data_6Y99 # _model_server_result.job_id OkLegvlEtghPp98G4jcjUQ _model_server_result.datetime_utc '2024-10-15 16:20:31' _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 6y99 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6Y99 # _exptl.entry_id 6Y99 _exptl.method 'X-RAY DIFFRACTION' # _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 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 6Y99 _cell.length_a 111.703 _cell.length_b 111.703 _cell.length_c 35.058 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y99 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -17.62 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 6Y99 _atom_sites.fract_transf_matrix[1][1] 0.008952 _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] 0.008952 _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] 0.028524 _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 1SY A 1 401 401 1SY 1SY . C 3 HOH A 1 501 4 HOH HOH . C 3 HOH A 2 502 3 HOH HOH . C 3 HOH A 3 503 1 HOH HOH . C 3 HOH A 4 504 2 HOH HOH . C 3 HOH A 5 505 5 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 C2 1SY . . . B 2 -22.171 14.3 -9.11 0.5 65.69 ? C2 1SY 401 A 1 HETATM 2 N N01 1SY . . . B 2 -18.637 13.979 -9.596 0.5 64.37 ? N01 1SY 401 A 1 HETATM 3 C C6 1SY . . . B 2 -19.875 14.513 -9.577 0.5 66.3 ? C6 1SY 401 A 1 HETATM 4 N N1 1SY . . . B 2 -20.932 13.822 -9.152 0.5 71.76 ? N1 1SY 401 A 1 HETATM 5 N N3 1SY . . . B 2 -22.459 15.524 -9.496 0.5 58.12 ? N3 1SY 401 A 1 HETATM 6 C C4 1SY . . . B 2 -21.499 16.308 -9.951 0.5 57.58 ? C4 1SY 401 A 1 HETATM 7 C C5 1SY . . . B 2 -20.14 15.864 -10.022 0.5 58.37 ? C5 1SY 401 A 1 HETATM 8 N N7 1SY . . . B 2 -19.442 16.878 -10.499 0.5 60.86 ? N7 1SY 401 A 1 HETATM 9 C C8 1SY . . . B 2 -20.29 17.896 -10.72 0.5 59.58 ? C8 1SY 401 A 1 HETATM 10 N N9 1SY . . . B 2 -21.506 17.517 -10.398 0.5 58.27 ? N9 1SY 401 A 1 HETATM 11 C C1' 1SY . . . B 2 -22.723 18.28 -10.439 0.5 59.24 ? C1' 1SY 401 A 1 HETATM 12 C C2' 1SY . . . B 2 -22.899 18.566 -8.992 0.5 66.61 ? C2' 1SY 401 A 1 HETATM 13 O O2' 1SY . . . B 2 -24.165 18.08 -8.567 0.5 58.99 ? O2' 1SY 401 A 1 HETATM 14 C C3' 1SY . . . B 2 -22.713 20.049 -8.902 0.5 63.19 ? C3' 1SY 401 A 1 HETATM 15 C C4' 1SY . . . B 2 -23.085 20.536 -10.274 0.5 63.19 ? C4' 1SY 401 A 1 HETATM 16 C C16 1SY . . . B 2 -22.372 21.781 -10.723 0.5 62.86 ? C16 1SY 401 A 1 HETATM 17 O O17 1SY . . . B 2 -20.988 21.558 -10.642 0.5 60.04 ? O17 1SY 401 A 1 HETATM 18 P P18 1SY . . . B 2 -20.037 22.713 -11.057 0.5 60.13 ? P18 1SY 401 A 1 HETATM 19 O O19 1SY . . . B 2 -18.936 22.19 -11.849 0.5 56.89 ? O19 1SY 401 A 1 HETATM 20 O O20 1SY . . . B 2 -19.357 23.328 -9.803 0.5 66.39 ? O20 1SY 401 A 1 HETATM 21 C C21 1SY . . . B 2 -19.661 22.658 -8.615 0.5 64.2 ? C21 1SY 401 A 1 HETATM 22 C C22 1SY . . . B 2 -20.963 23.169 -8.101 0.5 60.96 ? C22 1SY 401 A 1 HETATM 23 O O23 1SY . . . B 2 -21.159 24.548 -8.323 0.5 57.37 ? O23 1SY 401 A 1 HETATM 24 C C24 1SY . . . B 2 -20.791 22.936 -6.653 0.5 63.03 ? C24 1SY 401 A 1 HETATM 25 C C25 1SY . . . B 2 -21.049 21.498 -6.478 0.5 60.52 ? C25 1SY 401 A 1 HETATM 26 O O26 1SY . . . B 2 -22.295 21.355 -5.909 0.5 63.02 ? O26 1SY 401 A 1 HETATM 27 P P27 1SY . . . B 2 -22.962 20.092 -6.428 0.5 60.97 ? P27 1SY 401 A 1 HETATM 28 O O28 1SY . . . B 2 -23.482 20.511 -7.837 0.5 63.48 ? O28 1SY 401 A 1 HETATM 29 O O29 1SY . . . B 2 -21.995 19.042 -6.501 0.5 52.23 ? O29 1SY 401 A 1 HETATM 30 O O30 1SY . . . B 2 -24.086 19.801 -5.378 0.5 55.12 ? O30 1SY 401 A 1 HETATM 31 O O31 1SY . . . B 2 -19.436 23.085 -6.345 0.5 64.1 ? O31 1SY 401 A 1 HETATM 32 C C32 1SY . . . B 2 -18.674 22.878 -7.493 0.5 61.73 ? C32 1SY 401 A 1 HETATM 33 N N33 1SY . . . B 2 -17.844 21.683 -7.357 0.5 59.74 ? N33 1SY 401 A 1 HETATM 34 C C34 1SY . . . B 2 -18.14 20.452 -6.958 0.5 58.64 ? C34 1SY 401 A 1 HETATM 35 N N35 1SY . . . B 2 -17.067 19.657 -7.043 0.5 61.03 ? N35 1SY 401 A 1 HETATM 36 C C36 1SY . . . B 2 -16.604 21.692 -7.707 0.5 60.31 ? C36 1SY 401 A 1 HETATM 37 C C37 1SY . . . B 2 -16.077 20.377 -7.503 0.5 57.93 ? C37 1SY 401 A 1 HETATM 38 C C38 1SY . . . B 2 -14.694 20.138 -7.827 0.5 65.44 ? C38 1SY 401 A 1 HETATM 39 N N39 1SY . . . B 2 -14.013 21.165 -8.283 0.5 70.7 ? N39 1SY 401 A 1 HETATM 40 C C40 1SY . . . B 2 -14.57 22.355 -8.451 0.5 65.08 ? C40 1SY 401 A 1 HETATM 41 N N41 1SY . . . B 2 -13.836 23.363 -8.926 0.5 71.63 ? N41 1SY 401 A 1 HETATM 42 N N42 1SY . . . B 2 -15.83 22.637 -8.178 0.5 60.67 ? N42 1SY 401 A 1 HETATM 43 O O43 1SY . . . B 2 -14.183 19.019 -7.671 0.5 66.3 ? O43 1SY 401 A 1 HETATM 44 O O44 1SY . . . B 2 -20.791 23.699 -11.83 0.5 59.19 ? O44 1SY 401 A 1 HETATM 45 O O4' 1SY . . . B 2 -22.588 19.514 -11.095 0.5 61.5 ? O4' 1SY 401 A 1 HETATM 46 H H1 1SY . . . B 2 -22.967 13.664 -8.746 0.5 78.93 ? H1 1SY 401 A 1 HETATM 47 H H2 1SY . . . B 2 -18.491 13.031 -9.281 0.5 77.34 ? H2 1SY 401 A 1 HETATM 48 H H3 1SY . . . B 2 -17.855 14.527 -9.927 0.5 77.34 ? H3 1SY 401 A 1 HETATM 49 H H4 1SY . . . B 2 -20.017 18.865 -11.119 0.5 71.6 ? H4 1SY 401 A 1 HETATM 50 H H5 1SY . . . B 2 -23.566 17.691 -10.826 0.5 71.18 ? H5 1SY 401 A 1 HETATM 51 H H6 1SY . . . B 2 -22.099 18.091 -8.416 0.5 80.04 ? H6 1SY 401 A 1 HETATM 52 H H7 1SY . . . B 2 -24.858 18.485 -9.106 0.5 70.89 ? H7 1SY 401 A 1 HETATM 53 H H8 1SY . . . B 2 -21.646 20.224 -8.804 0.5 75.93 ? H8 1SY 401 A 1 HETATM 54 H H9 1SY . . . B 2 -24.174 20.646 -10.372 0.5 75.93 ? H9 1SY 401 A 1 HETATM 55 H H10 1SY . . . B 2 -22.63 21.968 -11.767 0.5 75.52 ? H10 1SY 401 A 1 HETATM 56 H H11 1SY . . . B 2 -22.695 22.654 -10.158 0.5 75.52 ? H11 1SY 401 A 1 HETATM 57 H H13 1SY . . . B 2 -19.717 21.582 -8.819 0.5 77.14 ? H13 1SY 401 A 1 HETATM 58 H H14 1SY . . . B 2 -21.806 22.558 -8.421 0.5 73.26 ? H14 1SY 401 A 1 HETATM 59 H H15 1SY . . . B 2 -21.966 24.837 -7.874 0.5 68.95 ? H15 1SY 401 A 1 HETATM 60 H H16 1SY . . . B 2 -21.457 23.559 -6.04 0.5 75.73 ? H16 1SY 401 A 1 HETATM 61 H H17 1SY . . . B 2 -20.871 20.881 -7.332 0.5 72.72 ? H17 1SY 401 A 1 HETATM 62 H H18 1SY . . . B 2 -20.37 21.175 -5.692 0.5 72.72 ? H18 1SY 401 A 1 HETATM 63 H H19 1SY . . . B 2 -23.86 19.719 -4.441 0.5 66.24 ? H19 1SY 401 A 1 HETATM 64 H H20 1SY . . . B 2 -18.06 23.762 -7.713 0.5 74.17 ? H20 1SY 401 A 1 HETATM 65 H H21 1SY . . . B 2 -19.078 20.073 -6.608 0.5 70.47 ? H21 1SY 401 A 1 HETATM 66 H H22 1SY . . . B 2 -14.253 24.27 -9.044 0.5 86.05 ? H22 1SY 401 A 1 HETATM 67 H H23 1SY . . . B 2 -12.866 23.224 -9.151 0.5 86.05 ? H23 1SY 401 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 67 #