data_6VG9 # _model_server_result.job_id FJ52s0wJ1HcPvVEdHfqsFg _model_server_result.datetime_utc '2024-11-16 06:44:49' _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 6vg9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 6VG9 # _exptl.entry_id 6VG9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.502 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'benzyl [2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate' _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 6VG9 _cell.length_a 90.571 _cell.length_b 90.571 _cell.length_c 133.829 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VG9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _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,E,F,G _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 E _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 A NE2 HIS 61 A HIS 41 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc2 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc4 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc6 B MN MN . A MN 201 1_555 E O01 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc7 B MN MN . A MN 201 1_555 E O02 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.743 ? metalc ? metalc8 C MN MN . A MN 202 1_555 E O03 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc9 C MN MN . A MN 202 1_555 E O02 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc10 C MN MN . A MN 202 1_555 G O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? # _chem_comp.formula 'C23 H25 N9 O5' _chem_comp.formula_weight 507.502 _chem_comp.id QVV _chem_comp.mon_nstd_flag . _chem_comp.name 'benzyl [2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms SJ000988248 # 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 O01 C01 QVV doub 386 n n O02 C02 QVV sing 387 n n C01 C02 QVV sing 388 n n C01 N01 QVV sing 389 n n C02 C03 QVV doub 390 n n N01 C07 QVV sing 391 n n C16 C15 QVV sing 392 n n O03 C04 QVV doub 393 n n C03 C04 QVV sing 394 n n C03 N03 QVV sing 395 n n C07 N03 QVV doub 396 n n C07 C15 QVV sing 397 n n C04 N02 QVV sing 398 n n C15 C17 QVV sing 399 n n C15 N04 QVV sing 400 n n N02 C05 QVV sing 401 n n C05 C06 QVV sing 402 n n C06 N05 QVV sing 403 n n N05 C18 QVV sing 404 n y N05 C19 QVV sing 405 n y C18 N06 QVV doub 406 n y C19 N07 QVV doub 407 n y C19 C20 QVV sing 408 n y N06 C20 QVV sing 409 n y N07 C22 QVV sing 410 n y C20 C21 QVV doub 411 n y C22 N09 QVV doub 412 n y C21 N09 QVV sing 413 n y C21 N08 QVV sing 414 n n C17 H1 QVV sing 415 n n C17 H2 QVV sing 416 n n C17 H3 QVV sing 417 n n C16 H4 QVV sing 418 n n C16 H5 QVV sing 419 n n C16 H6 QVV sing 420 n n C22 H7 QVV sing 421 n n C05 H8 QVV sing 422 n n C05 H9 QVV sing 423 n n C06 H10 QVV sing 424 n n C06 H11 QVV sing 425 n n C18 H12 QVV sing 426 n n N01 H13 QVV sing 427 n n N02 H14 QVV sing 428 n n N04 H15 QVV sing 429 n n N08 H18 QVV sing 430 n n N08 H19 QVV sing 431 n n O02 H20 QVV sing 432 n n N04 C1 QVV sing 433 n n C1 O1 QVV sing 434 n n O1 C3 QVV sing 435 n n C3 C4 QVV sing 436 n n C1 O2 QVV doub 437 n n C4 C2 QVV sing 438 n y C2 C5 QVV doub 439 n y C5 C6 QVV sing 440 n y C6 C7 QVV doub 441 n y C7 C8 QVV sing 442 n y C8 C4 QVV doub 443 n y C3 H16 QVV sing 444 n n C3 H17 QVV sing 445 n n C2 H21 QVV sing 446 n n C5 H22 QVV sing 447 n n C6 H23 QVV sing 448 n n C7 H24 QVV sing 449 n n C8 H25 QVV sing 450 n n # _atom_sites.entry_id 6VG9 _atom_sites.fract_transf_matrix[1][1] 0.011041 _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] 0.011041 _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] 0.007472 _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 MN A 1 201 201 MN MN . C 2 MN A 1 202 202 MN MN . D 3 QQ4 A 1 203 401 QQ4 PVP . E 4 QVV A 1 204 501 QVV 248 . F 5 SO4 A 1 205 1 SO4 SO4 . G 6 HOH A 1 301 9 HOH HOH . G 6 HOH A 2 302 27 HOH HOH . G 6 HOH A 3 303 8 HOH HOH . G 6 HOH A 4 304 7 HOH HOH . G 6 HOH A 5 305 17 HOH HOH . G 6 HOH A 6 306 22 HOH HOH . G 6 HOH A 7 307 19 HOH HOH . G 6 HOH A 8 308 5 HOH HOH . G 6 HOH A 9 309 29 HOH HOH . G 6 HOH A 10 310 13 HOH HOH . G 6 HOH A 11 311 23 HOH HOH . G 6 HOH A 12 312 21 HOH HOH . G 6 HOH A 13 313 24 HOH HOH . G 6 HOH A 14 314 12 HOH HOH . G 6 HOH A 15 315 16 HOH HOH . G 6 HOH A 16 316 14 HOH HOH . G 6 HOH A 17 317 30 HOH HOH . G 6 HOH A 18 318 15 HOH HOH . G 6 HOH A 19 319 1 HOH HOH . G 6 HOH A 20 320 25 HOH HOH . G 6 HOH A 21 321 26 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 C17 QVV . . . E 4 38.532 13.221 14.122 1 88.76 ? C17 QVV 204 A 1 HETATM 2 C C16 QVV . . . E 4 36.625 14.053 15.463 1 79.8 ? C16 QVV 204 A 1 HETATM 3 C C15 QVV . . . E 4 37.98 13.349 15.531 1 86.68 ? C15 QVV 204 A 1 HETATM 4 C C22 QVV . . . E 4 41.371 13.654 11.046 1 105.65 ? C22 QVV 204 A 1 HETATM 5 C C19 QVV . . . E 4 42.837 12.79 12.469 1 105.61 ? C19 QVV 204 A 1 HETATM 6 C C20 QVV . . . E 4 42.207 11.519 12.365 1 107.5 ? C20 QVV 204 A 1 HETATM 7 C C21 QVV . . . E 4 41.11 11.439 11.537 1 103.61 ? C21 QVV 204 A 1 HETATM 8 C C01 QVV . . . E 4 39.226 15.739 18.098 1 77.82 ? C01 QVV 204 A 1 HETATM 9 C C02 QVV . . . E 4 40.665 15.716 17.831 1 79.07 ? C02 QVV 204 A 1 HETATM 10 C C03 QVV . . . E 4 41.183 14.906 16.782 1 85.01 ? C03 QVV 204 A 1 HETATM 11 C C04 QVV . . . E 4 42.677 14.861 16.48 1 85 ? C04 QVV 204 A 1 HETATM 12 C C05 QVV . . . E 4 44.598 14.02 15.194 1 95.67 ? C05 QVV 204 A 1 HETATM 13 C C06 QVV . . . E 4 44.811 13.582 13.746 1 106.07 ? C06 QVV 204 A 1 HETATM 14 C C07 QVV . . . E 4 38.957 14.184 16.305 1 89.19 ? C07 QVV 204 A 1 HETATM 15 C C18 QVV . . . E 4 43.936 11.31 13.764 1 105.54 ? C18 QVV 204 A 1 HETATM 16 N N01 QVV . . . E 4 38.403 14.97 17.342 1 89.13 ? N01 QVV 204 A 1 HETATM 17 N N02 QVV . . . E 4 43.177 14.035 15.432 1 94.41 ? N02 QVV 204 A 1 HETATM 18 N N03 QVV . . . E 4 40.303 14.121 16.015 1 89.83 ? N03 QVV 204 A 1 HETATM 19 N N04 QVV . . . E 4 37.956 12.095 16.283 1 74.78 ? N04 QVV 204 A 1 HETATM 20 N N05 QVV . . . E 4 43.855 12.563 13.327 1 103.93 ? N05 QVV 204 A 1 HETATM 21 N N06 QVV . . . E 4 42.94 10.575 13.223 1 108.98 ? N06 QVV 204 A 1 HETATM 22 N N07 QVV . . . E 4 42.455 13.899 11.83 1 107.94 ? N07 QVV 204 A 1 HETATM 23 N N08 QVV . . . E 4 40.364 10.211 11.35 1 100.07 ? N08 QVV 204 A 1 HETATM 24 N N09 QVV . . . E 4 40.691 12.494 10.873 1 103.69 ? N09 QVV 204 A 1 HETATM 25 O O01 QVV . . . E 4 38.683 16.543 19.103 1 77.83 ? O01 QVV 204 A 1 HETATM 26 O O02 QVV . . . E 4 41.481 16.523 18.637 1 79.34 ? O02 QVV 204 A 1 HETATM 27 O O03 QVV . . . E 4 43.457 15.491 17.089 1 81.84 ? O03 QVV 204 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #