data_6VBR # _model_server_result.job_id ZpDtQZRN4ovwF8eBp2jCUg _model_server_result.datetime_utc '2024-11-16 06:35:55' _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 6vbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":204}' # _entry.id 6VBR # _exptl.entry_id 6VBR _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 6VBR _cell.length_a 90.79 _cell.length_b 90.79 _cell.length_c 134.118 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6VBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 1,2,3,4,5,6,7,8 # 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 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 90.79 90.79 0 3 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 90.79 0 0 4 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 90.79 0 5 'crystal symmetry operation' 5_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 90.79 0 0 6 'crystal symmetry operation' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 90.79 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 90.79 90.79 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 C MN MN . A MN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc5 A OE2 GLU 120 A GLU 119 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 B MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc7 B MN MN . A MN 201 1_555 E O01 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc8 B MN MN . A MN 201 1_555 E O02 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc9 C MN MN . A MN 202 1_555 E O02 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc10 C MN MN . A MN 202 1_555 E O03 QVV . A QVV 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc11 C MN MN . A MN 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _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 6VBR _atom_sites.fract_transf_matrix[1][1] 0.011014 _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] 0.011014 _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] 0.007456 _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 1 201 200 MN MN . C 2 MN A 1 202 201 MN MN . D 3 QQ4 A 1 203 202 QQ4 PVP . E 4 QVV A 1 204 501 QVV 248 . F 5 SO4 A 1 205 2 SO4 SO4 . G 6 HOH A 1 301 17 HOH HOH . G 6 HOH A 2 302 6 HOH HOH . G 6 HOH A 3 303 2 HOH HOH . G 6 HOH A 4 304 34 HOH HOH . G 6 HOH A 5 305 5 HOH HOH . G 6 HOH A 6 306 4 HOH HOH . G 6 HOH A 7 307 22 HOH HOH . G 6 HOH A 8 308 24 HOH HOH . G 6 HOH A 9 309 13 HOH HOH . G 6 HOH A 10 310 31 HOH HOH . G 6 HOH A 11 311 21 HOH HOH . G 6 HOH A 12 312 16 HOH HOH . G 6 HOH A 13 313 35 HOH HOH . G 6 HOH A 14 314 3 HOH HOH . G 6 HOH A 15 315 33 HOH HOH . G 6 HOH A 16 316 30 HOH HOH . G 6 HOH A 17 317 10 HOH HOH . G 6 HOH A 18 318 21 HOH HOH . G 6 HOH A 19 319 29 HOH HOH . G 6 HOH A 20 320 22 HOH HOH . G 6 HOH A 21 321 32 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 14.728 37.068 -14.719 1 96.06 ? C17 QVV 204 A 1 HETATM 2 C C16 QVV . . . E 4 12.82 37.232 -16.35 1 76.25 ? C16 QVV 204 A 1 HETATM 3 C C15 QVV . . . E 4 13.715 37.998 -15.386 1 100.37 ? C15 QVV 204 A 1 HETATM 4 C C22 QVV . . . E 4 12.942 41.423 -11.776 1 105.98 ? C22 QVV 204 A 1 HETATM 5 C C19 QVV . . . E 4 12.013 43.152 -12.804 1 90.98 ? C19 QVV 204 A 1 HETATM 6 C C20 QVV . . . E 4 10.751 42.811 -12.239 1 105.86 ? C20 QVV 204 A 1 HETATM 7 C C21 QVV . . . E 4 10.702 41.718 -11.431 1 100.72 ? C21 QVV 204 A 1 HETATM 8 C C01 QVV . . . E 4 15.997 39.522 -17.952 1 75.25 ? C01 QVV 204 A 1 HETATM 9 C C02 QVV . . . E 4 15.898 40.938 -17.609 1 93.21 ? C02 QVV 204 A 1 HETATM 10 C C03 QVV . . . E 4 15.079 41.341 -16.538 1 87.85 ? C03 QVV 204 A 1 HETATM 11 C C04 QVV . . . E 4 14.958 42.811 -16.158 1 86.97 ? C04 QVV 204 A 1 HETATM 12 C C05 QVV . . . E 4 14.013 44.595 -14.705 1 99.98 ? C05 QVV 204 A 1 HETATM 13 C C06 QVV . . . E 4 12.602 45.077 -14.359 1 104.81 ? C06 QVV 204 A 1 HETATM 14 C C07 QVV . . . E 4 14.48 39.048 -16.167 1 98.51 ? C07 QVV 204 A 1 HETATM 15 C C18 QVV . . . E 4 10.436 44.602 -13.467 1 110.92 ? C18 QVV 204 A 1 HETATM 16 N N01 QVV . . . E 4 15.299 38.606 -17.235 1 91.79 ? N01 QVV 204 A 1 HETATM 17 N N02 QVV . . . E 4 14.105 43.196 -15.066 1 81.63 ? N02 QVV 204 A 1 HETATM 18 N N03 QVV . . . E 4 14.358 40.375 -15.812 1 88.33 ? N03 QVV 204 A 1 HETATM 19 N N04 QVV . . . E 4 12.904 38.663 -14.387 1 99.52 ? N04 QVV 204 A 1 HETATM 20 N N05 QVV . . . E 4 11.722 44.25 -13.535 1 92.87 ? N05 QVV 204 A 1 HETATM 21 N N06 QVV . . . E 4 9.734 43.765 -12.68 1 116.8 ? N06 QVV 204 A 1 HETATM 22 N N07 QVV . . . E 4 13.141 42.482 -12.596 1 101.62 ? N07 QVV 204 A 1 HETATM 23 N N08 QVV . . . E 4 9.437 41.321 -10.826 1 95.65 ? N08 QVV 204 A 1 HETATM 24 N N09 QVV . . . E 4 11.793 41.018 -11.191 1 109.83 ? N09 QVV 204 A 1 HETATM 25 O O01 QVV . . . E 4 16.817 39.107 -18.999 1 68.33 ? O01 QVV 204 A 1 HETATM 26 O O02 QVV . . . E 4 16.625 41.87 -18.351 1 97.19 ? O02 QVV 204 A 1 HETATM 27 O O03 QVV . . . E 4 15.545 43.648 -16.744 1 90.56 ? O03 QVV 204 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #