data_8KBG # _model_server_result.job_id WRHINpzcifiArB2iLEUVsw _model_server_result.datetime_utc '2024-11-24 15:04:12' _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 8kbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 8KBG # _exptl.entry_id 8KBG _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.3 _cell.angle_gamma 90 _cell.entry_id 8KBG _cell.length_a 71.9 _cell.length_b 66.04 _cell.length_c 89.37 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8KBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_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 _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 # 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 H N N ? 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 8KBG _atom_sites.fract_transf_matrix[1][1] 0.013908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002029 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015142 _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] 0.011308 _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 1SY D 1 401 401 1SY 1SY . H 2 1SY E 1 401 401 1SY 1SY . I 2 1SY F 1 401 401 1SY 1SY . J 2 1SY G 1 401 401 1SY 1SY . K 2 1SY H 1 401 401 1SY 1SY . L 2 1SY I 1 401 401 1SY 1SY . M 3 HOH D 1 501 38 HOH HOH . M 3 HOH D 2 502 45 HOH HOH . M 3 HOH D 3 503 10 HOH HOH . M 3 HOH D 4 504 44 HOH HOH . M 3 HOH D 5 505 2 HOH HOH . M 3 HOH D 6 506 46 HOH HOH . M 3 HOH D 7 507 39 HOH HOH . M 3 HOH D 8 508 19 HOH HOH . M 3 HOH D 9 509 1 HOH HOH . M 3 HOH D 10 510 53 HOH HOH . M 3 HOH D 11 511 59 HOH HOH . M 3 HOH D 12 512 34 HOH HOH . M 3 HOH D 13 513 72 HOH HOH . M 3 HOH D 14 514 67 HOH HOH . M 3 HOH D 15 515 3 HOH HOH . M 3 HOH D 16 516 49 HOH HOH . M 3 HOH D 17 517 8 HOH HOH . M 3 HOH D 18 518 61 HOH HOH . M 3 HOH D 19 519 35 HOH HOH . M 3 HOH D 20 520 58 HOH HOH . M 3 HOH D 21 521 68 HOH HOH . M 3 HOH D 22 522 29 HOH HOH . M 3 HOH D 23 523 79 HOH HOH . M 3 HOH D 24 524 88 HOH HOH . M 3 HOH D 25 525 22 HOH HOH . M 3 HOH D 26 526 82 HOH HOH . M 3 HOH D 27 527 51 HOH HOH . M 3 HOH D 28 528 50 HOH HOH . M 3 HOH D 29 529 78 HOH HOH . N 3 HOH E 1 501 77 HOH HOH . N 3 HOH E 2 502 56 HOH HOH . N 3 HOH E 3 503 20 HOH HOH . N 3 HOH E 4 504 7 HOH HOH . N 3 HOH E 5 505 31 HOH HOH . N 3 HOH E 6 506 30 HOH HOH . N 3 HOH E 7 507 28 HOH HOH . N 3 HOH E 8 508 37 HOH HOH . N 3 HOH E 9 509 11 HOH HOH . N 3 HOH E 10 510 18 HOH HOH . N 3 HOH E 11 511 42 HOH HOH . N 3 HOH E 12 512 70 HOH HOH . N 3 HOH E 13 513 13 HOH HOH . N 3 HOH E 14 514 9 HOH HOH . N 3 HOH E 15 515 17 HOH HOH . N 3 HOH E 16 516 6 HOH HOH . N 3 HOH E 17 517 26 HOH HOH . N 3 HOH E 18 518 25 HOH HOH . N 3 HOH E 19 519 32 HOH HOH . N 3 HOH E 20 520 75 HOH HOH . N 3 HOH E 21 521 52 HOH HOH . N 3 HOH E 22 522 33 HOH HOH . N 3 HOH E 23 523 62 HOH HOH . N 3 HOH E 24 524 54 HOH HOH . N 3 HOH E 25 525 86 HOH HOH . N 3 HOH E 26 526 48 HOH HOH . N 3 HOH E 27 527 85 HOH HOH . N 3 HOH E 28 528 90 HOH HOH . N 3 HOH E 29 529 73 HOH HOH . O 3 HOH F 1 501 91 HOH HOH . O 3 HOH F 2 502 41 HOH HOH . O 3 HOH F 3 503 24 HOH HOH . O 3 HOH F 4 504 71 HOH HOH . O 3 HOH F 5 505 64 HOH HOH . O 3 HOH F 6 506 15 HOH HOH . O 3 HOH F 7 507 57 HOH HOH . P 3 HOH G 1 501 93 HOH HOH . P 3 HOH G 2 502 60 HOH HOH . P 3 HOH G 3 503 23 HOH HOH . P 3 HOH G 4 504 63 HOH HOH . P 3 HOH G 5 505 84 HOH HOH . P 3 HOH G 6 506 66 HOH HOH . P 3 HOH G 7 507 43 HOH HOH . P 3 HOH G 8 508 92 HOH HOH . P 3 HOH G 9 509 83 HOH HOH . Q 3 HOH H 1 501 16 HOH HOH . Q 3 HOH H 2 502 4 HOH HOH . Q 3 HOH H 3 503 74 HOH HOH . Q 3 HOH H 4 504 36 HOH HOH . Q 3 HOH H 5 505 69 HOH HOH . Q 3 HOH H 6 506 80 HOH HOH . Q 3 HOH H 7 507 27 HOH HOH . Q 3 HOH H 8 508 21 HOH HOH . Q 3 HOH H 9 509 47 HOH HOH . Q 3 HOH H 10 510 12 HOH HOH . Q 3 HOH H 11 511 55 HOH HOH . Q 3 HOH H 12 512 89 HOH HOH . R 3 HOH I 1 501 81 HOH HOH . R 3 HOH I 2 502 76 HOH HOH . R 3 HOH I 3 503 65 HOH HOH . R 3 HOH I 4 504 5 HOH HOH . R 3 HOH I 5 505 14 HOH HOH . R 3 HOH I 6 506 40 HOH HOH . R 3 HOH I 7 507 94 HOH HOH . R 3 HOH I 8 508 87 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 . . . J 2 -2.128 -2.747 -5.285 1 55.57 ? C2 1SY 401 G 1 HETATM 2 N N01 1SY . . . J 2 -3.987 -4.188 -7.935 1 49.55 ? N01 1SY 401 G 1 HETATM 3 C C6 1SY . . . J 2 -3.074 -4.035 -6.973 1 59.99 ? C6 1SY 401 G 1 HETATM 4 N N1 1SY . . . J 2 -3.049 -2.879 -6.252 1 55.59 ? N1 1SY 401 G 1 HETATM 5 N N3 1SY . . . J 2 -1.184 -3.612 -4.894 1 54.94 ? N3 1SY 401 G 1 HETATM 6 C C4 1SY . . . J 2 -1.235 -4.74 -5.62 1 51.71 ? C4 1SY 401 G 1 HETATM 7 C C5 1SY . . . J 2 -2.116 -5.026 -6.646 1 58.18 ? C5 1SY 401 G 1 HETATM 8 N N7 1SY . . . J 2 -1.877 -6.289 -7.148 1 58.36 ? N7 1SY 401 G 1 HETATM 9 C C8 1SY . . . J 2 -0.852 -6.745 -6.453 1 59.72 ? C8 1SY 401 G 1 HETATM 10 N N9 1SY . . . J 2 -0.399 -5.837 -5.514 1 59.75 ? N9 1SY 401 G 1 HETATM 11 C C1' 1SY . . . J 2 0.702 -6.109 -4.566 1 61.86 ? C1' 1SY 401 G 1 HETATM 12 C C2' 1SY . . . J 2 1.42 -4.889 -3.964 1 56.22 ? C2' 1SY 401 G 1 HETATM 13 O O2' 1SY . . . J 2 2.816 -5.115 -3.885 1 60.49 ? O2' 1SY 401 G 1 HETATM 14 C C3' 1SY . . . J 2 0.815 -4.839 -2.567 1 58.36 ? C3' 1SY 401 G 1 HETATM 15 C C4' 1SY . . . J 2 0.593 -6.31 -2.252 1 60.46 ? C4' 1SY 401 G 1 HETATM 16 C C16 1SY . . . J 2 -0.46 -6.557 -1.201 1 65.19 ? C16 1SY 401 G 1 HETATM 17 O O17 1SY . . . J 2 -1.688 -5.932 -1.66 1 71.86 ? O17 1SY 401 G 1 HETATM 18 P P18 1SY . . . J 2 -2.956 -5.771 -0.703 1 114.86 ? P18 1SY 401 G 1 HETATM 19 O O19 1SY . . . J 2 -4.027 -4.999 -1.389 1 73.61 ? O19 1SY 401 G 1 HETATM 20 O O20 1SY . . . J 2 -2.3 -4.819 0.401 1 60.18 ? O20 1SY 401 G 1 HETATM 21 C C21 1SY . . . J 2 -1.756 -3.56 0.06 1 61.46 ? C21 1SY 401 G 1 HETATM 22 C C22 1SY . . . J 2 -0.446 -3.329 0.806 1 66.28 ? C22 1SY 401 G 1 HETATM 23 O O23 1SY . . . J 2 -0.616 -3.744 2.157 1 71.65 ? O23 1SY 401 G 1 HETATM 24 C C24 1SY . . . J 2 -0.338 -1.798 0.791 1 66.22 ? C24 1SY 401 G 1 HETATM 25 C C25 1SY . . . J 2 0.608 -1.213 -0.23 1 63.27 ? C25 1SY 401 G 1 HETATM 26 O O26 1SY . . . J 2 0.669 -2.086 -1.365 1 63.08 ? O26 1SY 401 G 1 HETATM 27 P P27 1SY . . . J 2 2.101 -2.724 -1.669 1 59.01 ? P27 1SY 401 G 1 HETATM 28 O O28 1SY . . . J 2 1.695 -4.272 -1.619 1 54.06 ? O28 1SY 401 G 1 HETATM 29 O O29 1SY . . . J 2 2.512 -2.244 -3.02 1 68.35 ? O29 1SY 401 G 1 HETATM 30 O O30 1SY . . . J 2 3.007 -2.445 -0.52 1 65.82 ? O30 1SY 401 G 1 HETATM 31 O O31 1SY . . . J 2 -1.672 -1.299 0.543 1 66.32 ? O31 1SY 401 G 1 HETATM 32 C C32 1SY . . . J 2 -2.548 -2.412 0.658 1 67.53 ? C32 1SY 401 G 1 HETATM 33 N N33 1SY . . . J 2 -3.794 -2.064 -0.021 1 72.6 ? N33 1SY 401 G 1 HETATM 34 C C34 1SY . . . J 2 -4.016 -1.944 -1.37 1 72.6 ? C34 1SY 401 G 1 HETATM 35 N N35 1SY . . . J 2 -5.246 -1.594 -1.675 1 70.43 ? N35 1SY 401 G 1 HETATM 36 C C36 1SY . . . J 2 -4.99 -1.752 0.588 1 70.98 ? C36 1SY 401 G 1 HETATM 37 C C37 1SY . . . J 2 -5.885 -1.468 -0.446 1 69.37 ? C37 1SY 401 G 1 HETATM 38 C C38 1SY . . . J 2 -7.238 -1.112 -0.067 1 64.94 ? C38 1SY 401 G 1 HETATM 39 N N39 1SY . . . J 2 -7.591 -1.073 1.246 1 63.17 ? N39 1SY 401 G 1 HETATM 40 C C40 1SY . . . J 2 -6.7 -1.35 2.188 1 61.76 ? C40 1SY 401 G 1 HETATM 41 N N41 1SY . . . J 2 -7.053 -1.307 3.473 1 66.83 ? N41 1SY 401 G 1 HETATM 42 N N42 1SY . . . J 2 -5.416 -1.682 1.896 1 67.07 ? N42 1SY 401 G 1 HETATM 43 O O43 1SY . . . J 2 -8.094 -0.843 -0.88 1 60.14 ? O43 1SY 401 G 1 HETATM 44 O O44 1SY . . . J 2 -3.3 -7.094 -0.119 1 64.4 ? O44 1SY 401 G 1 HETATM 45 O O4' 1SY . . . J 2 0.176 -6.887 -3.498 1 57.33 ? O4' 1SY 401 G 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #