data_8JYL # _model_server_result.job_id VwdzFeQQG_KgcBKTPQDxtg _model_server_result.datetime_utc '2024-12-06 10:03:45' _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 8jyl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 8JYL # _exptl.entry_id 8JYL _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 500.569 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-decanoylsulfamate' _entity.pdbx_number_of_molecules 6 _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 8JYL _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R _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 ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N 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 OE1 GLU 322 A GLU 322 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc2 G O3 VUL . A VUL 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc3 B OE1 GLU 322 B GLU 322 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc4 I O3 VUL . B VUL 601 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 C OE1 GLU 322 C GLU 322 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc6 K O3 VUL . C VUL 601 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc7 D OE1 GLU 322 D GLU 322 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc8 M O3 VUL . D VUL 601 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc9 E OE1 GLU 322 E GLU 322 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc10 O O3 VUL . E VUL 601 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc11 F OE1 GLU 322 F GLU 322 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc12 Q O3 VUL . F VUL 601 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? # _chem_comp.formula 'C20 H32 N6 O7 S' _chem_comp.formula_weight 500.569 _chem_comp.id VUL _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-decanoylsulfamate' _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 VUL sing 374 n n C2 C3 VUL sing 375 n n C9 C8 VUL sing 376 n n C9 C10 VUL sing 377 n n C3 C4 VUL sing 378 n n C5 C4 VUL sing 379 n n C5 C6 VUL sing 380 n n O2 S1 VUL doub 381 n n C7 C8 VUL sing 382 n n C7 C6 VUL sing 383 n n N1 C10 VUL sing 384 n n N1 S1 VUL sing 385 n n C10 O1 VUL doub 386 n n S1 O3 VUL doub 387 n n S1 O4 VUL sing 388 n n O4 C11 VUL sing 389 n n C11 C12 VUL sing 390 n n C18 N3 VUL doub 391 n y C18 N2 VUL sing 392 n y N3 C17 VUL sing 393 n y O5 C12 VUL sing 394 n n O5 C15 VUL sing 395 n n C12 C13 VUL sing 396 n n N2 C15 VUL sing 397 n n N2 C16 VUL sing 398 n y C17 C20 VUL doub 399 n y C17 C16 VUL sing 400 n y N6 C20 VUL sing 401 n n C13 O7 VUL sing 402 n n C13 C14 VUL sing 403 n n C15 C14 VUL sing 404 n n C20 N5 VUL sing 405 n y C16 N4 VUL doub 406 n y C14 O6 VUL sing 407 n n N5 C19 VUL doub 408 n y N4 C19 VUL sing 409 n y C1 H1 VUL sing 410 n n C1 H2 VUL sing 411 n n C1 H3 VUL sing 412 n n C2 H4 VUL sing 413 n n C2 H5 VUL sing 414 n n C5 H6 VUL sing 415 n n C5 H7 VUL sing 416 n n C6 H8 VUL sing 417 n n C6 H9 VUL sing 418 n n C7 H10 VUL sing 419 n n C7 H11 VUL sing 420 n n C8 H12 VUL sing 421 n n C8 H13 VUL sing 422 n n N1 H14 VUL sing 423 n n C4 H15 VUL sing 424 n n C4 H16 VUL sing 425 n n C3 H17 VUL sing 426 n n C3 H18 VUL sing 427 n n N6 H19 VUL sing 428 n n N6 H20 VUL sing 429 n n O6 H21 VUL sing 430 n n O7 H22 VUL sing 431 n n C9 H23 VUL sing 432 n n C9 H24 VUL sing 433 n n C11 H25 VUL sing 434 n n C11 H26 VUL sing 435 n n C12 H27 VUL sing 436 n n C13 H28 VUL sing 437 n n C14 H29 VUL sing 438 n n C15 H30 VUL sing 439 n n C18 H31 VUL sing 440 n n C19 H32 VUL sing 441 n n # _atom_sites.entry_id 8JYL _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 2 VUL A 1 601 533 VUL NSA . H 3 MG A 1 602 534 MG MG . I 2 VUL B 1 601 533 VUL NSA . J 3 MG B 1 602 534 MG MG . K 2 VUL C 1 601 533 VUL NSA . L 3 MG C 1 602 534 MG MG . M 2 VUL D 1 601 533 VUL NSA . N 3 MG D 1 602 534 MG MG . O 2 VUL E 1 601 533 VUL NSA . P 3 MG E 1 602 534 MG MG . Q 2 VUL F 1 601 533 VUL NSA . R 3 MG F 1 602 534 MG MG . # 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 VUL . . . I 2 95.465 150.675 136.797 1 17.83 ? C1 VUL 601 B 1 HETATM 2 C C2 VUL . . . I 2 95.256 149.175 136.63 1 18.38 ? C2 VUL 601 B 1 HETATM 3 O O1 VUL . . . I 2 95.594 140.112 134.037 1 27.01 ? O1 VUL 601 B 1 HETATM 4 C C5 VUL . . . I 2 94.786 146.268 134.996 1 13.41 ? C5 VUL 601 B 1 HETATM 5 C C6 VUL . . . I 2 95.228 145.042 134.208 1 19.38 ? C6 VUL 601 B 1 HETATM 6 C C7 VUL . . . I 2 96.169 144.135 134.986 1 13.1 ? C7 VUL 601 B 1 HETATM 7 C C8 VUL . . . I 2 95.759 142.677 134.852 1 13.98 ? C8 VUL 601 B 1 HETATM 8 N N1 VUL . . . I 2 97.607 139.276 134.723 1 21.29 ? N1 VUL 601 B 1 HETATM 9 C C4 VUL . . . I 2 95.756 147.433 134.852 1 17.28 ? C4 VUL 601 B 1 HETATM 10 C C3 VUL . . . I 2 95.106 148.776 135.167 1 19.78 ? C3 VUL 601 B 1 HETATM 11 S S1 VUL . . . I 2 97.321 137.711 134.093 1 21.9 ? S1 VUL 601 B 1 HETATM 12 N N2 VUL . . . I 2 94.302 140.738 129.561 1 16.99 ? N2 VUL 601 B 1 HETATM 13 O O2 VUL . . . I 2 96.342 136.89 135.131 1 29.8 ? O2 VUL 601 B 1 HETATM 14 N N3 VUL . . . I 2 94.146 142.626 130.59 1 19.32 ? N3 VUL 601 B 1 HETATM 15 O O3 VUL . . . I 2 98.749 136.911 133.921 1 29.33 ? O3 VUL 601 B 1 HETATM 16 N N4 VUL . . . I 2 92.825 141.36 127.642 1 15.84 ? N4 VUL 601 B 1 HETATM 17 O O4 VUL . . . I 2 96.574 137.804 132.623 1 27.16 ? O4 VUL 601 B 1 HETATM 18 N N5 VUL . . . I 2 91.959 143.493 127.712 1 23.62 ? N5 VUL 601 B 1 HETATM 19 O O5 VUL . . . I 2 95.225 138.627 130.562 1 19.47 ? O5 VUL 601 B 1 HETATM 20 N N6 VUL . . . I 2 92.432 145.013 129.496 1 22.28 ? N6 VUL 601 B 1 HETATM 21 O O6 VUL . . . I 2 95.534 138.195 127.484 1 33.31 ? O6 VUL 601 B 1 HETATM 22 O O7 VUL . . . I 2 97.952 138.749 128.523 1 28.78 ? O7 VUL 601 B 1 HETATM 23 C C9 VUL . . . I 2 96.895 141.712 135.154 1 12.96 ? C9 VUL 601 B 1 HETATM 24 C C10 VUL . . . I 2 96.615 140.327 134.589 1 22.01 ? C10 VUL 601 B 1 HETATM 25 C C11 VUL . . . I 2 97.317 138.365 131.581 1 15.9 ? C11 VUL 601 B 1 HETATM 26 C C12 VUL . . . I 2 96.45 138.263 130.304 1 15.4 ? C12 VUL 601 B 1 HETATM 27 C C13 VUL . . . I 2 96.922 139.258 129.239 1 21.22 ? C13 VUL 601 B 1 HETATM 28 C C14 VUL . . . I 2 95.655 139.384 128.378 1 20.87 ? C14 VUL 601 B 1 HETATM 29 C C15 VUL . . . I 2 94.677 139.383 129.241 1 19.42 ? C15 VUL 601 B 1 HETATM 30 C C16 VUL . . . I 2 93.49 141.53 128.812 1 19.3 ? C16 VUL 601 B 1 HETATM 31 C C17 VUL . . . I 2 93.393 142.73 129.466 1 19.63 ? C17 VUL 601 B 1 HETATM 32 C C18 VUL . . . I 2 94.684 141.421 130.626 1 15.67 ? C18 VUL 601 B 1 HETATM 33 C C19 VUL . . . I 2 92.083 142.314 127.115 1 20.45 ? C19 VUL 601 B 1 HETATM 34 C C20 VUL . . . I 2 92.581 143.725 128.859 1 16.95 ? C20 VUL 601 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 225 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 34 #