data_8RV4 # _model_server_result.job_id yghJP4k7FVyClqFz2rtEoA _model_server_result.datetime_utc '2024-11-22 06:12:18' _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 8rv4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 8RV4 # _exptl.entry_id 8RV4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 493.535 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-phenyl-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 8RV4 _cell.length_a 168.545 _cell.length_b 168.545 _cell.length_c 52.174 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RV4 _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 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc2 B SG CYS 80 B CYS 77 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 B NE2 HIS 86 B HIS 83 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc4 B SG CYS 93 B CYS 90 1_555 E ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc5 B SG CYS 120 B CYS 117 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc6 B SG CYS 123 B CYS 120 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc7 B SG CYS 131 B CYS 128 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc8 B SG CYS 133 B CYS 130 1_555 F ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? # _chem_comp.formula 'C24 H23 N5 O5 S' _chem_comp.formula_weight 493.535 _chem_comp.id A1H3C _chem_comp.mon_nstd_flag . _chem_comp.name '5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-phenyl-benzoic acid' _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 C1 C2 A1H3C sing 1 n n C1 C5 A1H3C sing 2 n n O7 C1 A1H3C sing 3 n n C2 C3 A1H3C sing 4 n n O6 C2 A1H3C sing 5 n n O4 C3 A1H3C sing 6 n n C3 C9 A1H3C sing 7 n n C5 O4 A1H3C sing 8 n n N8 C5 A1H3C sing 9 n n C11 N8 A1H3C sing 10 n y C14 N8 A1H3C sing 11 n y C9 S10 A1H3C sing 12 n n S10 C20 A1H3C sing 13 n n C11 C12 A1H3C doub 14 n y N15 C11 A1H3C sing 15 n y C12 N13 A1H3C sing 16 n y C12 C18 A1H3C sing 17 n y N13 C14 A1H3C doub 18 n y C16 N15 A1H3C doub 19 n y N17 C16 A1H3C sing 20 n y C18 N17 A1H3C doub 21 n y N19 C18 A1H3C sing 22 n n C20 C21 A1H3C sing 23 n n C21 C22 A1H3C doub 24 n y C21 C26 A1H3C sing 25 n y C22 C23 A1H3C sing 26 n y C23 C24 A1H3C doub 27 n y C24 C25 A1H3C sing 28 n y C30 C24 A1H3C sing 29 n n C26 C25 A1H3C doub 30 n y C25 C27 A1H3C sing 31 n n O28 C27 A1H3C sing 32 n n C27 O29 A1H3C doub 33 n n C30 C31 A1H3C doub 34 n y C35 C30 A1H3C sing 35 n y C31 C32 A1H3C sing 36 n y C32 C33 A1H3C doub 37 n y C33 C34 A1H3C sing 38 n y C34 C35 A1H3C doub 39 n y C1 H36 A1H3C sing 40 n n C14 H44 A1H3C sing 41 n n C16 H45 A1H3C sing 42 n n C2 H37 A1H3C sing 43 n n C20 H48 A1H3C sing 44 n n C20 H49 A1H3C sing 45 n n C22 H50 A1H3C sing 46 n n C23 H51 A1H3C sing 47 n n C26 H52 A1H3C sing 48 n n C3 H38 A1H3C sing 49 n n C31 H53 A1H3C sing 50 n n C32 H54 A1H3C sing 51 n n C33 H55 A1H3C sing 52 n n C34 H56 A1H3C sing 53 n n C35 H57 A1H3C sing 54 n n C5 H39 A1H3C sing 55 n n C9 H43 A1H3C sing 56 n n C9 H42 A1H3C sing 57 n n N19 H47 A1H3C sing 58 n n N19 H46 A1H3C sing 59 n n O28 H1 A1H3C sing 60 n n O6 H40 A1H3C sing 61 n n O7 H41 A1H3C sing 62 n n # _atom_sites.entry_id 8RV4 _atom_sites.fract_transf_matrix[1][1] 0.005933 _atom_sites.fract_transf_matrix[1][2] 0.003425 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006851 _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] 0.019167 _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 1 301 301 MES MES . D 4 A1H3C A 1 302 303 A1H3C OBV . E 5 ZN B 1 201 201 ZN ZN . F 5 ZN B 1 202 202 ZN ZN . G 6 HOH A 1 401 394 HOH HOH . G 6 HOH A 2 402 358 HOH HOH . G 6 HOH A 3 403 355 HOH HOH . G 6 HOH A 4 404 368 HOH HOH . G 6 HOH A 5 405 320 HOH HOH . G 6 HOH A 6 406 354 HOH HOH . G 6 HOH A 7 407 321 HOH HOH . G 6 HOH A 8 408 319 HOH HOH . G 6 HOH A 9 409 338 HOH HOH . G 6 HOH A 10 410 343 HOH HOH . G 6 HOH A 11 411 353 HOH HOH . G 6 HOH A 12 412 357 HOH HOH . G 6 HOH A 13 413 332 HOH HOH . G 6 HOH A 14 414 315 HOH HOH . G 6 HOH A 15 415 318 HOH HOH . G 6 HOH A 16 416 348 HOH HOH . G 6 HOH A 17 417 314 HOH HOH . G 6 HOH A 18 418 381 HOH HOH . G 6 HOH A 19 419 342 HOH HOH . G 6 HOH A 20 420 328 HOH HOH . G 6 HOH A 21 421 356 HOH HOH . G 6 HOH A 22 422 341 HOH HOH . G 6 HOH A 23 423 366 HOH HOH . G 6 HOH A 24 424 378 HOH HOH . G 6 HOH A 25 425 367 HOH HOH . G 6 HOH A 26 426 380 HOH HOH . G 6 HOH A 27 427 388 HOH HOH . G 6 HOH A 28 428 370 HOH HOH . G 6 HOH A 29 429 393 HOH HOH . G 6 HOH A 30 430 362 HOH HOH . G 6 HOH A 31 431 329 HOH HOH . G 6 HOH A 32 432 326 HOH HOH . G 6 HOH A 33 433 323 HOH HOH . G 6 HOH A 34 434 390 HOH HOH . G 6 HOH A 35 435 331 HOH HOH . G 6 HOH A 36 436 335 HOH HOH . G 6 HOH A 37 437 364 HOH HOH . G 6 HOH A 38 438 372 HOH HOH . G 6 HOH A 39 439 359 HOH HOH . G 6 HOH A 40 440 313 HOH HOH . G 6 HOH A 41 441 336 HOH HOH . G 6 HOH A 42 442 371 HOH HOH . G 6 HOH A 43 443 346 HOH HOH . G 6 HOH A 44 444 361 HOH HOH . G 6 HOH A 45 445 396 HOH HOH . G 6 HOH A 46 446 363 HOH HOH . G 6 HOH A 47 447 384 HOH HOH . G 6 HOH A 48 448 386 HOH HOH . G 6 HOH A 49 449 325 HOH HOH . G 6 HOH A 50 450 334 HOH HOH . G 6 HOH A 51 451 327 HOH HOH . G 6 HOH A 52 452 387 HOH HOH . G 6 HOH A 53 453 352 HOH HOH . G 6 HOH A 54 454 322 HOH HOH . G 6 HOH A 55 455 312 HOH HOH . G 6 HOH A 56 456 339 HOH HOH . G 6 HOH A 57 457 376 HOH HOH . G 6 HOH A 58 458 333 HOH HOH . G 6 HOH A 59 459 373 HOH HOH . G 6 HOH A 60 460 369 HOH HOH . G 6 HOH A 61 461 385 HOH HOH . G 6 HOH A 62 462 392 HOH HOH . G 6 HOH A 63 463 345 HOH HOH . G 6 HOH A 64 464 389 HOH HOH . G 6 HOH A 65 465 379 HOH HOH . G 6 HOH A 66 466 395 HOH HOH . G 6 HOH A 67 467 391 HOH HOH . G 6 HOH A 68 468 360 HOH HOH . G 6 HOH A 69 469 377 HOH HOH . H 6 HOH B 1 301 316 HOH HOH . H 6 HOH B 2 302 382 HOH HOH . H 6 HOH B 3 303 324 HOH HOH . H 6 HOH B 4 304 317 HOH HOH . H 6 HOH B 5 305 375 HOH HOH . H 6 HOH B 6 306 383 HOH HOH . H 6 HOH B 7 307 344 HOH HOH . H 6 HOH B 8 308 350 HOH HOH . H 6 HOH B 9 309 365 HOH HOH . H 6 HOH B 10 310 330 HOH HOH . H 6 HOH B 11 311 349 HOH HOH . H 6 HOH B 12 312 337 HOH HOH . H 6 HOH B 13 313 374 HOH HOH . H 6 HOH B 14 314 340 HOH HOH . H 6 HOH B 15 315 347 HOH HOH . H 6 HOH B 16 316 351 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 C1 A1H3C . . . D 4 85.298 -13.418 29.607 1 61.96 ? C1 A1H3C 302 A 1 HETATM 2 C C11 A1H3C . . . D 4 81.891 -12.237 29.043 1 54.65 ? C11 A1H3C 302 A 1 HETATM 3 C C12 A1H3C . . . D 4 80.893 -11.977 30.026 1 53.53 ? C12 A1H3C 302 A 1 HETATM 4 C C14 A1H3C . . . D 4 82.236 -13.42 30.857 1 53.19 ? C14 A1H3C 302 A 1 HETATM 5 C C16 A1H3C . . . D 4 80.96 -10.791 27.602 1 51.08 ? C16 A1H3C 302 A 1 HETATM 6 C C18 A1H3C . . . D 4 79.887 -11.031 29.658 1 55.72 ? C18 A1H3C 302 A 1 HETATM 7 C C2 A1H3C . . . D 4 86.173 -14.558 29.052 1 60.04 ? C2 A1H3C 302 A 1 HETATM 8 C C20 A1H3C . . . D 4 86.911 -17.075 31.264 1 85.31 ? C20 A1H3C 302 A 1 HETATM 9 C C21 A1H3C . . . D 4 87.436 -18.253 32.08 1 95.53 ? C21 A1H3C 302 A 1 HETATM 10 C C22 A1H3C . . . D 4 86.64 -18.821 33.079 1 94.87 ? C22 A1H3C 302 A 1 HETATM 11 C C23 A1H3C . . . D 4 87.086 -19.908 33.858 1 95.56 ? C23 A1H3C 302 A 1 HETATM 12 C C24 A1H3C . . . D 4 88.358 -20.487 33.681 1 108.42 ? C24 A1H3C 302 A 1 HETATM 13 C C25 A1H3C . . . D 4 89.19 -19.896 32.65 1 115.36 ? C25 A1H3C 302 A 1 HETATM 14 C C26 A1H3C . . . D 4 88.715 -18.801 31.879 1 108.55 ? C26 A1H3C 302 A 1 HETATM 15 C C27 A1H3C . . . D 4 90.587 -20.331 32.266 1 114.61 ? C27 A1H3C 302 A 1 HETATM 16 C C3 A1H3C . . . D 4 85.151 -15.552 28.457 1 58.75 ? C3 A1H3C 302 A 1 HETATM 17 C C30 A1H3C . . . D 4 88.67 -21.629 34.599 1 111.87 ? C30 A1H3C 302 A 1 HETATM 18 C C31 A1H3C . . . D 4 89.29 -22.827 34.166 1 110.02 ? C31 A1H3C 302 A 1 HETATM 19 C C32 A1H3C . . . D 4 89.571 -23.889 35.056 1 109.33 ? C32 A1H3C 302 A 1 HETATM 20 C C33 A1H3C . . . D 4 89.227 -23.784 36.417 1 113.66 ? C33 A1H3C 302 A 1 HETATM 21 C C34 A1H3C . . . D 4 88.604 -22.61 36.876 1 117.92 ? C34 A1H3C 302 A 1 HETATM 22 C C35 A1H3C . . . D 4 88.328 -21.549 35.978 1 113.37 ? C35 A1H3C 302 A 1 HETATM 23 C C5 A1H3C . . . D 4 83.959 -13.707 28.907 1 57.69 ? C5 A1H3C 302 A 1 HETATM 24 C C9 A1H3C . . . D 4 85.382 -17.003 28.894 1 60.47 ? C9 A1H3C 302 A 1 HETATM 25 N N13 A1H3C . . . D 4 81.146 -12.748 31.152 1 57.43 ? N13 A1H3C 302 A 1 HETATM 26 N N15 A1H3C . . . D 4 81.966 -11.653 27.802 1 52.34 ? N15 A1H3C 302 A 1 HETATM 27 N N17 A1H3C . . . D 4 79.954 -10.457 28.424 1 51.45 ? N17 A1H3C 302 A 1 HETATM 28 N N19 A1H3C . . . D 4 78.879 -10.684 30.474 1 52.75 ? N19 A1H3C 302 A 1 HETATM 29 N N8 A1H3C . . . D 4 82.752 -13.16 29.603 1 56.13 ? N8 A1H3C 302 A 1 HETATM 30 O O28 A1H3C . . . D 4 91.584 -19.687 32.683 1 110.05 ? O28 A1H3C 302 A 1 HETATM 31 O O29 A1H3C . . . D 4 90.709 -21.319 31.498 1 113.11 ? O29 A1H3C 302 A 1 HETATM 32 O O4 A1H3C . . . D 4 83.884 -15.088 28.92 1 58.08 ? O4 A1H3C 302 A 1 HETATM 33 O O6 A1H3C . . . D 4 87.091 -14.154 28.047 1 60.31 ? O6 A1H3C 302 A 1 HETATM 34 O O7 A1H3C . . . D 4 85.835 -12.126 29.374 1 60.08 ? O7 A1H3C 302 A 1 HETATM 35 S S10 A1H3C . . . D 4 85.195 -17.173 30.69 1 70.95 ? S10 A1H3C 302 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #