data_6UO8 # _model_server_result.job_id 60ApoG3LjAUVXnOPuSWOIw _model_server_result.datetime_utc '2025-02-05 15:50:50' _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 6uo8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1009}' # _entry.id 6UO8 # _exptl.entry_id 6UO8 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 337.44 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine _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 6UO8 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UO8 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG A 1401 NAG 3 n C NAG 2 C 2 NAG A 1606 NAG 4 n D NAG 1 D 1 NAG A 1608 NAG 4 n D NAG 2 D 2 NAG A 1609 NAG 4 n D BMA 3 D 3 BMA A 1610 BMA 3 n E NAG 1 E 1 NAG B 801 NAG 3 n E NAG 2 E 2 NAG B 901 NAG # 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 disulf ? disulf1 A SG CYS 57 A CYS 220 1_555 A SG CYS 83 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 213 A CYS 376 1_555 A SG CYS 247 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 500 A CYS 663 1_555 A SG CYS 598 A CYS 761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 B SG CYS 68 B CYS 108 1_555 B SG CYS 95 B CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 197 B CYS 237 1_555 B SG CYS 226 B CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 225 B CYS 265 1_555 B SG CYS 262 B CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 B SG CYS 513 B CYS 553 1_555 B SG CYS 608 B CYS 648 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 277 A ASN 440 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 319 A ASN 482 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 339 A ASN 502 1_555 H C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 351 A ASN 514 1_555 G C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 50 B ASN 90 1_555 M C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 B ND2 ASN 258 B ASN 298 1_555 J C1 NAG . B NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 B ND2 ASN 349 B ASN 389 1_555 L C1 NAG . B NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 B ND2 ASN 364 B ASN 404 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 B ND2 ASN 413 B ASN 453 1_555 K C1 NAG . B NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale12 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _chem_comp.formula 'C15 H23 N5 O2 S' _chem_comp.formula_weight 337.44 _chem_comp.id QDA _chem_comp.mon_nstd_flag . _chem_comp.name N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine _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 C15 S14 QDA sing 348 n n S14 C13 QDA sing 349 n n C13 N12 QDA doub 350 n y C13 N16 QDA sing 351 n y N12 C05 QDA sing 352 n y C23 C22 QDA sing 353 n n C23 C19 QDA sing 354 n n N16 C17 QDA doub 355 n y C22 C21 QDA sing 356 n n C05 N06 QDA sing 357 n n C05 C04 QDA doub 358 n y N06 C07 QDA sing 359 n n C17 C04 QDA sing 360 n y C17 N18 QDA sing 361 n n C19 N18 QDA sing 362 n n C19 C20 QDA sing 363 n n C04 N02 QDA sing 364 n n O01 N02 QDA doub 365 n n C21 C20 QDA sing 366 n n C11 C07 QDA sing 367 n n C11 C10 QDA sing 368 n n N02 O03 QDA sing 369 n n C07 C08 QDA sing 370 n n C10 C09 QDA sing 371 n n C08 C09 QDA sing 372 n n C07 H1 QDA sing 373 n n C08 H2 QDA sing 374 n n C08 H3 QDA sing 375 n n C09 H4 QDA sing 376 n n C09 H5 QDA sing 377 n n C10 H6 QDA sing 378 n n C10 H7 QDA sing 379 n n C11 H8 QDA sing 380 n n C11 H9 QDA sing 381 n n C15 H10 QDA sing 382 n n C15 H11 QDA sing 383 n n C15 H12 QDA sing 384 n n C19 H13 QDA sing 385 n n C20 H14 QDA sing 386 n n C20 H15 QDA sing 387 n n C21 H16 QDA sing 388 n n C21 H17 QDA sing 389 n n C22 H18 QDA sing 390 n n C22 H19 QDA sing 391 n n C23 H20 QDA sing 392 n n C23 H21 QDA sing 393 n n N06 H22 QDA sing 394 n n N18 H23 QDA sing 395 n n # _atom_sites.entry_id 6UO8 _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 F 5 QD7 A 1 1001 1000 QD7 QD7 . G 6 NAG A 1 1002 1101 NAG NAG . H 6 NAG A 1 1005 1501 NAG NAG . I 7 QDA A 1 1009 1301 QDA QDA . J 6 NAG B 1 903 902 NAG NAG . K 6 NAG B 1 904 1001 NAG NAG . L 6 NAG B 1 905 1101 NAG NAG . M 6 NAG B 1 906 1201 NAG NAG . # 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 C04 QDA . . . I 7 143.322 139.423 78.843 1 137.34 ? C04 QDA 1009 A 1 HETATM 2 C C05 QDA . . . I 7 142.602 138.261 78.422 1 137.34 ? C05 QDA 1009 A 1 HETATM 3 C C07 QDA . . . I 7 140.749 136.644 78.73 1 137.34 ? C07 QDA 1009 A 1 HETATM 4 C C08 QDA . . . I 7 139.29 136.68 79.211 1 137.34 ? C08 QDA 1009 A 1 HETATM 5 C C09 QDA . . . I 7 139.208 135.682 80.362 1 137.34 ? C09 QDA 1009 A 1 HETATM 6 C C10 QDA . . . I 7 140.583 135.402 80.762 1 137.34 ? C10 QDA 1009 A 1 HETATM 7 C C11 QDA . . . I 7 141.353 135.462 79.475 1 137.34 ? C11 QDA 1009 A 1 HETATM 8 C C13 QDA . . . I 7 144.276 137.855 76.921 1 137.34 ? C13 QDA 1009 A 1 HETATM 9 C C15 QDA . . . I 7 146.367 136.138 76.39 1 137.34 ? C15 QDA 1009 A 1 HETATM 10 C C17 QDA . . . I 7 144.575 139.709 78.216 1 137.34 ? C17 QDA 1009 A 1 HETATM 11 C C19 QDA . . . I 7 146.606 141.107 77.997 1 137.34 ? C19 QDA 1009 A 1 HETATM 12 C C20 QDA . . . I 7 146.639 142.544 77.452 1 137.34 ? C20 QDA 1009 A 1 HETATM 13 C C21 QDA . . . I 7 147.636 143.283 78.322 1 137.34 ? C21 QDA 1009 A 1 HETATM 14 C C22 QDA . . . I 7 148.591 142.27 78.735 1 137.34 ? C22 QDA 1009 A 1 HETATM 15 C C23 QDA . . . I 7 147.739 141.06 79.031 1 137.34 ? C23 QDA 1009 A 1 HETATM 16 N N02 QDA . . . I 7 142.773 140.319 79.834 1 137.34 ? N02 QDA 1009 A 1 HETATM 17 N N06 QDA . . . I 7 141.451 137.89 79.011 1 137.34 ? N06 QDA 1009 A 1 HETATM 18 N N12 QDA . . . I 7 143.102 137.491 77.446 1 137.34 ? N12 QDA 1009 A 1 HETATM 19 N N16 QDA . . . I 7 145.035 138.906 77.249 1 137.34 ? N16 QDA 1009 A 1 HETATM 20 N N18 QDA . . . I 7 145.314 140.771 78.581 1 137.34 ? N18 QDA 1009 A 1 HETATM 21 O O01 QDA . . . I 7 141.661 140.078 80.278 1 137.34 ? O01 QDA 1009 A 1 HETATM 22 O O03 QDA . . . I 7 143.453 141.267 80.192 1 137.34 ? O03 QDA 1009 A 1 HETATM 23 S S14 QDA . . . I 7 144.894 136.831 75.641 1 137.34 ? S14 QDA 1009 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 23 #