data_6V53 # _model_server_result.job_id O_j0EY5hVBkpdXf6UfUApA _model_server_result.datetime_utc '2024-11-28 13:22:40' _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 6v53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6V53 # _exptl.entry_id 6V53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 519.513 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate' _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 6V53 _cell.length_a 89.731 _cell.length_b 89.731 _cell.length_c 132.135 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V53 _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 ? _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,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 2 _struct_asym.id B _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 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc2 A OE1 GLU 81 A GLU 61 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc3 A OD2 ASP 109 A ASP 89 1_555 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc4 A OD1 ASP 109 A ASP 89 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc5 A OE2 GLU 120 A GLU 100 1_555 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 A O ILE 121 A ILE 101 1_555 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc7 B O1 QPY . A QPY 201 1_555 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc8 B O2 QPY . A QPY 201 1_555 D MN MN . A MN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc9 B O2 QPY . A QPY 201 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc10 B O3 QPY . A QPY 201 1_555 E MN MN . A MN 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc11 E MN MN . A MN 204 1_555 H O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc12 E MN MN . A MN 204 1_555 H O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? # _chem_comp.formula 'C24 H25 N9 O5' _chem_comp.formula_weight 519.513 _chem_comp.id QPY _chem_comp.mon_nstd_flag . _chem_comp.name 'benzyl (2S)-2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)pyrrolidine-1-carboxylate' _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 N6 C10 QPY doub 277 n y N6 C11 QPY sing 278 n y N7 C11 QPY sing 279 n n C10 N5 QPY sing 280 n y C11 C8 QPY doub 281 n y N5 C9 QPY doub 282 n y C8 C9 QPY sing 283 n y C8 N4 QPY sing 284 n y C9 N3 QPY sing 285 n y N4 C7 QPY doub 286 n y N3 C7 QPY sing 287 n y N3 C6 QPY sing 288 n n C19 C20 QPY doub 289 n y C19 C18 QPY sing 290 n y C20 C21 QPY sing 291 n y C18 C17 QPY doub 292 n y C6 C5 QPY sing 293 n n O5 C14 QPY doub 294 n n C17 C16 QPY sing 295 n y C21 C16 QPY doub 296 n y O4 C14 QPY sing 297 n n O4 C15 QPY sing 298 n n C16 C15 QPY sing 299 n n C14 N9 QPY sing 300 n n C5 N2 QPY sing 301 n n N2 C4 QPY sing 302 n n N9 C22 QPY sing 303 n n N9 C13 QPY sing 304 n n C22 C23 QPY sing 305 n n C4 O3 QPY doub 306 n n C4 C3 QPY sing 307 n n N8 C3 QPY sing 308 n n N8 C12 QPY doub 309 n n C3 C2 QPY doub 310 n n C13 C12 QPY sing 311 n n C13 C24 QPY sing 312 n n C12 N1 QPY sing 313 n n C2 O2 QPY sing 314 n n C2 C1 QPY sing 315 n n C23 C24 QPY sing 316 n n N1 C1 QPY sing 317 n n C1 O1 QPY doub 318 n n C15 H1 QPY sing 319 n n C15 H2 QPY sing 320 n n C17 H3 QPY sing 321 n n C10 H4 QPY sing 322 n n C13 H5 QPY sing 323 n n C18 H6 QPY sing 324 n n C19 H7 QPY sing 325 n n C20 H8 QPY sing 326 n n C21 H9 QPY sing 327 n n C22 H10 QPY sing 328 n n C22 H11 QPY sing 329 n n C23 H12 QPY sing 330 n n C23 H13 QPY sing 331 n n C24 H14 QPY sing 332 n n C24 H15 QPY sing 333 n n C5 H16 QPY sing 334 n n C5 H17 QPY sing 335 n n C6 H18 QPY sing 336 n n C6 H19 QPY sing 337 n n C7 H20 QPY sing 338 n n N1 H21 QPY sing 339 n n N2 H22 QPY sing 340 n n N7 H23 QPY sing 341 n n N7 H24 QPY sing 342 n n O2 H25 QPY sing 343 n n # _atom_sites.entry_id 6V53 _atom_sites.fract_transf_matrix[1][1] 0.011144 _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] 0.011144 _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] 0.007568 _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 QPY A 1 201 181 QPY 494 . C 3 QQ4 A 1 202 201 QQ4 PVP . D 4 MN A 1 203 1 MN MN . E 4 MN A 1 204 2 MN MN . F 5 SO4 A 1 205 1 SO4 SO4 . G 5 SO4 A 1 206 2 SO4 SO4 . H 6 HOH A 1 301 9 HOH HOH . H 6 HOH A 2 302 2 HOH HOH . H 6 HOH A 3 303 14 HOH HOH . H 6 HOH A 4 304 39 HOH HOH . H 6 HOH A 5 305 15 HOH HOH . H 6 HOH A 6 306 11 HOH HOH . H 6 HOH A 7 307 7 HOH HOH . H 6 HOH A 8 308 3 HOH HOH . H 6 HOH A 9 309 57 HOH HOH . H 6 HOH A 10 310 25 HOH HOH . H 6 HOH A 11 311 16 HOH HOH . H 6 HOH A 12 312 8 HOH HOH . H 6 HOH A 13 313 35 HOH HOH . H 6 HOH A 14 314 4 HOH HOH . H 6 HOH A 15 315 5 HOH HOH . H 6 HOH A 16 316 13 HOH HOH . H 6 HOH A 17 317 42 HOH HOH . H 6 HOH A 18 318 47 HOH HOH . H 6 HOH A 19 319 51 HOH HOH . H 6 HOH A 20 320 1 HOH HOH . H 6 HOH A 21 321 10 HOH HOH . H 6 HOH A 22 322 22 HOH HOH . H 6 HOH A 23 323 6 HOH HOH . H 6 HOH A 24 324 38 HOH HOH . H 6 HOH A 25 325 48 HOH HOH . H 6 HOH A 26 326 55 HOH HOH . H 6 HOH A 27 327 58 HOH HOH . H 6 HOH A 28 328 34 HOH HOH . H 6 HOH A 29 329 27 HOH HOH . H 6 HOH A 30 330 17 HOH HOH . H 6 HOH A 31 331 18 HOH HOH . H 6 HOH A 32 332 24 HOH HOH . H 6 HOH A 33 333 12 HOH HOH . H 6 HOH A 34 334 36 HOH HOH . H 6 HOH A 35 335 31 HOH HOH . H 6 HOH A 36 336 32 HOH HOH . H 6 HOH A 37 337 29 HOH HOH . H 6 HOH A 38 338 43 HOH HOH . H 6 HOH A 39 339 23 HOH HOH . H 6 HOH A 40 340 19 HOH HOH . H 6 HOH A 41 341 56 HOH HOH . H 6 HOH A 42 342 49 HOH HOH . H 6 HOH A 43 343 30 HOH HOH . H 6 HOH A 44 344 37 HOH HOH . H 6 HOH A 45 345 26 HOH HOH . H 6 HOH A 46 346 40 HOH HOH . H 6 HOH A 47 347 28 HOH HOH . H 6 HOH A 48 348 45 HOH HOH . H 6 HOH A 49 349 46 HOH HOH . H 6 HOH A 50 350 44 HOH HOH . H 6 HOH A 51 351 41 HOH HOH . H 6 HOH A 52 352 21 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 C15 QPY . . . B 2 -6.745 -32.301 14.585 1 114.56 ? C15 QPY 201 A 1 HETATM 2 C C17 QPY . . . B 2 -5.875 -29.836 14.969 1 93.71 ? C17 QPY 201 A 1 HETATM 3 C C1 QPY . . . B 2 -4.952 -29.802 18.15 1 81.21 ? C1 QPY 201 A 1 HETATM 4 C C10 QPY . . . B 2 -3.454 -30.594 10.842 1 115.2 ? C10 QPY 201 A 1 HETATM 5 C C11 QPY . . . B 2 -3.81 -32.908 10.846 1 119.39 ? C11 QPY 201 A 1 HETATM 6 C C12 QPY . . . B 2 -4.934 -32.154 17.541 1 103.32 ? C12 QPY 201 A 1 HETATM 7 C C13 QPY . . . B 2 -5.61 -33.531 17.555 1 116.12 ? C13 QPY 201 A 1 HETATM 8 C C14 QPY . . . B 2 -5.304 -34.102 15.038 1 119.7 ? C14 QPY 201 A 1 HETATM 9 C C16 QPY . . . B 2 -6.724 -30.83 14.18 1 111.75 ? C16 QPY 201 A 1 HETATM 10 C C18 QPY . . . B 2 -5.851 -28.565 14.626 1 84.25 ? C18 QPY 201 A 1 HETATM 11 C C19 QPY . . . B 2 -6.677 -28.087 13.435 1 87.22 ? C19 QPY 201 A 1 HETATM 12 C C2 QPY . . . B 2 -3.657 -29.656 17.495 1 68.41 ? C2 QPY 201 A 1 HETATM 13 C C20 QPY . . . B 2 -7.409 -28.945 12.756 1 88.62 ? C20 QPY 201 A 1 HETATM 14 C C21 QPY . . . B 2 -7.436 -30.419 13.153 1 109.8 ? C21 QPY 201 A 1 HETATM 15 C C22 QPY . . . B 2 -4.245 -35.422 17.039 1 115.23 ? C22 QPY 201 A 1 HETATM 16 C C23 QPY . . . B 2 -4.569 -35.468 18.547 1 115.13 ? C23 QPY 201 A 1 HETATM 17 C C24 QPY . . . B 2 -5.334 -34.215 18.87 1 117.12 ? C24 QPY 201 A 1 HETATM 18 C C3 QPY . . . B 2 -3.048 -30.764 16.886 1 92.91 ? C3 QPY 201 A 1 HETATM 19 C C4 QPY . . . B 2 -1.689 -30.682 16.179 1 89.86 ? C4 QPY 201 A 1 HETATM 20 C C5 QPY . . . B 2 0.156 -31.821 14.893 1 93.5 ? C5 QPY 201 A 1 HETATM 21 C C6 QPY . . . B 2 -0.083 -31.475 13.42 1 105.02 ? C6 QPY 201 A 1 HETATM 22 C C7 QPY . . . B 2 -1.044 -33.657 12.965 1 112.71 ? C7 QPY 201 A 1 HETATM 23 C C8 QPY . . . B 2 -2.735 -33.047 11.653 1 116.85 ? C8 QPY 201 A 1 HETATM 24 C C9 QPY . . . B 2 -2.027 -31.937 12.046 1 117.73 ? C9 QPY 201 A 1 HETATM 25 N N1 QPY . . . B 2 -5.572 -31.023 18.169 1 87.49 ? N1 QPY 201 A 1 HETATM 26 N N2 QPY . . . B 2 -1.123 -31.876 15.574 1 95.27 ? N2 QPY 201 A 1 HETATM 27 N N3 QPY . . . B 2 -1.07 -32.357 12.804 1 111.2 ? N3 QPY 201 A 1 HETATM 28 N N4 QPY . . . B 2 -2.083 -34.254 12.271 1 114.03 ? N4 QPY 201 A 1 HETATM 29 N N5 QPY . . . B 2 -2.366 -30.723 11.657 1 121.21 ? N5 QPY 201 A 1 HETATM 30 N N6 QPY . . . B 2 -4.161 -31.693 10.448 1 113.29 ? N6 QPY 201 A 1 HETATM 31 N N7 QPY . . . B 2 -4.577 -34.064 10.415 1 118.65 ? N7 QPY 201 A 1 HETATM 32 N N8 QPY . . . B 2 -3.697 -32.007 16.916 1 96.18 ? N8 QPY 201 A 1 HETATM 33 N N9 QPY . . . B 2 -5.072 -34.336 16.454 1 115.75 ? N9 QPY 201 A 1 HETATM 34 O O1 QPY . . . B 2 -5.57 -28.701 18.759 1 61.89 ? O1 QPY 201 A 1 HETATM 35 O O2 QPY . . . B 2 -3.043 -28.399 17.487 1 58.92 ? O2 QPY 201 A 1 HETATM 36 O O3 QPY . . . B 2 -1.085 -29.665 16.114 1 71.32 ? O3 QPY 201 A 1 HETATM 37 O O4 QPY . . . B 2 -5.436 -32.793 14.562 1 117.72 ? O4 QPY 201 A 1 HETATM 38 O O5 QPY . . . B 2 -5.383 -35.014 14.285 1 127.67 ? O5 QPY 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 38 #