data_6YWB
#
_model_server_result.job_id            nZY74DUVDV8ogiYYA2vGqQ 
_model_server_result.datetime_utc      '2024-10-19 03:35:40' 
_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          6ywb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    6YWB 
#
_exptl.entry_id    6YWB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              680.475 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3',3'-c-[2'FdAMP-2'FdAM(PS)]" 
_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            6YWB 
_cell.length_a            110.906 
_cell.length_b            110.906 
_cell.length_c            35.67 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YWB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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 'point symmetry operation' ? ? 0 -1 0 -1 0 0 0 0 -1 0 0 -17.835 
#
_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 H24 F2 N10 O9 P2 S 2' 
_chem_comp.formula_weight    680.475 
_chem_comp.id                PWB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3',3'-c-[2'FdAMP-2'FdAM(PS)]" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     9-[(1~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3-oxidanyl-3,12-bis(oxidanylidene)-12-sulfanyl-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]purin-6-amine 
#
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
C10 N4 PWB doub 277 n y 
C10 N5 PWB sing 278 n y 
N4 C13 PWB sing 279 n y 
N5 C11 PWB doub 280 n y 
C13 N10 PWB sing 281 n n 
C13 C12 PWB doub 282 n y 
C11 C12 PWB sing 283 n y 
C11 N6 PWB sing 284 n y 
C12 N7 PWB sing 285 n y 
F1 C16 PWB sing 286 n n 
N6 C17 PWB sing 287 n n 
N6 C14 PWB sing 288 n y 
C17 C16 PWB sing 289 n n 
C17 O5 PWB sing 290 n n 
C16 C15 PWB sing 291 n n 
N7 C14 PWB doub 292 n y 
O5 C18 PWB sing 293 n n 
O P PWB doub 294 n n 
C15 C18 PWB sing 295 n n 
C15 O7 PWB sing 296 n n 
C18 C19 PWB sing 297 n n 
O7 P PWB sing 298 n n 
P S1 PWB sing 299 n n 
P O2 PWB sing 300 n n 
N11 C3 PWB sing 301 n n 
C19 O8 PWB sing 302 n n 
N3 C2 PWB sing 303 n y 
N3 C4 PWB doub 304 n y 
O8 P1 PWB sing 305 n n 
O2 C9 PWB sing 306 n n 
C3 C2 PWB doub 307 n y 
C3 N PWB sing 308 n y 
C2 C1 PWB sing 309 n y 
C4 N2 PWB sing 310 n y 
N C PWB doub 311 n y 
C9 C8 PWB sing 312 n n 
O22 P1 PWB doub 313 n n 
P1 O4 PWB sing 314 n n 
P1 O10 PWB sing 315 n n 
C1 N2 PWB sing 316 n y 
C1 N1 PWB doub 317 n y 
N2 C7 PWB sing 318 n n 
C5 O10 PWB sing 319 n n 
C5 C8 PWB sing 320 n n 
C5 C6 PWB sing 321 n n 
C N1 PWB sing 322 n y 
C8 O1 PWB sing 323 n n 
O1 C7 PWB sing 324 n n 
C6 C7 PWB sing 325 n n 
C6 F2 PWB sing 326 n n 
C H PWB sing 327 n n 
C10 H10 PWB sing 328 n n 
C14 H14 PWB sing 329 n n 
C15 H15 PWB sing 330 n n 
C16 H16 PWB sing 331 n n 
C17 H17 PWB sing 332 n n 
C18 H18 PWB sing 333 n n 
C19 H192 PWB sing 334 n n 
C19 H191 PWB sing 335 n n 
C4 H4 PWB sing 336 n n 
C5 H5 PWB sing 337 n n 
C6 H6 PWB sing 338 n n 
C7 H7 PWB sing 339 n n 
C8 H8 PWB sing 340 n n 
C9 H91 PWB sing 341 n n 
C9 H92 PWB sing 342 n n 
N10 HN5 PWB sing 343 n n 
N10 HN4 PWB sing 344 n n 
O4 H1 PWB sing 345 n n 
S1 HS1 PWB sing 346 n n 
N11 HN3 PWB sing 347 n n 
N11 HN1 PWB sing 348 n n 
HN2 N11 PWB sing 349 n n 
N10 HN6 PWB sing 350 n n 
#
_atom_sites.entry_id                     6YWB 
_atom_sites.fract_transf_matrix[1][1]    0.009017 
_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]    0.009017 
_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]    0.028035 
_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 PWB A 1 401 401 PWB 95B . 
C 3 HOH A 1 501 36 HOH HOH . 
C 3 HOH A 2 502 30 HOH HOH . 
C 3 HOH A 3 503 14 HOH HOH . 
C 3 HOH A 4 504 35 HOH HOH . 
C 3 HOH A 5 505 4 HOH HOH . 
C 3 HOH A 6 506 28 HOH HOH . 
C 3 HOH A 7 507 2 HOH HOH . 
C 3 HOH A 8 508 7 HOH HOH . 
C 3 HOH A 9 509 33 HOH HOH . 
C 3 HOH A 10 510 10 HOH HOH . 
C 3 HOH A 11 511 9 HOH HOH . 
C 3 HOH A 12 512 16 HOH HOH . 
C 3 HOH A 13 513 20 HOH HOH . 
C 3 HOH A 14 514 18 HOH HOH . 
C 3 HOH A 15 515 6 HOH HOH . 
C 3 HOH A 16 516 21 HOH HOH . 
C 3 HOH A 17 517 1 HOH HOH . 
C 3 HOH A 18 518 23 HOH HOH . 
C 3 HOH A 19 519 39 HOH HOH . 
C 3 HOH A 20 520 3 HOH HOH . 
C 3 HOH A 21 521 27 HOH HOH . 
C 3 HOH A 22 522 5 HOH HOH . 
C 3 HOH A 23 523 29 HOH HOH . 
C 3 HOH A 24 524 32 HOH HOH . 
C 3 HOH A 25 525 8 HOH HOH . 
C 3 HOH A 26 526 11 HOH HOH . 
C 3 HOH A 27 527 17 HOH HOH . 
C 3 HOH A 28 528 15 HOH HOH . 
C 3 HOH A 29 529 19 HOH HOH . 
C 3 HOH A 30 530 38 HOH HOH . 
C 3 HOH A 31 531 12 HOH HOH . 
C 3 HOH A 32 532 31 HOH HOH . 
C 3 HOH A 33 533 22 HOH HOH . 
C 3 HOH A 34 534 25 HOH HOH . 
C 3 HOH A 35 535 24 HOH HOH . 
C 3 HOH A 36 536 34 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 PWB . . . B 2 -13.917 20.152 -8.387 0.49 30.41 ? N PWB 401 A 1 
HETATM 2 C C PWB . . . B 2 -14.115 21.421 -8.673 0.49 30.62 ? C PWB 401 A 1 
HETATM 3 O O PWB . . . B 2 -21.762 19.082 -6.187 0.49 27.1 ? O PWB 401 A 1 
HETATM 4 C C1 PWB . . . B 2 -16.192 21.484 -7.679 0.49 27.71 ? C1 PWB 401 A 1 
HETATM 5 C C10 PWB . . . B 2 -21.415 14.112 -9.148 0.49 30.48 ? C10 PWB 401 A 1 
HETATM 6 C C11 PWB . . . B 2 -21.479 16.187 -10.145 0.49 30.07 ? C11 PWB 401 A 1 
HETATM 7 C C12 PWB . . . B 2 -20.098 16.053 -10.496 0.49 26.49 ? C12 PWB 401 A 1 
HETATM 8 C C13 PWB . . . B 2 -19.436 14.814 -10.087 0.49 30.88 ? C13 PWB 401 A 1 
HETATM 9 C C14 PWB . . . B 2 -20.844 17.918 -11.187 0.49 28.67 ? C14 PWB 401 A 1 
HETATM 10 C C15 PWB . . . B 2 -22.752 19.57 -8.936 0.49 28.49 ? C15 PWB 401 A 1 
HETATM 11 C C16 PWB . . . B 2 -23.268 18.17 -8.993 0.49 29.14 ? C16 PWB 401 A 1 
HETATM 12 C C17 PWB . . . B 2 -23.201 17.873 -10.454 0.49 29.05 ? C17 PWB 401 A 1 
HETATM 13 C C18 PWB . . . B 2 -23.343 20.148 -10.184 0.49 28.68 ? C18 PWB 401 A 1 
HETATM 14 C C19 PWB . . . B 2 -22.643 21.373 -10.689 0.49 27.27 ? C19 PWB 401 A 1 
HETATM 15 C C2 PWB . . . B 2 -16.056 20.104 -7.323 0.49 27.6 ? C2 PWB 401 A 1 
HETATM 16 C C3 PWB . . . B 2 -14.815 19.443 -7.728 0.49 31.12 ? C3 PWB 401 A 1 
HETATM 17 C C4 PWB . . . B 2 -17.923 20.848 -6.637 0.49 28.84 ? C4 PWB 401 A 1 
HETATM 18 C C5 PWB . . . B 2 -19.581 22.762 -8.917 0.49 28.78 ? C5 PWB 401 A 1 
HETATM 19 C C6 PWB . . . B 2 -18.178 23.271 -8.843 0.49 28.25 ? C6 PWB 401 A 1 
HETATM 20 C C7 PWB . . . B 2 -17.882 23.204 -7.381 0.49 29.21 ? C7 PWB 401 A 1 
HETATM 21 C C8 PWB . . . B 2 -20.157 23.346 -7.663 0.49 28.68 ? C8 PWB 401 A 1 
HETATM 22 C C9 PWB . . . B 2 -21.374 22.638 -7.152 0.49 27.31 ? C9 PWB 401 A 1 
HETATM 23 F F1 PWB . . . B 2 -24.532 18.122 -8.598 0.49 26.55 ? F1 PWB 401 A 1 
HETATM 24 F F2 PWB . . . B 2 -18.123 24.537 -9.231 0.49 26.54 ? F2 PWB 401 A 1 
HETATM 25 N N1 PWB . . . B 2 -15.206 22.078 -8.341 0.49 32.39 ? N1 PWB 401 A 1 
HETATM 26 N N10 PWB . . . B 2 -18.023 14.561 -10.386 0.49 31.32 ? N10 PWB 401 A 1 
HETATM 27 N N2 PWB . . . B 2 -17.337 21.869 -7.22 0.49 29.28 ? N2 PWB 401 A 1 
HETATM 28 N N3 PWB . . . B 2 -17.154 19.778 -6.685 0.49 25.87 ? N3 PWB 401 A 1 
HETATM 29 N N4 PWB . . . B 2 -20.144 13.916 -9.429 0.49 30.35 ? N4 PWB 401 A 1 
HETATM 30 N N5 PWB . . . B 2 -22.074 15.2 -9.482 0.49 32.44 ? N5 PWB 401 A 1 
HETATM 31 N N6 PWB . . . B 2 -21.865 17.33 -10.608 0.49 29.26 ? N6 PWB 401 A 1 
HETATM 32 N N7 PWB . . . B 2 -19.771 17.151 -11.135 0.49 26.13 ? N7 PWB 401 A 1 
HETATM 33 O O1 PWB . . . B 2 -19.117 23.267 -6.711 0.49 30.54 ? O1 PWB 401 A 1 
HETATM 34 O O10 PWB . . . B 2 -20.213 23.197 -10.089 0.49 30.71 ? O10 PWB 401 A 1 
HETATM 35 O O2 PWB . . . B 2 -21.131 21.271 -6.973 0.49 30.14 ? O2 PWB 401 A 1 
HETATM 36 O O22 PWB . . . B 2 -19.072 21.753 -11.638 0.49 27.07 ? O22 PWB 401 A 1 
HETATM 37 O O4 PWB . . . B 2 -20.897 23.061 -12.452 0.49 25.74 ? O4 PWB 401 A 1 
HETATM 38 O O5 PWB . . . B 2 -23.263 19.105 -11.13 0.49 30.59 ? O5 PWB 401 A 1 
HETATM 39 O O7 PWB . . . B 2 -23.175 20.211 -7.769 0.49 29.69 ? O7 PWB 401 A 1 
HETATM 40 O O8 PWB . . . B 2 -21.272 21.153 -10.871 0.49 30.11 ? O8 PWB 401 A 1 
HETATM 41 P P PWB . . . B 2 -22.271 20.325 -6.526 0.49 29.03 ? P PWB 401 A 1 
HETATM 42 P P1 PWB . . . B 2 -20.342 22.3 -11.338 0.49 28.23 ? P1 PWB 401 A 1 
HETATM 43 S S1 PWB . . . B 2 -23.351 21.091 -5.023 0.49 25.29 ? S1 PWB 401 A 1 
HETATM 44 N N11 PWB . . . B 2 -14.558 18.032 -7.422 0.49 32.68 ? N11 PWB 401 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           44 
#