data_5N2R # _model_server_result.job_id Ajz6kWOgRUsInaeYI2V0FA _model_server_result.datetime_utc '2024-11-16 23:19:11' _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 5n2r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2401}' # _entry.id 5N2R # _exptl.entry_id 5N2R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.472 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-butyl-3-[(~{E})-3-oxidanylprop-1-enyl]-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione _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 5N2R _cell.length_a 39.254 _cell.length_b 180.739 _cell.length_c 140.641 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N2R _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _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 3 _struct_asym.id C _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 disulf ? disulf1 A SG CYS 80 A CYS 71 1_555 A SG CYS 168 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 83 A CYS 74 1_555 A SG CYS 155 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 86 A CYS 77 1_555 A SG CYS 175 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 364 A CYS 259 1_555 A SG CYS 367 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc1 A OD1 ASP 61 A ASP 52 1_555 B NA NA . A NA 2400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc2 A OG SER 100 A SER 91 1_555 B NA NA . A NA 2400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc3 B NA NA . A NA 2400 1_555 HA O HOH . A HOH 2514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc4 B NA NA . A NA 2400 1_555 HA O HOH . A HOH 2534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? # _chem_comp.formula 'C21 H28 N4 O3' _chem_comp.formula_weight 384.472 _chem_comp.id 8JN _chem_comp.mon_nstd_flag . _chem_comp.name 1-butyl-3-[(~{E})-3-oxidanylprop-1-enyl]-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione _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 O12 C11 8JN sing 1 n n C11 C10 8JN sing 2 n n C10 C09 8JN doub 3 e n C01 C02 8JN sing 4 n n C09 N08 8JN sing 5 n n C25 C24 8JN sing 6 n n C25 C18 8JN sing 7 n n C02 C03 8JN sing 8 n n C24 C26 8JN sing 9 n n C24 C23 8JN sing 10 n n C26 C20 8JN sing 11 n n C19 C18 8JN sing 12 n n C19 C20 8JN sing 13 n n N08 C13 8JN sing 14 n n N08 C06 8JN sing 15 n n N17 C13 8JN sing 16 n y N17 C16 8JN doub 17 n y O07 C06 8JN doub 18 n n C13 C14 8JN doub 19 n y C06 N05 8JN sing 20 n n C18 C16 8JN sing 21 n n C18 C22 8JN sing 22 n n C16 N15 8JN sing 23 n y C03 C04 8JN sing 24 n n C20 C21 8JN sing 25 n n C14 N15 8JN sing 26 n y C14 C27 8JN sing 27 n n N05 C27 8JN sing 28 n n N05 C04 8JN sing 29 n n C23 C22 8JN sing 30 n n C27 O28 8JN doub 31 n n C22 C21 8JN sing 32 n n C10 H1 8JN sing 33 n n C21 H2 8JN sing 34 n n C21 H3 8JN sing 35 n n C22 H4 8JN sing 36 n n C23 H5 8JN sing 37 n n C23 H6 8JN sing 38 n n C24 H7 8JN sing 39 n n C25 H8 8JN sing 40 n n C25 H9 8JN sing 41 n n C26 H10 8JN sing 42 n n C26 H11 8JN sing 43 n n C01 H12 8JN sing 44 n n C01 H13 8JN sing 45 n n C01 H14 8JN sing 46 n n C02 H15 8JN sing 47 n n C02 H16 8JN sing 48 n n C03 H17 8JN sing 49 n n C03 H18 8JN sing 50 n n C04 H19 8JN sing 51 n n C04 H20 8JN sing 52 n n C09 H21 8JN sing 53 n n C11 H22 8JN sing 54 n n C11 H23 8JN sing 55 n n O12 H24 8JN sing 56 n n N15 H25 8JN sing 57 n n C19 H27 8JN sing 58 n n C19 H28 8JN sing 59 n n C20 H29 8JN sing 60 n n # _atom_sites.entry_id 5N2R _atom_sites.fract_transf_matrix[1][1] 0.025475 _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] 0.005533 _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] 0.00711 _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 NA A 1 2400 2400 NA NA . C 3 8JN A 1 2401 2401 8JN PSB . D 4 CLR A 1 2402 2402 CLR CLR . E 4 CLR A 1 2403 2403 CLR CLR . F 4 CLR A 1 2404 2404 CLR CLR . G 5 OLA A 1 2405 2405 OLA OLA . H 5 OLA A 1 2406 2406 OLA OLA . I 5 OLA A 1 2407 2407 OLA OLA . J 5 OLA A 1 2408 2408 OLA OLA . K 5 OLA A 1 2409 2409 OLA OLA . L 5 OLA A 1 2410 2410 OLA OLA . M 5 OLA A 1 2411 2411 OLA OLA . N 5 OLA A 1 2412 2412 OLA OLA . O 5 OLA A 1 2413 2413 OLA OLA . P 5 OLA A 1 2414 2414 OLA OLA . Q 5 OLA A 1 2415 2415 OLA OLA . R 5 OLA A 1 2416 2416 OLA OLA . S 5 OLA A 1 2417 2417 OLA OLA . T 5 OLA A 1 2418 2418 OLA OLA . U 5 OLA A 1 2419 2419 OLA OLA . V 5 OLA A 1 2420 2420 OLA OLA . W 5 OLA A 1 2421 2421 OLA OLA . X 5 OLA A 1 2422 2422 OLA OLA . Y 5 OLA A 1 2423 2423 OLA OLA . Z 5 OLA A 1 2424 2424 OLA OLA . AA 5 OLA A 1 2425 2425 OLA OLA . BA 6 OLC A 1 2426 2426 OLC OLC . CA 6 OLC A 1 2427 2427 OLC OLC . DA 6 OLC A 1 2428 2428 OLC OLC . EA 6 OLC A 1 2429 2429 OLC OLC . FA 6 OLC A 1 2430 2430 OLC OLC . GA 7 TAR A 1 2431 2431 TAR TAR . HA 8 HOH A 1 2501 16 HOH HOH . HA 8 HOH A 2 2502 10 HOH HOH . HA 8 HOH A 3 2503 32 HOH HOH . HA 8 HOH A 4 2504 29 HOH HOH . HA 8 HOH A 5 2505 3 HOH HOH . HA 8 HOH A 6 2506 12 HOH HOH . HA 8 HOH A 7 2507 14 HOH HOH . HA 8 HOH A 8 2508 30 HOH HOH . HA 8 HOH A 9 2509 1 HOH HOH . HA 8 HOH A 10 2510 17 HOH HOH . HA 8 HOH A 11 2511 25 HOH HOH . HA 8 HOH A 12 2512 7 HOH HOH . HA 8 HOH A 13 2513 11 HOH HOH . HA 8 HOH A 14 2514 20 HOH HOH . HA 8 HOH A 15 2515 22 HOH HOH . HA 8 HOH A 16 2516 34 HOH HOH . HA 8 HOH A 17 2517 4 HOH HOH . HA 8 HOH A 18 2518 13 HOH HOH . HA 8 HOH A 19 2519 31 HOH HOH . HA 8 HOH A 20 2520 26 HOH HOH . HA 8 HOH A 21 2521 18 HOH HOH . HA 8 HOH A 22 2522 15 HOH HOH . HA 8 HOH A 23 2523 27 HOH HOH . HA 8 HOH A 24 2524 37 HOH HOH . HA 8 HOH A 25 2525 28 HOH HOH . HA 8 HOH A 26 2526 9 HOH HOH . HA 8 HOH A 27 2527 36 HOH HOH . HA 8 HOH A 28 2528 2 HOH HOH . HA 8 HOH A 29 2529 8 HOH HOH . HA 8 HOH A 30 2530 23 HOH HOH . HA 8 HOH A 31 2531 5 HOH HOH . HA 8 HOH A 32 2532 21 HOH HOH . HA 8 HOH A 33 2533 35 HOH HOH . HA 8 HOH A 34 2534 19 HOH HOH . HA 8 HOH A 35 2535 24 HOH HOH . HA 8 HOH A 36 2536 33 HOH HOH . HA 8 HOH A 37 2537 6 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 C10 8JN . . . C 3 22.19 171.293 15.602 1 74.95 ? C10 8JN 2401 A 1 HETATM 2 C C13 8JN . . . C 3 20.304 172.803 17.581 1 47.66 ? C13 8JN 2401 A 1 HETATM 3 C C14 8JN . . . C 3 19.389 173.61 18.283 1 43.39 ? C14 8JN 2401 A 1 HETATM 4 C C16 8JN . . . C 3 18.363 171.597 17.809 1 59.9 ? C16 8JN 2401 A 1 HETATM 5 C C18 8JN . . . C 3 17.288 170.444 17.727 1 80.64 ? C18 8JN 2401 A 1 HETATM 6 C C21 8JN . . . C 3 15.447 169.654 19.346 1 93.6 ? C21 8JN 2401 A 1 HETATM 7 C C22 8JN . . . C 3 16.96 169.58 19.024 1 84.99 ? C22 8JN 2401 A 1 HETATM 8 C C23 8JN . . . C 3 17.209 168.182 18.548 1 79.37 ? C23 8JN 2401 A 1 HETATM 9 C C24 8JN . . . C 3 16.49 168.166 17.105 1 88.23 ? C24 8JN 2401 A 1 HETATM 10 C C25 8JN . . . C 3 17.369 169.284 16.538 1 84.75 ? C25 8JN 2401 A 1 HETATM 11 C C26 8JN . . . C 3 15.022 168.649 17.123 1 94.79 ? C26 8JN 2401 A 1 HETATM 12 C C27 8JN . . . C 3 19.737 175.014 18.756 1 39.51 ? C27 8JN 2401 A 1 HETATM 13 C C01 8JN . . . C 3 22.172 179.345 15.781 1 81.74 ? C01 8JN 2401 A 1 HETATM 14 C C02 8JN . . . C 3 22.414 178.165 16.774 1 70.77 ? C02 8JN 2401 A 1 HETATM 15 C C03 8JN . . . C 3 21.273 178.01 17.829 1 62.94 ? C03 8JN 2401 A 1 HETATM 16 C C04 8JN . . . C 3 21.513 176.886 18.886 1 45.42 ? C04 8JN 2401 A 1 HETATM 17 N N05 8JN . . . C 3 21.078 175.446 18.422 1 41.79 ? N05 8JN 2401 A 1 HETATM 18 C C06 8JN . . . C 3 22.057 174.651 17.703 1 58.08 ? C06 8JN 2401 A 1 HETATM 19 O O07 8JN . . . C 3 23.147 175.068 17.463 1 72.88 ? O07 8JN 2401 A 1 HETATM 20 N N08 8JN . . . C 3 21.624 173.294 17.284 1 50.13 ? N08 8JN 2401 A 1 HETATM 21 C C09 8JN . . . C 3 22.714 172.478 16.511 1 67.25 ? C09 8JN 2401 A 1 HETATM 22 C C11 8JN . . . C 3 23.267 170.451 14.824 1 74.18 ? C11 8JN 2401 A 1 HETATM 23 O O12 8JN . . . C 3 24.236 171.315 14.282 1 69.12 ? O12 8JN 2401 A 1 HETATM 24 N N15 8JN . . . C 3 18.205 172.848 18.41 1 51.44 ? N15 8JN 2401 A 1 HETATM 25 N N17 8JN . . . C 3 19.646 171.569 17.303 1 53.72 ? N17 8JN 2401 A 1 HETATM 26 C C19 8JN . . . C 3 15.843 170.854 17.252 1 84.79 ? C19 8JN 2401 A 1 HETATM 27 C C20 8JN . . . C 3 14.875 169.875 17.986 1 90.23 ? C20 8JN 2401 A 1 HETATM 28 O O28 8JN . . . C 3 19.015 175.726 19.342 1 56.04 ? O28 8JN 2401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #