data_8KBL
#
_model_server_result.job_id            Pz58OFLkUdeES3rGXev0MA 
_model_server_result.datetime_utc      '2024-11-14 19:49:49' 
_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          8kbl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    8KBL 
#
_exptl.entry_id    8KBL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              690.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_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            8KBL 
_cell.length_a            63.729 
_cell.length_b            63.729 
_cell.length_c            63.153 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8KBL 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        93 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 42 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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 
#
_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 
#
_chem_comp.formula           'C20 H24 N10 O14 P2' 
_chem_comp.formula_weight    690.411 
_chem_comp.id                C2E 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'c-di-GMP;Cyclic diguanosine monophosphate' 
#
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
P1 O2P C2E sing 70 n n 
O1P P1 C2E doub 71 n n 
O5' P1 C2E sing 72 n n 
C5' O5' C2E sing 73 n n 
C4' O4' C2E sing 74 n n 
C4' C5' C2E sing 75 n n 
C3' C4' C2E sing 76 n n 
O3' P11 C2E sing 77 n n 
O3' C3' C2E sing 78 n n 
C2' C3' C2E sing 79 n n 
C2' C1' C2E sing 80 n n 
O2' C2' C2E sing 81 n n 
C1' O4' C2E sing 82 n n 
C1' N9 C2E sing 83 n n 
N9 C4 C2E sing 84 n y 
N9 C8 C2E sing 85 n y 
C8 N7 C2E doub 86 n y 
C5 N7 C2E sing 87 n y 
C5 C6 C2E sing 88 n n 
C6 O6 C2E doub 89 n n 
N1 C6 C2E sing 90 n n 
C2 N1 C2E sing 91 n n 
N2 C2 C2E sing 92 n n 
N3 C2 C2E doub 93 n n 
N3 C4 C2E sing 94 n n 
C4 C5 C2E doub 95 n y 
P11 O21 C2E sing 96 n n 
P11 O5A C2E sing 97 n n 
O11 P11 C2E doub 98 n n 
C5A O5A C2E sing 99 n n 
C5A C4A C2E sing 100 n n 
C4A O4A C2E sing 101 n n 
C4A C3A C2E sing 102 n n 
O4A C1A C2E sing 103 n n 
C3A C2A C2E sing 104 n n 
O3A C3A C2E sing 105 n n 
O3A P1 C2E sing 106 n n 
C2A O2A C2E sing 107 n n 
C1A C2A C2E sing 108 n n 
C1A N91 C2E sing 109 n n 
N91 C41 C2E sing 110 n y 
C81 N71 C2E doub 111 n y 
C81 N91 C2E sing 112 n y 
N71 C51 C2E sing 113 n y 
C51 C41 C2E doub 114 n y 
C51 C61 C2E sing 115 n n 
C61 O61 C2E doub 116 n n 
C61 N11 C2E sing 117 n n 
C21 N11 C2E sing 118 n n 
C21 N21 C2E sing 119 n n 
N31 C21 C2E doub 120 n n 
C41 N31 C2E sing 121 n n 
O2P HO2P C2E sing 122 n n 
C5' "H5'1" C2E sing 123 n n 
C5' "H5'2" C2E sing 124 n n 
C4' H4' C2E sing 125 n n 
C3' H3' C2E sing 126 n n 
C2' H2' C2E sing 127 n n 
O2' HO2' C2E sing 128 n n 
C1' H1' C2E sing 129 n n 
C8 H8 C2E sing 130 n n 
N1 HN1 C2E sing 131 n n 
N2 HN21 C2E sing 132 n n 
N2 HN22 C2E sing 133 n n 
O21 HO21 C2E sing 134 n n 
C5A H511 C2E sing 135 n n 
C5A H512 C2E sing 136 n n 
C4A H4A C2E sing 137 n n 
C3A H3A C2E sing 138 n n 
C2A H2A C2E sing 139 n n 
O2A HO2A C2E sing 140 n n 
C1A H1A C2E sing 141 n n 
C81 H81 C2E sing 142 n n 
N11 HN11 C2E sing 143 n n 
N21 HN24 C2E sing 144 n n 
N21 HN23 C2E sing 145 n n 
#
_atom_sites.entry_id                     8KBL 
_atom_sites.fract_transf_matrix[1][1]    0.015691 
_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]    0.015691 
_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]    0.015835 
_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 OJC A 1 201 201 OJC OJC . 
C 3 C2E A 1 202 202 C2E C2E . 
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 . 
D 4 HOH A 84 384 384 HOH HOH . 
D 4 HOH A 85 385 385 HOH HOH . 
D 4 HOH A 86 386 386 HOH HOH . 
D 4 HOH A 87 387 387 HOH HOH . 
D 4 HOH A 88 388 388 HOH HOH . 
D 4 HOH A 89 389 389 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 P1 C2E . . . C 3 29.269 -0.969 25.576 0.37 20 ? P1 C2E 202 A 1 
HETATM 2 O O2P C2E . . . C 3 28.53 -0.878 24.288 0.37 20 ? O2P C2E 202 A 1 
HETATM 3 O O1P C2E . . . C 3 28.606 -1.668 26.709 0.37 20 ? O1P C2E 202 A 1 
HETATM 4 O O5' C2E . . . C 3 30.649 -1.71 25.27 0.37 20 ? O5' C2E 202 A 1 
HETATM 5 C C5' C2E . . . C 3 31.371 -2.248 26.387 0.37 20 ? C5' C2E 202 A 1 
HETATM 6 C C4' C2E . . . C 3 32.785 -2.543 25.958 0.37 20 ? C4' C2E 202 A 1 
HETATM 7 O O4' C2E . . . C 3 32.791 -3.653 25.039 0.37 20 ? O4' C2E 202 A 1 
HETATM 8 C C3' C2E . . . C 3 33.472 -1.418 25.195 0.37 20 ? C3' C2E 202 A 1 
HETATM 9 O O3' C2E . . . C 3 33.983 -0.458 26.107 0.37 20 ? O3' C2E 202 A 1 
HETATM 10 C C2' C2E . . . C 3 34.584 -2.191 24.491 0.37 20 ? C2' C2E 202 A 1 
HETATM 11 O O2' C2E . . . C 3 35.631 -2.455 25.398 0.37 20 ? O2' C2E 202 A 1 
HETATM 12 C C1' C2E . . . C 3 33.865 -3.488 24.119 0.37 20 ? C1' C2E 202 A 1 
HETATM 13 N N9 C2E . . . C 3 33.339 -3.543 22.755 0.37 20 ? N9 C2E 202 A 1 
HETATM 14 C C8 C2E . . . C 3 32.025 -3.583 22.37 0.37 20 ? C8 C2E 202 A 1 
HETATM 15 N N7 C2E . . . C 3 31.856 -3.624 21.073 0.37 20 ? N7 C2E 202 A 1 
HETATM 16 C C5 C2E . . . C 3 33.148 -3.606 20.568 0.37 20 ? C5 C2E 202 A 1 
HETATM 17 C C6 C2E . . . C 3 33.595 -3.628 19.225 0.37 20 ? C6 C2E 202 A 1 
HETATM 18 O O6 C2E . . . C 3 32.911 -3.674 18.195 0.37 20 ? O6 C2E 202 A 1 
HETATM 19 N N1 C2E . . . C 3 34.985 -3.589 19.148 0.37 20 ? N1 C2E 202 A 1 
HETATM 20 C C2 C2E . . . C 3 35.836 -3.535 20.227 0.37 20 ? C2 C2E 202 A 1 
HETATM 21 N N2 C2E . . . C 3 37.146 -3.503 19.961 0.37 20 ? N2 C2E 202 A 1 
HETATM 22 N N3 C2E . . . C 3 35.423 -3.512 21.49 0.37 20 ? N3 C2E 202 A 1 
HETATM 23 C C4 C2E . . . C 3 34.073 -3.549 21.585 0.37 20 ? C4 C2E 202 A 1 
HETATM 24 P P11 C2E . . . C 3 34.483 0.988 25.622 0.37 20 ? P11 C2E 202 A 1 
HETATM 25 O O21 C2E . . . C 3 35.273 0.921 24.364 0.37 20 ? O21 C2E 202 A 1 
HETATM 26 O O11 C2E . . . C 3 35.092 1.691 26.784 0.37 20 ? O11 C2E 202 A 1 
HETATM 27 O O5A C2E . . . C 3 33.104 1.715 25.281 0.37 20 ? O5A C2E 202 A 1 
HETATM 28 C C5A C2E . . . C 3 32.38 2.27 26.389 0.37 20 ? C5A C2E 202 A 1 
HETATM 29 C C4A C2E . . . C 3 30.965 2.561 25.96 0.37 20 ? C4A C2E 202 A 1 
HETATM 30 O O4A C2E . . . C 3 30.95 3.684 25.058 0.37 20 ? O4A C2E 202 A 1 
HETATM 31 C C3A C2E . . . C 3 30.278 1.446 25.183 0.37 20 ? C3A C2E 202 A 1 
HETATM 32 O O3A C2E . . . C 3 29.776 0.468 26.082 0.37 20 ? O3A C2E 202 A 1 
HETATM 33 C C2A C2E . . . C 3 29.151 2.231 24.519 0.37 20 ? C2A C2E 202 A 1 
HETATM 34 O O2A C2E . . . C 3 28.152 2.474 25.483 0.37 20 ? O2A C2E 202 A 1 
HETATM 35 C C1A C2E . . . C 3 29.87 3.527 24.142 0.37 20 ? C1A C2E 202 A 1 
HETATM 36 N N91 C2E . . . C 3 30.392 3.578 22.777 0.37 20 ? N91 C2E 202 A 1 
HETATM 37 C C81 C2E . . . C 3 31.705 3.605 22.391 0.37 20 ? C81 C2E 202 A 1 
HETATM 38 N N71 C2E . . . C 3 31.875 3.644 21.094 0.37 20 ? N71 C2E 202 A 1 
HETATM 39 C C51 C2E . . . C 3 30.583 3.638 20.589 0.37 20 ? C51 C2E 202 A 1 
HETATM 40 C C61 C2E . . . C 3 30.136 3.664 19.245 0.37 20 ? C61 C2E 202 A 1 
HETATM 41 O O61 C2E . . . C 3 30.817 3.703 18.213 0.37 20 ? O61 C2E 202 A 1 
HETATM 42 N N11 C2E . . . C 3 28.746 3.639 19.173 0.37 20 ? N11 C2E 202 A 1 
HETATM 43 C C21 C2E . . . C 3 27.894 3.593 20.25 0.37 20 ? C21 C2E 202 A 1 
HETATM 44 N N21 C2E . . . C 3 26.583 3.574 19.982 0.37 20 ? N21 C2E 202 A 1 
HETATM 45 N N31 C2E . . . C 3 28.307 3.566 21.512 0.37 20 ? N31 C2E 202 A 1 
HETATM 46 C C41 C2E . . . C 3 29.657 3.591 21.607 0.37 20 ? C41 C2E 202 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           371 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           46 
#