data_8IK3 # _model_server_result.job_id -qmbx-ir3MZl1notmOpxIA _model_server_result.datetime_utc '2025-07-31 22:02:37' _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 8ik3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 8IK3 # _exptl.entry_id 8IK3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 674.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description cGAMP _entity.pdbx_number_of_molecules 4 _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 8IK3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IK3 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _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 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _chem_comp.formula 'C20 H24 N10 O13 P2' _chem_comp.formula_weight 674.411 _chem_comp.id 1SY _chem_comp.mon_nstd_flag . _chem_comp.name cGAMP _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2',3' cGAMP;c-GMP-AMP;c[G(2',5')pA(3',5')p]" # 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 O44 P18 1SY doub 1 n n O19 P18 1SY sing 2 n n P18 O17 1SY sing 3 n n P18 O20 1SY sing 4 n n O17 C16 1SY sing 5 n n O4' C4' 1SY sing 6 n n O4' C1' 1SY sing 7 n n C16 C4' 1SY sing 8 n n C8 N7 1SY doub 9 n y C8 N9 1SY sing 10 n y N7 C5 1SY sing 11 n y O20 C21 1SY sing 12 n n N9 C1' 1SY sing 13 n n N9 C4 1SY sing 14 n y N41 C40 1SY sing 15 n n C4' C3' 1SY sing 16 n n C1' C2' 1SY sing 17 n n C5 C4 1SY doub 18 n y C5 C6 1SY sing 19 n y N01 C6 1SY sing 20 n n C4 N3 1SY sing 21 n y C40 N42 1SY sing 22 n n C40 N39 1SY doub 23 n n C6 N1 1SY doub 24 n y N42 C36 1SY sing 25 n n N39 C38 1SY sing 26 n n C21 C22 1SY sing 27 n n C21 C32 1SY sing 28 n n O23 C22 1SY sing 29 n n N3 C2 1SY doub 30 n y C3' C2' 1SY sing 31 n n C3' O28 1SY sing 32 n n N1 C2 1SY sing 33 n y C2' O2' 1SY sing 34 n n C36 C37 1SY doub 35 n y C36 N33 1SY sing 36 n y C38 O43 1SY doub 37 n n C38 C37 1SY sing 38 n n C22 C24 1SY sing 39 n n C32 N33 1SY sing 40 n n C32 O31 1SY sing 41 n n C37 N35 1SY sing 42 n y N33 C34 1SY sing 43 n y O28 P27 1SY sing 44 n n N35 C34 1SY doub 45 n y O31 C24 1SY sing 46 n n C24 C25 1SY sing 47 n n O26 P27 1SY sing 48 n n O26 C25 1SY sing 49 n n P27 O29 1SY doub 50 n n P27 O30 1SY sing 51 n n C2 H1 1SY sing 52 n n N01 H2 1SY sing 53 n n N01 H3 1SY sing 54 n n C8 H4 1SY sing 55 n n C1' H5 1SY sing 56 n n C2' H6 1SY sing 57 n n O2' H7 1SY sing 58 n n C3' H8 1SY sing 59 n n C4' H9 1SY sing 60 n n C16 H10 1SY sing 61 n n C16 H11 1SY sing 62 n n O19 H12 1SY sing 63 n n C21 H13 1SY sing 64 n n C22 H14 1SY sing 65 n n O23 H15 1SY sing 66 n n C24 H16 1SY sing 67 n n C25 H17 1SY sing 68 n n C25 H18 1SY sing 69 n n O30 H19 1SY sing 70 n n C32 H20 1SY sing 71 n n C34 H21 1SY sing 72 n n N41 H22 1SY sing 73 n n N41 H23 1SY sing 74 n n N42 H24 1SY sing 75 n n # _atom_sites.entry_id 8IK3 _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 I 2 1SY B 1 601 401 1SY 1SY . J 2 1SY D 1 601 401 1SY 1SY . K 2 1SY G 1 601 401 1SY 1SY . L 2 1SY F 1 601 401 1SY 1SY . # 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 C2 1SY . A . J 2 104.65 119.75 127.739 0.5 68.72 ? C2 1SY 601 D 1 HETATM 2 C C2 1SY . B . J 2 93.664 119.107 127.57 0.5 68.72 ? C2 1SY 601 D 1 HETATM 3 N N01 1SY . A . J 2 101.883 120.451 129.793 0.5 68.72 ? N01 1SY 601 D 1 HETATM 4 N N01 1SY . B . J 2 96.433 118.623 129.68 0.5 68.72 ? N01 1SY 601 D 1 HETATM 5 C C6 1SY . A . J 2 102.554 120.332 128.524 0.5 68.72 ? C6 1SY 601 D 1 HETATM 6 C C6 1SY . B . J 2 95.752 118.597 128.411 0.5 68.72 ? C6 1SY 601 D 1 HETATM 7 N N1 1SY . A . J 2 103.792 119.944 128.764 0.5 68.72 ? N1 1SY 601 D 1 HETATM 8 N N1 1SY . B . J 2 94.522 119.029 128.609 0.5 68.72 ? N1 1SY 601 D 1 HETATM 9 N N3 1SY . A . J 2 104.24 119.954 126.471 0.5 68.72 ? N3 1SY 601 D 1 HETATM 10 N N3 1SY . B . J 2 94.066 118.744 126.334 0.5 68.72 ? N3 1SY 601 D 1 HETATM 11 C C4 1SY . A . J 2 102.983 120.347 126.228 0.5 68.72 ? C4 1SY 601 D 1 HETATM 12 C C4 1SY . B . J 2 95.315 118.304 126.136 0.5 68.72 ? C4 1SY 601 D 1 HETATM 13 C C5 1SY . A . J 2 102.137 120.539 127.234 0.5 68.72 ? C5 1SY 601 D 1 HETATM 14 C C5 1SY . B . J 2 96.161 118.226 127.156 0.5 68.72 ? C5 1SY 601 D 1 HETATM 15 N N7 1SY . A . J 2 100.964 120.925 126.717 0.5 68.72 ? N7 1SY 601 D 1 HETATM 16 N N7 1SY . B . J 2 97.328 117.762 126.69 0.5 68.72 ? N7 1SY 601 D 1 HETATM 17 C C8 1SY . A . J 2 101.092 120.972 125.393 0.5 68.72 ? C8 1SY 601 D 1 HETATM 18 C C8 1SY . B . J 2 97.196 117.553 125.382 0.5 68.72 ? C8 1SY 601 D 1 HETATM 19 N N9 1SY . A . J 2 102.34 120.617 125.094 0.5 68.72 ? N9 1SY 601 D 1 HETATM 20 N N9 1SY . B . J 2 95.951 117.886 125.042 0.5 68.72 ? N9 1SY 601 D 1 HETATM 21 C C1' 1SY . A . J 2 102.802 120.569 123.765 0.5 68.72 ? C1' 1SY 601 D 1 HETATM 22 C C1' 1SY . B . J 2 95.492 117.781 123.715 0.5 68.72 ? C1' 1SY 601 D 1 HETATM 23 C C2' 1SY . A . J 2 102.694 119.162 123.272 0.5 68.72 ? C2' 1SY 601 D 1 HETATM 24 C C2' 1SY . B . J 2 95.624 119.126 123.078 0.5 68.72 ? C2' 1SY 601 D 1 HETATM 25 O O2' 1SY . A . J 2 103.771 118.94 122.385 0.5 68.72 ? O2' 1SY 601 D 1 HETATM 26 O O2' 1SY . B . J 2 94.572 119.268 122.147 0.5 68.72 ? O2' 1SY 601 D 1 HETATM 27 C C3' 1SY . A . J 2 101.445 119.161 122.531 0.5 68.72 ? C3' 1SY 601 D 1 HETATM 28 C C3' 1SY . B . J 2 96.897 119.05 122.379 0.5 68.72 ? C3' 1SY 601 D 1 HETATM 29 C C4' 1SY . A . J 2 101.517 120.44 121.87 0.5 68.72 ? C4' 1SY 601 D 1 HETATM 30 C C4' 1SY . B . J 2 96.864 117.702 121.865 0.5 68.72 ? C4' 1SY 601 D 1 HETATM 31 C C16 1SY . A . J 2 100.107 120.909 121.439 0.5 68.72 ? C16 1SY 601 D 1 HETATM 32 C C16 1SY . B . J 2 98.301 117.189 121.593 0.5 68.72 ? C16 1SY 601 D 1 HETATM 33 O O17 1SY . A . J 2 99.253 121.025 122.63 0.5 68.72 ? O17 1SY 601 D 1 HETATM 34 O O17 1SY . B . J 2 99.101 117.24 122.831 0.5 68.72 ? O17 1SY 601 D 1 HETATM 35 P P18 1SY . A . J 2 97.66 121.643 122.437 0.5 68.72 ? P18 1SY 601 D 1 HETATM 36 P P18 1SY . B . J 2 100.708 116.613 122.82 0.5 68.72 ? P18 1SY 601 D 1 HETATM 37 O O19 1SY . A . J 2 97.279 122.638 123.498 0.5 68.72 ? O19 1SY 601 D 1 HETATM 38 O O19 1SY . B . J 2 101.021 115.753 124.012 0.5 68.72 ? O19 1SY 601 D 1 HETATM 39 O O20 1SY . A . J 2 96.44 120.498 122.117 0.5 68.72 ? O20 1SY 601 D 1 HETATM 40 O O20 1SY . B . J 2 101.95 117.722 122.465 0.5 68.72 ? O20 1SY 601 D 1 HETATM 41 C C21 1SY . A . J 2 96.874 119.131 122.529 0.5 68.72 ? C21 1SY 601 D 1 HETATM 42 C C21 1SY . B . J 2 101.482 119.118 122.704 0.5 68.72 ? C21 1SY 601 D 1 HETATM 43 C C22 1SY . A . J 2 97.36 118.414 121.35 0.5 68.72 ? C22 1SY 601 D 1 HETATM 44 C C22 1SY . B . J 2 101.065 119.701 121.429 0.5 68.72 ? C22 1SY 601 D 1 HETATM 45 O O23 1SY . A . J 2 96.643 118.843 120.199 0.5 68.72 ? O23 1SY 601 D 1 HETATM 46 O O23 1SY . B . J 2 101.873 119.183 120.38 0.5 68.72 ? O23 1SY 601 D 1 HETATM 47 C C24 1SY . A . J 2 97.056 116.982 121.613 0.5 68.72 ? C24 1SY 601 D 1 HETATM 48 C C24 1SY . B . J 2 101.323 121.158 121.573 0.5 68.72 ? C24 1SY 601 D 1 HETATM 49 C C25 1SY . A . J 2 98.189 116.296 122.257 0.5 68.72 ? C25 1SY 601 D 1 HETATM 50 C C25 1SY . B . J 2 100.161 121.87 122.127 0.5 68.72 ? C25 1SY 601 D 1 HETATM 51 O O26 1SY . A . J 2 99.203 117.251 122.745 0.5 68.72 ? O26 1SY 601 D 1 HETATM 52 O O26 1SY . B . J 2 99.104 120.924 122.523 0.5 68.72 ? O26 1SY 601 D 1 HETATM 53 P P27 1SY . A . J 2 100.759 116.659 122.463 0.5 68.72 ? P27 1SY 601 D 1 HETATM 54 P P27 1SY . B . J 2 97.6 121.525 122.064 0.5 68.72 ? P27 1SY 601 D 1 HETATM 55 O O28 1SY . A . J 2 101.433 118.029 121.613 0.5 68.72 ? O28 1SY 601 D 1 HETATM 56 O O28 1SY . B . J 2 96.94 120.077 121.342 0.5 68.72 ? O28 1SY 601 D 1 HETATM 57 O O29 1SY . A . J 2 100.664 115.521 121.478 0.5 68.72 ? O29 1SY 601 D 1 HETATM 58 O O29 1SY . B . J 2 97.829 122.532 120.966 0.5 68.72 ? O29 1SY 601 D 1 HETATM 59 O O30 1SY . A . J 2 101.489 116.14 123.664 0.5 68.72 ? O30 1SY 601 D 1 HETATM 60 O O30 1SY . B . J 2 96.823 122.209 123.148 0.5 68.72 ? O30 1SY 601 D 1 HETATM 61 O O31 1SY . A . J 2 95.881 117.014 122.505 0.5 68.72 ? O31 1SY 601 D 1 HETATM 62 O O31 1SY . B . J 2 102.459 121.233 122.509 0.5 68.72 ? O31 1SY 601 D 1 HETATM 63 C C32 1SY . A . J 2 95.8 118.366 123.02 0.5 68.72 ? C32 1SY 601 D 1 HETATM 64 C C32 1SY . B . J 2 102.522 119.943 123.163 0.5 68.72 ? C32 1SY 601 D 1 HETATM 65 N N33 1SY . A . J 2 95.917 118.27 124.517 0.5 68.72 ? N33 1SY 601 D 1 HETATM 66 N N33 1SY . B . J 2 102.347 120.196 124.635 0.5 68.72 ? N33 1SY 601 D 1 HETATM 67 C C34 1SY . A . J 2 97.001 117.712 125.091 0.5 68.72 ? C34 1SY 601 D 1 HETATM 68 C C34 1SY . B . J 2 101.243 120.787 125.132 0.5 68.72 ? C34 1SY 601 D 1 HETATM 69 N N35 1SY . A . J 2 96.837 117.761 126.433 0.5 68.72 ? N35 1SY 601 D 1 HETATM 70 N N35 1SY . B . J 2 101.385 120.877 126.476 0.5 68.72 ? N35 1SY 601 D 1 HETATM 71 C C36 1SY . A . J 2 95.091 118.658 125.488 0.5 68.72 ? C36 1SY 601 D 1 HETATM 72 C C36 1SY . B . J 2 103.16 119.93 125.651 0.5 68.72 ? C36 1SY 601 D 1 HETATM 73 C C37 1SY . A . J 2 95.665 118.341 126.683 0.5 68.72 ? C37 1SY 601 D 1 HETATM 74 C C37 1SY . B . J 2 102.564 120.349 126.8 0.5 68.72 ? C37 1SY 601 D 1 HETATM 75 C C38 1SY . A . J 2 94.936 118.673 127.993 0.5 68.72 ? C38 1SY 601 D 1 HETATM 76 C C38 1SY . B . J 2 103.288 120.161 128.142 0.5 68.72 ? C38 1SY 601 D 1 HETATM 77 N N39 1SY . A . J 2 93.659 119.311 127.961 0.5 68.72 ? N39 1SY 601 D 1 HETATM 78 N N39 1SY . B . J 2 104.579 119.545 128.176 0.5 68.72 ? N39 1SY 601 D 1 HETATM 79 C C40 1SY . A . J 2 93.06 119.646 126.696 0.5 68.72 ? C40 1SY 601 D 1 HETATM 80 C C40 1SY . B . J 2 105.196 119.102 126.953 0.5 68.72 ? C40 1SY 601 D 1 HETATM 81 N N41 1SY . A . J 2 91.754 120.301 126.655 0.5 68.72 ? N41 1SY 601 D 1 HETATM 82 N N41 1SY . B . J 2 106.512 118.468 126.958 0.5 68.72 ? N41 1SY 601 D 1 HETATM 83 N N42 1SY . A . J 2 93.76 119.329 125.444 0.5 68.72 ? N42 1SY 601 D 1 HETATM 84 N N42 1SY . B . J 2 104.502 119.287 125.678 0.5 68.72 ? N42 1SY 601 D 1 HETATM 85 O O43 1SY . A . J 2 95.431 118.399 129.035 0.5 68.72 ? O43 1SY 601 D 1 HETATM 86 O O43 1SY . B . J 2 102.776 120.525 129.149 0.5 68.72 ? O43 1SY 601 D 1 HETATM 87 O O44 1SY . A . J 2 97.743 122.447 121.16 0.5 68.72 ? O44 1SY 601 D 1 HETATM 88 O O44 1SY . B . J 2 100.734 115.665 121.645 0.5 68.72 ? O44 1SY 601 D 1 HETATM 89 O O4' 1SY . A . J 2 101.985 121.353 122.886 0.5 68.72 ? O4' 1SY 601 D 1 HETATM 90 O O4' 1SY . B . J 2 96.308 116.901 122.93 0.5 68.72 ? O4' 1SY 601 D 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 90 #