data_2I2D
#
_model_server_result.job_id            J7ot7C0r9hmpLpAflq4hBg 
_model_server_result.datetime_utc      '2024-11-13 19:17:56' 
_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          2i2d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":273}' 
#
_entry.id    2I2D 
#
_exptl.entry_id    2I2D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              676.427 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE' 
_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            2I2D 
_cell.length_a            62.481 
_cell.length_b            75.851 
_cell.length_c            118.35 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2I2D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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    1,2,3,4 
#
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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 62.481 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.481 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C20 H26 N10 O13 P2' 
_chem_comp.formula_weight    676.427 
_chem_comp.id                A2D 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "BIS(ADENOSINE)-5'-DIPHOSPHATE" 
#
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
PA O5D A2D sing 1 n n 
PA O3A A2D sing 2 n n 
PA O2A A2D doub 3 n n 
PA O1A A2D sing 4 n n 
O1A HO1A A2D sing 5 n n 
O3A PB A2D sing 6 n n 
PB O5E A2D sing 7 n n 
PB O1B A2D doub 8 n n 
PB O2B A2D sing 9 n n 
O2B HO2B A2D sing 10 n n 
O5D C5D A2D sing 11 n n 
C5D C4D A2D sing 12 n n 
C5D HD1 A2D sing 13 n n 
C5D HD2 A2D sing 14 n n 
C4D O4D A2D sing 15 n n 
C4D C3D A2D sing 16 n n 
C4D H4D A2D sing 17 n n 
O4D C1D A2D sing 18 n n 
C3D C2D A2D sing 19 n n 
C3D O3D A2D sing 20 n n 
C3D H3CA A2D sing 21 n n 
O3D H3OA A2D sing 22 n n 
C2D C1D A2D sing 23 n n 
C2D O2D A2D sing 24 n n 
C2D H2CA A2D sing 25 n n 
O2D H2OA A2D sing 26 n n 
C1D N9A A2D sing 27 n n 
C1D H1D A2D sing 28 n n 
N9A C8A A2D sing 29 n y 
N9A C4A A2D sing 30 n y 
C8A N7A A2D doub 31 n y 
C8A H8A A2D sing 32 n n 
N7A C5A A2D sing 33 n y 
C5A C6A A2D sing 34 n y 
C5A C4A A2D doub 35 n y 
C6A N6A A2D sing 36 n n 
C6A N1A A2D doub 37 n y 
N6A H6A1 A2D sing 38 n n 
N6A H6A2 A2D sing 39 n n 
N1A C2A A2D sing 40 n y 
C2A N3A A2D doub 41 n y 
C2A H2A A2D sing 42 n n 
N3A C4A A2D sing 43 n y 
O5E C5E A2D sing 44 n n 
C5E C4E A2D sing 45 n n 
C5E HE1 A2D sing 46 n n 
C5E HE2 A2D sing 47 n n 
C4E C3E A2D sing 48 n n 
C4E O4E A2D sing 49 n n 
C4E H4E A2D sing 50 n n 
O4E C1E A2D sing 51 n n 
C3E C2E A2D sing 52 n n 
C3E O3E A2D sing 53 n n 
C3E H3CB A2D sing 54 n n 
O3E H3OB A2D sing 55 n n 
C2E O2E A2D sing 56 n n 
C2E C1E A2D sing 57 n n 
C2E H2CB A2D sing 58 n n 
O2E H2OB A2D sing 59 n n 
C1E N9B A2D sing 60 n n 
C1E H1E A2D sing 61 n n 
N9B C8B A2D sing 62 n y 
N9B C4B A2D sing 63 n y 
C8B N7B A2D doub 64 n y 
C8B H8B A2D sing 65 n n 
N7B C5B A2D sing 66 n y 
C5B C6B A2D doub 67 n y 
C5B C4B A2D sing 68 n y 
C6B N6B A2D sing 69 n n 
C6B N1B A2D sing 70 n y 
N6B H6B1 A2D sing 71 n n 
N6B H6B2 A2D sing 72 n n 
N1B C2B A2D doub 73 n y 
C2B N3B A2D sing 74 n y 
C2B H2B A2D sing 75 n n 
N3B C4B A2D doub 76 n y 
#
_atom_sites.entry_id                     2I2D 
_atom_sites.fract_transf_matrix[1][1]    0.016005 
_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]    0.013184 
_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]    0.00845 
_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 A2D A 1 273 101 A2D A2D . 
C 3 CIT A 1 274 201 CIT CIT . 
D 4 HOH A 1 275 1 HOH HOH . 
D 4 HOH A 2 276 2 HOH HOH . 
D 4 HOH A 3 277 3 HOH HOH . 
D 4 HOH A 4 278 4 HOH HOH . 
D 4 HOH A 5 279 5 HOH HOH . 
D 4 HOH A 6 280 6 HOH HOH . 
D 4 HOH A 7 281 7 HOH HOH . 
D 4 HOH A 8 282 8 HOH HOH . 
D 4 HOH A 9 283 9 HOH HOH . 
D 4 HOH A 10 284 10 HOH HOH . 
D 4 HOH A 11 285 11 HOH HOH . 
D 4 HOH A 12 286 12 HOH HOH . 
D 4 HOH A 13 287 13 HOH HOH . 
D 4 HOH A 14 288 14 HOH HOH . 
D 4 HOH A 15 289 15 HOH HOH . 
D 4 HOH A 16 290 16 HOH HOH . 
D 4 HOH A 17 291 17 HOH HOH . 
D 4 HOH A 18 292 18 HOH HOH . 
D 4 HOH A 19 293 19 HOH HOH . 
D 4 HOH A 20 294 20 HOH HOH . 
D 4 HOH A 21 295 21 HOH HOH . 
D 4 HOH A 22 296 22 HOH HOH . 
D 4 HOH A 23 297 23 HOH HOH . 
D 4 HOH A 24 298 24 HOH HOH . 
D 4 HOH A 25 299 25 HOH HOH . 
D 4 HOH A 26 300 26 HOH HOH . 
D 4 HOH A 27 301 27 HOH HOH . 
D 4 HOH A 28 302 28 HOH HOH . 
D 4 HOH A 29 303 29 HOH HOH . 
D 4 HOH A 30 304 30 HOH HOH . 
D 4 HOH A 31 305 31 HOH HOH . 
D 4 HOH A 32 306 32 HOH HOH . 
D 4 HOH A 33 307 33 HOH HOH . 
D 4 HOH A 34 308 34 HOH HOH . 
D 4 HOH A 35 309 35 HOH HOH . 
D 4 HOH A 36 310 36 HOH HOH . 
D 4 HOH A 37 311 37 HOH HOH . 
D 4 HOH A 38 312 38 HOH HOH . 
D 4 HOH A 39 313 39 HOH HOH . 
D 4 HOH A 40 314 40 HOH HOH . 
D 4 HOH A 41 315 41 HOH HOH . 
D 4 HOH A 42 316 42 HOH HOH . 
D 4 HOH A 43 317 43 HOH HOH . 
D 4 HOH A 44 318 44 HOH HOH . 
D 4 HOH A 45 319 45 HOH HOH . 
D 4 HOH A 46 320 46 HOH HOH . 
D 4 HOH A 47 321 47 HOH HOH . 
D 4 HOH A 48 322 48 HOH HOH . 
D 4 HOH A 49 323 49 HOH HOH . 
D 4 HOH A 50 324 50 HOH HOH . 
D 4 HOH A 51 325 51 HOH HOH . 
D 4 HOH A 52 326 52 HOH HOH . 
D 4 HOH A 53 327 53 HOH HOH . 
D 4 HOH A 54 328 54 HOH HOH . 
D 4 HOH A 55 329 55 HOH HOH . 
D 4 HOH A 56 330 56 HOH HOH . 
D 4 HOH A 57 331 57 HOH HOH . 
D 4 HOH A 58 332 58 HOH HOH . 
D 4 HOH A 59 333 59 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 PA A2D . . . B 2 14.306 7.549 13.388 0.8 37.22 ? PA A2D 273 A 1 
HETATM 2 O O1A A2D . . . B 2 14.649 8.597 14.574 0.8 36.83 ? O1A A2D 273 A 1 
HETATM 3 O O2A A2D . . . B 2 13.697 6.304 13.461 0.8 37.36 ? O2A A2D 273 A 1 
HETATM 4 O O3A A2D . . . B 2 13.678 8.439 12.658 0.8 35.93 ? O3A A2D 273 A 1 
HETATM 5 P PB A2D . . . B 2 12.904 9.645 12.912 0.8 56.17 ? PB A2D 273 A 1 
HETATM 6 O O1B A2D . . . B 2 11.422 9.477 12.862 0.8 56.09 ? O1B A2D 273 A 1 
HETATM 7 O O2B A2D . . . B 2 13.409 10.767 13.768 0.8 57.34 ? O2B A2D 273 A 1 
HETATM 8 O O5D A2D . . . B 2 15.729 7.529 12.628 0.8 35.66 ? O5D A2D 273 A 1 
HETATM 9 C C5D A2D . . . B 2 16.702 6.539 12.946 1 35.56 ? C5D A2D 273 A 1 
HETATM 10 C C4D A2D . . . B 2 17.86 7.216 13.655 1 34.95 ? C4D A2D 273 A 1 
HETATM 11 O O4D A2D . . . B 2 18.258 8.362 12.91 1 34.22 ? O4D A2D 273 A 1 
HETATM 12 C C3D A2D . . . B 2 17.509 7.712 15.053 1 35.01 ? C3D A2D 273 A 1 
HETATM 13 O O3D A2D . . . B 2 18.279 6.961 15.994 1 35.27 ? O3D A2D 273 A 1 
HETATM 14 C C2D A2D . . . B 2 17.869 9.195 15.059 1 34.73 ? C2D A2D 273 A 1 
HETATM 15 O O2D A2D . . . B 2 18.548 9.601 16.257 1 36.19 ? O2D A2D 273 A 1 
HETATM 16 C C1D A2D . . . B 2 18.78 9.292 13.847 1 32.74 ? C1D A2D 273 A 1 
HETATM 17 N N9A A2D . . . B 2 18.895 10.622 13.204 1 32.76 ? N9A A2D 273 A 1 
HETATM 18 C C8A A2D . . . B 2 17.931 11.479 12.822 1 31.47 ? C8A A2D 273 A 1 
HETATM 19 N N7A A2D . . . B 2 18.525 12.558 12.267 1 31.9 ? N7A A2D 273 A 1 
HETATM 20 C C5A A2D . . . B 2 19.874 12.364 12.291 1 32.84 ? C5A A2D 273 A 1 
HETATM 21 C C6A A2D . . . B 2 21.002 13.092 11.875 1 32.2 ? C6A A2D 273 A 1 
HETATM 22 N N6A A2D . . . B 2 20.907 14.308 11.279 1 31.43 ? N6A A2D 273 A 1 
HETATM 23 N N1A A2D . . . B 2 22.228 12.556 12.072 1 31.69 ? N1A A2D 273 A 1 
HETATM 24 C C2A A2D . . . B 2 22.402 11.361 12.651 1 31.72 ? C2A A2D 273 A 1 
HETATM 25 N N3A A2D . . . B 2 21.354 10.64 13.059 1 31.79 ? N3A A2D 273 A 1 
HETATM 26 C C4A A2D . . . B 2 20.089 11.126 12.882 1 33.11 ? C4A A2D 273 A 1 
HETATM 27 O O5E A2D . . . B 2 13.267 10.41 11.563 0.8 54.67 ? O5E A2D 273 A 1 
HETATM 28 C C5E A2D . . . B 2 13.666 9.672 10.419 1 50.72 ? C5E A2D 273 A 1 
HETATM 29 C C4E A2D . . . B 2 15.126 9.934 10.14 1 50.81 ? C4E A2D 273 A 1 
HETATM 30 O O4E A2D . . . B 2 15.853 8.724 10.026 1 50.12 ? O4E A2D 273 A 1 
HETATM 31 C C3E A2D . . . B 2 15.275 10.609 8.812 1 50.04 ? C3E A2D 273 A 1 
HETATM 32 O O3E A2D . . . B 2 16.49 11.327 8.89 1 49.81 ? O3E A2D 273 A 1 
HETATM 33 C C2E A2D . . . B 2 15.622 9.506 7.884 1 48.16 ? C2E A2D 273 A 1 
HETATM 34 O O2E A2D . . . B 2 16.393 10.14 6.876 1 46.31 ? O2E A2D 273 A 1 
HETATM 35 C C1E A2D . . . B 2 16.496 8.65 8.767 1 45.15 ? C1E A2D 273 A 1 
HETATM 36 N N9B A2D . . . B 2 16.533 7.246 8.296 1 44.26 ? N9B A2D 273 A 1 
HETATM 37 C C8B A2D . . . B 2 15.506 6.569 7.803 1 43.16 ? C8B A2D 273 A 1 
HETATM 38 N N7B A2D . . . B 2 15.903 5.331 7.474 1 41.95 ? N7B A2D 273 A 1 
HETATM 39 C C5B A2D . . . B 2 17.197 5.226 7.775 1 42.85 ? C5B A2D 273 A 1 
HETATM 40 C C6B A2D . . . B 2 18.118 4.202 7.662 1 43.87 ? C6B A2D 273 A 1 
HETATM 41 N N6B A2D . . . B 2 17.78 2.999 7.161 1 43.12 ? N6B A2D 273 A 1 
HETATM 42 N N1B A2D . . . B 2 19.37 4.419 8.069 1 41.84 ? N1B A2D 273 A 1 
HETATM 43 C C2B A2D . . . B 2 19.722 5.6 8.563 1 42.08 ? C2B A2D 273 A 1 
HETATM 44 N N3B A2D . . . B 2 18.857 6.599 8.686 1 42.12 ? N3B A2D 273 A 1 
HETATM 45 C C4B A2D . . . B 2 17.585 6.439 8.295 1 43.03 ? C4B A2D 273 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           45 
#