data_8SMD
#
_model_server_result.job_id            M_NN9HhJZhcA1y411H1SzQ 
_model_server_result.datetime_utc      '2024-11-16 15:31:30' 
_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          8smd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    8SMD 
#
_exptl.entry_id    8SMD 
_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            8SMD 
_cell.length_a            95.969 
_cell.length_b            95.969 
_cell.length_c            95.969 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SMD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    'P 2ac 2ab 3' 
_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                     8SMD 
_atom_sites.fract_transf_matrix[1][1]    0.01042 
_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]    0.01042 
_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]    0.01042 
_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 LIG . 
D 2 OJC B 1 201 201 OJC LIG . 
E 3 HOH A 1 301 30 HOH HOH . 
E 3 HOH A 2 302 48 HOH HOH . 
E 3 HOH A 3 303 39 HOH HOH . 
E 3 HOH A 4 304 43 HOH HOH . 
E 3 HOH A 5 305 14 HOH HOH . 
E 3 HOH A 6 306 25 HOH HOH . 
E 3 HOH A 7 307 44 HOH HOH . 
E 3 HOH A 8 308 45 HOH HOH . 
E 3 HOH A 9 309 27 HOH HOH . 
E 3 HOH A 10 310 19 HOH HOH . 
E 3 HOH A 11 311 55 HOH HOH . 
E 3 HOH A 12 312 11 HOH HOH . 
E 3 HOH A 13 313 5 HOH HOH . 
E 3 HOH A 14 314 38 HOH HOH . 
E 3 HOH A 15 315 17 HOH HOH . 
E 3 HOH A 16 316 35 HOH HOH . 
E 3 HOH A 17 317 60 HOH HOH . 
E 3 HOH A 18 318 42 HOH HOH . 
E 3 HOH A 19 319 12 HOH HOH . 
E 3 HOH A 20 320 9 HOH HOH . 
E 3 HOH A 21 321 28 HOH HOH . 
E 3 HOH A 22 322 3 HOH HOH . 
E 3 HOH A 23 323 18 HOH HOH . 
E 3 HOH A 24 324 10 HOH HOH . 
E 3 HOH A 25 325 37 HOH HOH . 
E 3 HOH A 26 326 59 HOH HOH . 
E 3 HOH A 27 327 23 HOH HOH . 
E 3 HOH A 28 328 36 HOH HOH . 
E 3 HOH A 29 329 1 HOH HOH . 
E 3 HOH A 30 330 49 HOH HOH . 
E 3 HOH A 31 331 47 HOH HOH . 
E 3 HOH A 32 332 51 HOH HOH . 
F 3 HOH B 1 301 46 HOH HOH . 
F 3 HOH B 2 302 41 HOH HOH . 
F 3 HOH B 3 303 13 HOH HOH . 
F 3 HOH B 4 304 58 HOH HOH . 
F 3 HOH B 5 305 54 HOH HOH . 
F 3 HOH B 6 306 16 HOH HOH . 
F 3 HOH B 7 307 15 HOH HOH . 
F 3 HOH B 8 308 4 HOH HOH . 
F 3 HOH B 9 309 56 HOH HOH . 
F 3 HOH B 10 310 22 HOH HOH . 
F 3 HOH B 11 311 2 HOH HOH . 
F 3 HOH B 12 312 32 HOH HOH . 
F 3 HOH B 13 313 21 HOH HOH . 
F 3 HOH B 14 314 8 HOH HOH . 
F 3 HOH B 15 315 24 HOH HOH . 
F 3 HOH B 16 316 6 HOH HOH . 
F 3 HOH B 17 317 34 HOH HOH . 
F 3 HOH B 18 318 29 HOH HOH . 
F 3 HOH B 19 319 57 HOH HOH . 
F 3 HOH B 20 320 33 HOH HOH . 
F 3 HOH B 21 321 20 HOH HOH . 
F 3 HOH B 22 322 7 HOH HOH . 
F 3 HOH B 23 323 52 HOH HOH . 
F 3 HOH B 24 324 40 HOH HOH . 
F 3 HOH B 25 325 26 HOH HOH . 
F 3 HOH B 26 326 31 HOH HOH . 
F 3 HOH B 27 327 50 HOH HOH . 
F 3 HOH B 28 328 53 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 5.967 -16.445 -26.626 1 47.06 ? N OJC 201 B 1 
HETATM 2 C C OJC . . . D 2 4.646 -16.309 -26.657 1 49.69 ? C OJC 201 B 1 
HETATM 3 O O OJC . . . D 2 1.869 -20.008 -25.543 1 50.44 ? O OJC 201 B 1 
HETATM 4 C C1 OJC . . . D 2 6.538 -17.434 -25.95 1 54.11 ? C1 OJC 201 B 1 
HETATM 5 C C2 OJC . . . D 2 5.714 -18.342 -25.265 1 48.12 ? C2 OJC 201 B 1 
HETATM 6 C C3 OJC . . . D 2 4.348 -18.175 -25.315 1 50.6 ? C3 OJC 201 B 1 
HETATM 7 C C10 OJC . . . D 2 1.139 -14.989 -28.034 1 52.61 ? C10 OJC 201 B 1 
HETATM 8 C C11 OJC . . . D 2 0.275 -14.863 -26.82 1 53.82 ? C11 OJC 201 B 1 
HETATM 9 C C12 OJC . . . D 2 1.12 -14.762 -25.581 1 55.26 ? C12 OJC 201 B 1 
HETATM 10 C C13 OJC . . . D 2 0.228 -15.238 -24.524 1 50.81 ? C13 OJC 201 B 1 
HETATM 11 C C14 OJC . . . D 2 -0.722 -16.176 -25.204 1 57.46 ? C14 OJC 201 B 1 
HETATM 12 C C4 OJC . . . D 2 4.795 -19.917 -24.1 1 49.35 ? C4 OJC 201 B 1 
HETATM 13 C C5 OJC . . . D 2 2.45 -19.407 -24.354 1 44.79 ? C5 OJC 201 B 1 
HETATM 14 C C6 OJC . . . D 2 1.683 -18.118 -24.104 1 51.35 ? C6 OJC 201 B 1 
HETATM 15 C C7 OJC . . . D 2 0.782 -17.964 -25.235 1 49.01 ? C7 OJC 201 B 1 
HETATM 16 C C8 OJC . . . D 2 0.624 -19.309 -25.792 1 49.99 ? C8 OJC 201 B 1 
HETATM 17 C C9 OJC . . . D 2 0.353 -19.232 -27.279 1 46.32 ? C9 OJC 201 B 1 
HETATM 18 N N1 OJC . . . D 2 3.841 -17.147 -26.022 1 51.15 ? N1 OJC 201 B 1 
HETATM 19 N N2 OJC . . . D 2 3.812 -19.171 -24.579 1 56.58 ? N2 OJC 201 B 1 
HETATM 20 N N3 OJC . . . D 2 5.954 -19.425 -24.506 1 52.11 ? N3 OJC 201 B 1 
HETATM 21 N N4 OJC . . . D 2 7.984 -17.574 -25.921 1 49.56 ? N4 OJC 201 B 1 
HETATM 22 O O1 OJC . . . D 2 1.546 -18.978 -27.958 1 53.33 ? O1 OJC 201 B 1 
HETATM 23 O O10 OJC . . . D 2 -0.494 -14.139 -23.964 1 46.1 ? O10 OJC 201 B 1 
HETATM 24 O O11 OJC . . . D 2 1.512 -13.412 -25.334 1 46.89 ? O11 OJC 201 B 1 
HETATM 25 O O12 OJC . . . D 2 0.926 -18.23 -22.904 1 48.98 ? O12 OJC 201 B 1 
HETATM 26 O O2 OJC . . . D 2 2.723 -17.879 -29.88 1 50.63 -1 O2 OJC 201 B 1 
HETATM 27 O O3 OJC . . . D 2 1.409 -19.797 -30.45 1 56.84 -1 O3 OJC 201 B 1 
HETATM 28 O O4 OJC . . . D 2 0.22 -17.507 -29.849 1 60.21 ? O4 OJC 201 B 1 
HETATM 29 O O5 OJC . . . D 2 1.807 -15.853 -30.913 1 48.6 -1 O5 OJC 201 B 1 
HETATM 30 O O6 OJC . . . D 2 -0.483 -15.612 -31.548 1 50.68 -1 O6 OJC 201 B 1 
HETATM 31 O O7 OJC . . . D 2 0.326 -14.824 -29.17 1 47.79 ? O7 OJC 201 B 1 
HETATM 32 O O8 OJC . . . D 2 -0.497 -16.052 -26.633 1 57.48 ? O8 OJC 201 B 1 
HETATM 33 O O9 OJC . . . D 2 -0.512 -17.467 -24.784 1 47.31 ? O9 OJC 201 B 1 
HETATM 34 P P OJC . . . D 2 1.434 -18.588 -29.546 1 51.56 ? P OJC 201 B 1 
HETATM 35 P P1 OJC . . . D 2 0.398 -15.948 -30.371 1 52.09 ? P1 OJC 201 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           35 
#