HOH . 
E 3 HOH A 6 306 33 HOH HOH . 
E 3 HOH A 7 307 8 HOH HOH . 
E 3 HOH A 8 308 14 HOH HOH . 
E 3 HOH A 9 309 25 HOH HOH . 
E 3 HOH A 10 310 6 HOH HOH . 
E 3 HOH A 11 311 42 HOH HOH . 
E 3 HOH A 12 312 13 HOH HOH . 
E 3 HOH A 13 313 32 HOH HOH . 
E 3 HOH A 14 314 15 HOH HOH . 
E 3 HOH A 15 315 35 HOH HOH . 
E 3 HOH A 16 316 41 HOH HOH . 
E 3 HOH A 17 317 17 HOH HOH . 
E 3 HOH A 18 318 38 HOH HOH . 
E 3 HOH A 19 319 5 HOH HOH . 
E 3 HOH A 20 320 44 HOH HOH . 
E 3 HOH A 21 321 27 HOH HOH . 
E 3 HOH A 22 322 31 HOH HOH . 
F 3 HOH B 1 301 37 HOH HOH . 
F 3 HOH B 2 302 21 HOH HOH . 
F 3 HOH B 3 303 4 HOH HOH . 
F 3 HOH B 4 304 24 HOH HOH . 
F 3 HOH B 5 305 28 HOH HOH . 
F 3 HOH B 6 306 9 HOH HOH . 
F 3 HOH B 7 307 29 HOH HOH . 
F 3 HOH B 8 308 22 HOH HOH . 
F 3 HOH B 9 309 1 HOH HOH . 
F 3 HOH B 10 310 18 HOH HOH . 
F 3 HOH B 11 311 3 HOH HOH . 
F 3 HOH B 12 312 26 HOH HOH . 
F 3 HOH B 13 313 16 HOH HOH . 
F 3 HOH B 14 314 23 HOH HOH . 
F 3 HOH B 15 315 10 HOH HOH . 
F 3 HOH B 16 316 11 HOH HOH . 
F 3 HOH B 17 317 30 HOH HOH . 
F 3 HOH B 18 318 40 HOH HOH . 
F 3 HOH B 19 319 45 HOH HOH . 
F 3 HOH B 20 320 12 HOH HOH . 
F 3 HOH B 21 321 39 HOH HOH . 
F 3 HOH B 22 322 34 HOH HOH . 
F 3 HOH B 23 323 43 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 N OJC . . . D 2 27.652 -0.287 -22.921 1 48.37 ? N OJC 201 B 1 
HETATM 2 C C OJC . . . D 2 27.669 -1.63 -22.945 1 46.2 ? C OJC 201 B 1 
HETATM 3 O O OJC . . . D 2 31.541 -4.11 -21.354 1 53.38 ? O OJC 201 B 1 
HETATM 4 C C1 OJC . . . D 2 28.532 0.352 -22.103 1 49.3 ? C1 OJC 201 B 1 
HETATM 5 C C2 OJC . . . D 2 29.388 -0.435 -21.339 1 51.14 ? C2 OJC 201 B 1 
HETATM 6 C C3 OJC . . . D 2 29.297 -1.81 -21.457 1 51.53 ? C3 OJC 201 B 1 
HETATM 7 C C10 OJC . . . D 2 26.926 -5.283 -25.05 1 51.76 ? C10 OJC 201 B 1 
HETATM 8 C C11 OJC . . . D 2 26.614 -6.147 -23.858 1 50.3 ? C11 OJC 201 B 1 
HETATM 9 C C12 OJC . . . D 2 26.276 -5.386 -22.576 1 53.99 ? C12 OJC 201 B 1 
HETATM 10 C C13 OJC . . . D 2 26.838 -6.293 -21.476 1 50.43 ? C13 OJC 201 B 1 
HETATM 11 C C14 OJC . . . D 2 27.909 -7.127 -22.172 1 49.46 ? C14 OJC 201 B 1 
HETATM 12 C C4 OJC . . . D 2 30.856 -1.258 -20.024 1 47.31 ? C4 OJC 201 B 1 
HETATM 13 C C5 OJC . . . D 2 30.612 -3.717 -20.327 1 56.34 ? C5 OJC 201 B 1 
HETATM 14 C C6 OJC . . . D 2 29.552 -4.811 -20.263 1 48.04 ? C6 OJC 201 B 1 
HETATM 15 C C7 OJC . . . D 2 29.634 -5.421 -21.666 1 49.28 ? C7 OJC 201 B 1 
HETATM 16 C C8 OJC . . . D 2 31.138 -5.362 -21.921 1 55.41 ? C8 OJC 201 B 1 
HETATM 17 C C9 OJC . . . D 2 31.513 -5.378 -23.393 1 54.98 ? C9 OJC 201 B 1 
HETATM 18 N N1 OJC . . . D 2 28.44 -2.47 -22.273 1 48.25 ? N1 OJC 201 B 1 
HETATM 19 N N2 OJC . . . D 2 30.245 -2.335 -20.628 1 51.32 ? N2 OJC 201 B 1 
HETATM 20 N N3 OJC . . . D 2 30.387 -0.105 -20.413 1 55.13 ? N3 OJC 201 B 1 
HETATM 21 N N4 OJC . . . D 2 28.525 1.689 -22.079 1 49.77 ? N4 OJC 201 B 1 
HETATM 22 O O1 OJC . . . D 2 30.654 -4.407 -24.059 1 54.3 ? O1 OJC 201 B 1 
HETATM 23 O O10 OJC . . . D 2 25.843 -7.148 -20.93 1 52.07 ? O10 OJC 201 B 1 
HETATM 24 O O11 OJC . . . D 2 24.882 -5.133 -22.409 1 53.85 ? O11 OJC 201 B 1 
HETATM 25 O O12 OJC . . . D 2 29.89 -5.788 -19.302 1 53.69 ? O12 OJC 201 B 1 
HETATM 26 O O2 OJC . . . D 2 30.486 -2.676 -25.852 1 47.04 ? O2 OJC 201 B 1 
HETATM 27 O O3 OJC . . . D 2 32.092 -4.638 -26.202 1 56.38 ? O3 OJC 201 B 1 
HETATM 28 O O4 OJC . . . D 2 29.537 -4.988 -25.938 1 50.03 ? O4 OJC 201 B 1 
HETATM 29 O O5 OJC . . . D 2 29.04 -6.409 -28.038 1 57.85 ? O5 OJC 201 B 1 
HETATM 30 O O6 OJC . . . D 2 27.909 -4.157 -27.644 1 47.13 ? O6 OJC 201 B 1 
HETATM 31 O O7 OJC . . . D 2 27.493 -6.116 -26.087 1 56.72 ? O7 OJC 201 B 1 
HETATM 32 O O8 OJC . . . D 2 27.837 -6.834 -23.547 1 53.29 ? O8 OJC 201 B 1 
HETATM 33 O O9 OJC . . . D 2 29.183 -6.771 -21.677 1 51.36 ? O9 OJC 201 B 1 
HETATM 34 P P OJC . . . D 2 30.837 -4.104 -25.625 1 54.55 ? P OJC 201 B 1 
HETATM 35 P P1 OJC . . . D 2 28.512 -5.402 -27.088 1 55.18 ? P1 OJC 201 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           35 
#