data_8RZC # _model_server_result.job_id pGDdisRGpLTMVqFZeBMpuQ _model_server_result.datetime_utc '2024-11-22 06:58:50' _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 8rzc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 8RZC # _exptl.entry_id 8RZC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.5 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-imidazol-1-yl-benzoic acid' _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 120 _cell.entry_id 8RZC _cell.length_a 168.202 _cell.length_b 168.202 _cell.length_c 51.991 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RZC _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _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,G,H _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 B SG CYS 77 B CYS 74 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc2 B SG CYS 80 B CYS 77 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 B NE2 HIS 86 B HIS 83 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc4 B SG CYS 93 B CYS 90 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc5 B SG CYS 120 B CYS 117 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc6 B SG CYS 123 B CYS 120 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 B SG CYS 131 B CYS 128 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc8 B SG CYS 133 B CYS 130 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? # _chem_comp.formula 'C21 H21 N7 O5 S' _chem_comp.formula_weight 483.5 _chem_comp.id A1H4D _chem_comp.mon_nstd_flag n _chem_comp.name '3-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-imidazol-1-yl-benzoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3-(((((2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)thio)methyl)-5-(1H-imidazol-1-yl)benzoic acid' # 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 O3' C3' A1H4D sing 1 n n C3' C2' A1H4D sing 2 n n C3' C4' A1H4D sing 3 n n C4' C5' A1H4D sing 4 n n O4' C4' A1H4D sing 5 n n C5' S1 A1H4D sing 6 n n S1 C3 A1H4D sing 7 n n C3 C7 A1H4D sing 8 n n C7 C20 A1H4D doub 9 n y C7 C1 A1H4D sing 10 n y C1 C9 A1H4D doub 11 n y C9 C10 A1H4D sing 12 n n C13 C9 A1H4D sing 13 n y O11 C10 A1H4D sing 14 n n C10 O12 A1H4D doub 15 n n C14 C13 A1H4D doub 16 n y N15 C14 A1H4D sing 17 n n C20 C14 A1H4D sing 18 n y C19 N15 A1H4D sing 19 n y N15 C16 A1H4D sing 20 n y C16 C17 A1H4D doub 21 n y C17 N18 A1H4D sing 22 n y N18 C19 A1H4D doub 23 n y C1' O4' A1H4D sing 24 n n N9 C1' A1H4D sing 25 n n C2' C1' A1H4D sing 26 n n C8 N9 A1H4D sing 27 n y N9 C4 A1H4D sing 28 n y C4 N3 A1H4D sing 29 n y C4 C5 A1H4D doub 30 n y N3 C2 A1H4D doub 31 n y C2 N1 A1H4D sing 32 n y N1 C6 A1H4D doub 33 n y C6 C5 A1H4D sing 34 n y N6 C6 A1H4D sing 35 n n C5 N7 A1H4D sing 36 n y N7 C8 A1H4D doub 37 n y O2' C2' A1H4D sing 38 n n C13 H45 A1H4D sing 39 n n C16 H46 A1H4D sing 40 n n C17 H47 A1H4D sing 41 n n C19 H48 A1H4D sing 42 n n C3' H3' A1H4D sing 43 n n C20 H49 A1H4D sing 44 n n C1' H1' A1H4D sing 45 n n C2 H2 A1H4D sing 46 n n C4' H4' A1H4D sing 47 n n C8 H8 A1H4D sing 48 n n C2' H2' A1H4D sing 49 n n C5' "H5'2" A1H4D sing 50 n n C5' "H5'1" A1H4D sing 51 n n C3 H42 A1H4D sing 52 n n C3 H43 A1H4D sing 53 n n C1 H44 A1H4D sing 54 n n N6 HN61 A1H4D sing 55 n n N6 HN62 A1H4D sing 56 n n O3' HO3' A1H4D sing 57 n n O11 H1 A1H4D sing 58 n n O2' HO2' A1H4D sing 59 n n # _atom_sites.entry_id 8RZC _atom_sites.fract_transf_matrix[1][1] 0.005945 _atom_sites.fract_transf_matrix[1][2] 0.003432 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006865 _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] 0.019234 _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 3 MES A 1 301 302 MES MES . D 4 A1H4D A 1 302 303 A1H4D OBV . E 5 ZN B 1 201 141 ZN ZN . F 5 ZN B 1 202 142 ZN ZN . G 6 HOH A 1 401 420 HOH HOH . G 6 HOH A 2 402 373 HOH HOH . G 6 HOH A 3 403 395 HOH HOH . G 6 HOH A 4 404 377 HOH HOH . G 6 HOH A 5 405 384 HOH HOH . G 6 HOH A 6 406 368 HOH HOH . G 6 HOH A 7 407 339 HOH HOH . G 6 HOH A 8 408 374 HOH HOH . G 6 HOH A 9 409 352 HOH HOH . G 6 HOH A 10 410 419 HOH HOH . G 6 HOH A 11 411 347 HOH HOH . G 6 HOH A 12 412 408 HOH HOH . G 6 HOH A 13 413 380 HOH HOH . G 6 HOH A 14 414 356 HOH HOH . G 6 HOH A 15 415 405 HOH HOH . G 6 HOH A 16 416 398 HOH HOH . G 6 HOH A 17 417 422 HOH HOH . G 6 HOH A 18 418 397 HOH HOH . G 6 HOH A 19 419 367 HOH HOH . G 6 HOH A 20 420 338 HOH HOH . G 6 HOH A 21 421 358 HOH HOH . G 6 HOH A 22 422 330 HOH HOH . G 6 HOH A 23 423 424 HOH HOH . G 6 HOH A 24 424 360 HOH HOH . G 6 HOH A 25 425 382 HOH HOH . G 6 HOH A 26 426 423 HOH HOH . G 6 HOH A 27 427 378 HOH HOH . G 6 HOH A 28 428 381 HOH HOH . G 6 HOH A 29 429 353 HOH HOH . G 6 HOH A 30 430 371 HOH HOH . G 6 HOH A 31 431 346 HOH HOH . G 6 HOH A 32 432 326 HOH HOH . G 6 HOH A 33 433 335 HOH HOH . G 6 HOH A 34 434 379 HOH HOH . G 6 HOH A 35 435 341 HOH HOH . G 6 HOH A 36 436 325 HOH HOH . G 6 HOH A 37 437 322 HOH HOH . G 6 HOH A 38 438 421 HOH HOH . G 6 HOH A 39 439 416 HOH HOH . G 6 HOH A 40 440 388 HOH HOH . G 6 HOH A 41 441 350 HOH HOH . G 6 HOH A 42 442 364 HOH HOH . G 6 HOH A 43 443 375 HOH HOH . G 6 HOH A 44 444 323 HOH HOH . G 6 HOH A 45 445 355 HOH HOH . G 6 HOH A 46 446 383 HOH HOH . G 6 HOH A 47 447 409 HOH HOH . G 6 HOH A 48 448 328 HOH HOH . G 6 HOH A 49 449 357 HOH HOH . G 6 HOH A 50 450 336 HOH HOH . G 6 HOH A 51 451 399 HOH HOH . G 6 HOH A 52 452 334 HOH HOH . G 6 HOH A 53 453 333 HOH HOH . G 6 HOH A 54 454 349 HOH HOH . G 6 HOH A 55 455 400 HOH HOH . G 6 HOH A 56 456 329 HOH HOH . G 6 HOH A 57 457 361 HOH HOH . G 6 HOH A 58 458 344 HOH HOH . G 6 HOH A 59 459 407 HOH HOH . G 6 HOH A 60 460 348 HOH HOH . G 6 HOH A 61 461 376 HOH HOH . G 6 HOH A 62 462 413 HOH HOH . G 6 HOH A 63 463 354 HOH HOH . G 6 HOH A 64 464 332 HOH HOH . G 6 HOH A 65 465 365 HOH HOH . G 6 HOH A 66 466 363 HOH HOH . G 6 HOH A 67 467 331 HOH HOH . G 6 HOH A 68 468 369 HOH HOH . G 6 HOH A 69 469 324 HOH HOH . G 6 HOH A 70 470 393 HOH HOH . G 6 HOH A 71 471 411 HOH HOH . G 6 HOH A 72 472 321 HOH HOH . G 6 HOH A 73 473 392 HOH HOH . G 6 HOH A 74 474 387 HOH HOH . G 6 HOH A 75 475 401 HOH HOH . G 6 HOH A 76 476 417 HOH HOH . G 6 HOH A 77 477 390 HOH HOH . G 6 HOH A 78 478 362 HOH HOH . G 6 HOH A 79 479 386 HOH HOH . G 6 HOH A 80 480 415 HOH HOH . G 6 HOH A 81 481 394 HOH HOH . G 6 HOH A 82 482 404 HOH HOH . G 6 HOH A 83 483 414 HOH HOH . G 6 HOH A 84 484 418 HOH HOH . G 6 HOH A 85 485 396 HOH HOH . G 6 HOH A 86 486 389 HOH HOH . G 6 HOH A 87 487 351 HOH HOH . G 6 HOH A 88 488 391 HOH HOH . H 6 HOH B 1 301 340 HOH HOH . H 6 HOH B 2 302 342 HOH HOH . H 6 HOH B 3 303 402 HOH HOH . H 6 HOH B 4 304 345 HOH HOH . H 6 HOH B 5 305 337 HOH HOH . H 6 HOH B 6 306 410 HOH HOH . H 6 HOH B 7 307 359 HOH HOH . H 6 HOH B 8 308 406 HOH HOH . H 6 HOH B 9 309 412 HOH HOH . H 6 HOH B 10 310 385 HOH HOH . H 6 HOH B 11 311 327 HOH HOH . H 6 HOH B 12 312 343 HOH HOH . H 6 HOH B 13 313 403 HOH HOH . H 6 HOH B 14 314 372 HOH HOH . H 6 HOH B 15 315 370 HOH HOH . H 6 HOH B 16 316 366 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 C C10 A1H4D . . . D 4 87.712 -20.441 34.542 1 86.28 ? C10 A1H4D 302 A 1 HETATM 2 C C13 A1H4D . . . D 4 88.493 -18.066 35.112 1 97.84 ? C13 A1H4D 302 A 1 HETATM 3 C C14 A1H4D . . . D 4 88.648 -16.701 34.791 1 103.75 ? C14 A1H4D 302 A 1 HETATM 4 C C16 A1H4D . . . D 4 89.017 -14.445 35.882 1 106.25 ? C16 A1H4D 302 A 1 HETATM 5 C C17 A1H4D . . . D 4 89.862 -14.017 36.899 1 108.19 ? C17 A1H4D 302 A 1 HETATM 6 C C19 A1H4D . . . D 4 90.241 -16.059 36.653 1 109.63 ? C19 A1H4D 302 A 1 HETATM 7 C C3' A1H4D . . . D 4 86.182 -14.525 28.924 1 58.68 ? C3' A1H4D 302 A 1 HETATM 8 C C20 A1H4D . . . D 4 88.18 -16.252 33.542 1 101.64 ? C20 A1H4D 302 A 1 HETATM 9 C C1' A1H4D . . . D 4 83.94 -13.727 28.871 1 58.6 ? C1' A1H4D 302 A 1 HETATM 10 C C4 A1H4D . . . D 4 81.86 -12.177 29.07 1 54.47 ? C4 A1H4D 302 A 1 HETATM 11 C C2 A1H4D . . . D 4 80.883 -10.662 27.749 1 54.93 ? C2 A1H4D 302 A 1 HETATM 12 C C6 A1H4D . . . D 4 79.885 -10.974 29.824 1 56.02 ? C6 A1H4D 302 A 1 HETATM 13 C C4' A1H4D . . . D 4 85.204 -15.611 28.427 1 57.08 ? C4' A1H4D 302 A 1 HETATM 14 C C5 A1H4D . . . D 4 80.912 -11.95 30.071 1 55.46 ? C5 A1H4D 302 A 1 HETATM 15 C C8 A1H4D . . . D 4 82.238 -13.428 30.804 1 55.31 ? C8 A1H4D 302 A 1 HETATM 16 C C2' A1H4D . . . D 4 85.296 -13.444 29.551 1 60.65 ? C2' A1H4D 302 A 1 HETATM 17 C C5' A1H4D . . . D 4 85.411 -17.005 29.048 1 61.98 ? C5' A1H4D 302 A 1 HETATM 18 C C3 A1H4D . . . D 4 87.075 -16.664 31.288 1 81.22 ? C3 A1H4D 302 A 1 HETATM 19 C C7 A1H4D . . . D 4 87.572 -17.143 32.64 1 91.8 ? C7 A1H4D 302 A 1 HETATM 20 C C1 A1H4D . . . D 4 87.431 -18.492 32.973 1 85.49 ? C1 A1H4D 302 A 1 HETATM 21 C C9 A1H4D . . . D 4 87.885 -18.978 34.214 1 89.78 ? C9 A1H4D 302 A 1 HETATM 22 N N15 A1H4D . . . D 4 89.26 -15.797 35.709 1 107.95 ? N15 A1H4D 302 A 1 HETATM 23 N N18 A1H4D . . . D 4 90.605 -15.01 37.362 1 112.87 ? N18 A1H4D 302 A 1 HETATM 24 N N9 A1H4D . . . D 4 82.706 -13.146 29.564 1 58.12 ? N9 A1H4D 302 A 1 HETATM 25 N N3 A1H4D . . . D 4 81.895 -11.549 27.863 1 52.45 ? N3 A1H4D 302 A 1 HETATM 26 N N1 A1H4D . . . D 4 79.889 -10.334 28.612 1 51.34 ? N1 A1H4D 302 A 1 HETATM 27 N N6 A1H4D . . . D 4 78.87 -10.649 30.737 1 54.59 ? N6 A1H4D 302 A 1 HETATM 28 N N7 A1H4D . . . D 4 81.163 -12.74 31.136 1 57.82 ? N7 A1H4D 302 A 1 HETATM 29 O O3' A1H4D . . . D 4 87.096 -14.035 27.958 1 61.04 ? O3' A1H4D 302 A 1 HETATM 30 O O11 A1H4D . . . D 4 87.806 -20.803 35.744 1 85.56 ? O11 A1H4D 302 A 1 HETATM 31 O O12 A1H4D . . . D 4 87.454 -21.219 33.583 1 85.57 ? O12 A1H4D 302 A 1 HETATM 32 O O4' A1H4D . . . D 4 83.911 -15.125 28.805 1 58.5 ? O4' A1H4D 302 A 1 HETATM 33 O O2' A1H4D . . . D 4 85.72 -12.105 29.318 1 63.96 ? O2' A1H4D 302 A 1 HETATM 34 S S1 A1H4D . . . D 4 85.348 -17.096 30.868 1 75.83 ? S1 A1H4D 302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #