data_4O67 # _model_server_result.job_id P16DBSdNJb3xLnlPH8sPew _model_server_result.datetime_utc '2024-11-24 13:32:46' _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 4o67 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1101}' # _entry.id 4O67 # _exptl.entry_id 4O67 _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 2 _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 4O67 _cell.length_a 47.822 _cell.length_b 118.542 _cell.length_c 124.025 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O67 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 B,E,F,H 2 1 A,C,D,G 3 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 C N N ? 2 E N 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 metalc ? metalc1 A NE2 HIS 231 A HIS 390 1_555 D ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A SG CYS 237 A CYS 396 1_555 D ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc3 A SG CYS 238 A CYS 397 1_555 D ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc4 A SG CYS 245 A CYS 404 1_555 D ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc5 B NE2 HIS 231 B HIS 390 1_555 F ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc6 B SG CYS 237 B CYS 396 1_555 F ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc7 B SG CYS 238 B CYS 397 1_555 F ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc8 B SG CYS 245 B CYS 404 1_555 F ZN ZN . B ZN 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? # _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 4O67 _atom_sites.fract_transf_matrix[1][1] 0.020911 _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] 0.008436 _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] 0.008063 _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 C 2 1SY A 1 601 1100 1SY 1SY . D 3 ZN A 1 602 1 ZN ZN . E 2 1SY B 1 1101 1101 1SY 1SY . F 3 ZN B 1 1102 2 ZN ZN . G 4 HOH A 1 701 2 HOH HOH . G 4 HOH A 2 702 3 HOH HOH . G 4 HOH A 3 703 7 HOH HOH . G 4 HOH A 4 704 10 HOH HOH . G 4 HOH A 5 705 11 HOH HOH . G 4 HOH A 6 706 15 HOH HOH . G 4 HOH A 7 707 16 HOH HOH . G 4 HOH A 8 708 18 HOH HOH . G 4 HOH A 9 709 24 HOH HOH . G 4 HOH A 10 710 26 HOH HOH . G 4 HOH A 11 711 27 HOH HOH . G 4 HOH A 12 712 32 HOH HOH . G 4 HOH A 13 713 35 HOH HOH . G 4 HOH A 14 714 36 HOH HOH . G 4 HOH A 15 715 38 HOH HOH . G 4 HOH A 16 716 41 HOH HOH . G 4 HOH A 17 717 43 HOH HOH . G 4 HOH A 18 718 45 HOH HOH . G 4 HOH A 19 719 46 HOH HOH . G 4 HOH A 20 720 47 HOH HOH . G 4 HOH A 21 721 48 HOH HOH . G 4 HOH A 22 722 50 HOH HOH . G 4 HOH A 23 723 52 HOH HOH . G 4 HOH A 24 724 53 HOH HOH . G 4 HOH A 25 725 54 HOH HOH . G 4 HOH A 26 726 56 HOH HOH . G 4 HOH A 27 727 57 HOH HOH . G 4 HOH A 28 728 59 HOH HOH . G 4 HOH A 29 729 61 HOH HOH . G 4 HOH A 30 730 65 HOH HOH . G 4 HOH A 31 731 67 HOH HOH . G 4 HOH A 32 732 68 HOH HOH . G 4 HOH A 33 733 73 HOH HOH . G 4 HOH A 34 734 74 HOH HOH . G 4 HOH A 35 735 78 HOH HOH . G 4 HOH A 36 736 80 HOH HOH . G 4 HOH A 37 737 81 HOH HOH . G 4 HOH A 38 738 86 HOH HOH . G 4 HOH A 39 739 87 HOH HOH . G 4 HOH A 40 740 93 HOH HOH . G 4 HOH A 41 741 94 HOH HOH . G 4 HOH A 42 742 102 HOH HOH . G 4 HOH A 43 743 104 HOH HOH . G 4 HOH A 44 744 106 HOH HOH . G 4 HOH A 45 745 107 HOH HOH . H 4 HOH B 1 1201 4 HOH HOH . H 4 HOH B 2 1202 5 HOH HOH . H 4 HOH B 3 1203 6 HOH HOH . H 4 HOH B 4 1204 8 HOH HOH . H 4 HOH B 5 1205 9 HOH HOH . H 4 HOH B 6 1206 12 HOH HOH . H 4 HOH B 7 1207 13 HOH HOH . H 4 HOH B 8 1208 14 HOH HOH . H 4 HOH B 9 1209 17 HOH HOH . H 4 HOH B 10 1210 19 HOH HOH . H 4 HOH B 11 1211 20 HOH HOH . H 4 HOH B 12 1212 21 HOH HOH . H 4 HOH B 13 1213 22 HOH HOH . H 4 HOH B 14 1214 23 HOH HOH . H 4 HOH B 15 1215 25 HOH HOH . H 4 HOH B 16 1216 28 HOH HOH . H 4 HOH B 17 1217 29 HOH HOH . H 4 HOH B 18 1218 30 HOH HOH . H 4 HOH B 19 1219 33 HOH HOH . H 4 HOH B 20 1220 34 HOH HOH . H 4 HOH B 21 1221 39 HOH HOH . H 4 HOH B 22 1222 40 HOH HOH . H 4 HOH B 23 1223 42 HOH HOH . H 4 HOH B 24 1224 49 HOH HOH . H 4 HOH B 25 1225 51 HOH HOH . H 4 HOH B 26 1226 55 HOH HOH . H 4 HOH B 27 1227 60 HOH HOH . H 4 HOH B 28 1228 62 HOH HOH . H 4 HOH B 29 1229 63 HOH HOH . H 4 HOH B 30 1230 69 HOH HOH . H 4 HOH B 31 1231 70 HOH HOH . H 4 HOH B 32 1232 71 HOH HOH . H 4 HOH B 33 1233 75 HOH HOH . H 4 HOH B 34 1234 77 HOH HOH . H 4 HOH B 35 1235 83 HOH HOH . H 4 HOH B 36 1236 91 HOH HOH . H 4 HOH B 37 1237 92 HOH HOH . H 4 HOH B 38 1238 95 HOH HOH . H 4 HOH B 39 1239 96 HOH HOH . H 4 HOH B 40 1240 97 HOH HOH . H 4 HOH B 41 1241 98 HOH HOH . H 4 HOH B 42 1242 99 HOH HOH . H 4 HOH B 43 1243 100 HOH HOH . H 4 HOH B 44 1244 105 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 . . . E 2 14.439 100.175 134.151 1 54.21 ? C2 1SY 1101 B 1 HETATM 2 N N01 1SY . . . E 2 12.023 99.304 136.812 1 63.37 ? N01 1SY 1101 B 1 HETATM 3 C C6 1SY . . . E 2 12.584 99.787 135.533 1 58.81 ? C6 1SY 1101 B 1 HETATM 4 N N1 1SY . . . E 2 13.915 99.749 135.322 1 49.89 ? N1 1SY 1101 B 1 HETATM 5 N N3 1SY . . . E 2 13.673 100.646 133.165 1 52.09 ? N3 1SY 1101 B 1 HETATM 6 C C4 1SY . . . E 2 12.319 100.719 133.288 1 46.65 ? C4 1SY 1101 B 1 HETATM 7 C C5 1SY . . . E 2 11.714 100.281 134.502 1 45.54 ? C5 1SY 1101 B 1 HETATM 8 N N7 1SY . . . E 2 10.357 100.463 134.364 1 63.98 ? N7 1SY 1101 B 1 HETATM 9 C C8 1SY . . . E 2 10.101 100.994 133.133 1 73.27 ? C8 1SY 1101 B 1 HETATM 10 N N9 1SY . . . E 2 11.274 101.145 132.494 1 54.65 ? N9 1SY 1101 B 1 HETATM 11 C C1' 1SY . . . E 2 11.724 101.659 131.217 1 59.54 ? C1' 1SY 1101 B 1 HETATM 12 C C2' 1SY . . . E 2 11.7 100.638 130.169 1 59.97 ? C2' 1SY 1101 B 1 HETATM 13 O O2' 1SY . . . E 2 12.803 100.817 129.28 1 68.46 ? O2' 1SY 1101 B 1 HETATM 14 C C3' 1SY . . . E 2 10.459 100.903 129.44 1 62.49 ? C3' 1SY 1101 B 1 HETATM 15 C C4' 1SY . . . E 2 10.143 102.333 129.609 1 55.69 ? C4' 1SY 1101 B 1 HETATM 16 C C16 1SY . . . E 2 8.659 102.516 129.829 1 57.83 ? C16 1SY 1101 B 1 HETATM 17 O O17 1SY . . . E 2 8.211 101.558 130.745 1 50.42 ? O17 1SY 1101 B 1 HETATM 18 P P18 1SY . . . E 2 6.65 101.336 131.028 1 59 ? P18 1SY 1101 B 1 HETATM 19 O O19 1SY . . . E 2 6.103 102.174 132.193 1 71.67 ? O19 1SY 1101 B 1 HETATM 20 O O20 1SY . . . E 2 6.229 99.78 131.108 1 68.78 ? O20 1SY 1101 B 1 HETATM 21 C C21 1SY . . . E 2 6.988 98.874 130.333 1 61.84 ? C21 1SY 1101 B 1 HETATM 22 C C22 1SY . . . E 2 6.31 98.538 129.05 1 65.23 ? C22 1SY 1101 B 1 HETATM 23 O O23 1SY . . . E 2 4.95 98.307 129.298 1 47.43 ? O23 1SY 1101 B 1 HETATM 24 C C24 1SY . . . E 2 6.883 97.26 128.635 1 59.76 ? C24 1SY 1101 B 1 HETATM 25 C C25 1SY . . . E 2 8.094 97.427 127.751 1 46.85 ? C25 1SY 1101 B 1 HETATM 26 O O26 1SY . . . E 2 8.62 98.746 127.869 1 48.06 ? O26 1SY 1101 B 1 HETATM 27 P P27 1SY . . . E 2 10.198 98.987 127.687 1 56.36 ? P27 1SY 1101 B 1 HETATM 28 O O28 1SY . . . E 2 10.675 100.532 128.052 1 58.76 ? O28 1SY 1101 B 1 HETATM 29 O O29 1SY . . . E 2 11.106 97.961 128.317 1 41.37 ? O29 1SY 1101 B 1 HETATM 30 O O30 1SY . . . E 2 10.364 98.856 126.217 1 56.68 ? O30 1SY 1101 B 1 HETATM 31 O O31 1SY . . . E 2 7.19 96.567 129.874 1 44.41 ? O31 1SY 1101 B 1 HETATM 32 C C32 1SY . . . E 2 7.048 97.535 130.959 1 50.56 ? C32 1SY 1101 B 1 HETATM 33 N N33 1SY . . . E 2 8.154 97.446 131.723 1 52.18 ? N33 1SY 1101 B 1 HETATM 34 C C34 1SY . . . E 2 9.386 97.448 131.279 1 50.5 ? C34 1SY 1101 B 1 HETATM 35 N N35 1SY . . . E 2 10.225 97.314 132.314 1 47.19 ? N35 1SY 1101 B 1 HETATM 36 C C36 1SY . . . E 2 8.149 97.302 133.08 1 49.08 ? C36 1SY 1101 B 1 HETATM 37 C C37 1SY . . . E 2 9.486 97.221 133.448 1 44.72 ? C37 1SY 1101 B 1 HETATM 38 C C38 1SY . . . E 2 9.852 97.057 134.889 1 54.12 ? C38 1SY 1101 B 1 HETATM 39 N N39 1SY . . . E 2 8.82 96.979 135.867 1 53.68 ? N39 1SY 1101 B 1 HETATM 40 C C40 1SY . . . E 2 7.448 97.07 135.475 1 44.06 ? C40 1SY 1101 B 1 HETATM 41 N N41 1SY . . . E 2 6.431 96.992 136.469 1 58.4 ? N41 1SY 1101 B 1 HETATM 42 N N42 1SY . . . E 2 7.088 97.23 134.074 1 62.46 ? N42 1SY 1101 B 1 HETATM 43 O O43 1SY . . . E 2 11.058 96.989 135.219 1 39.7 ? O43 1SY 1101 B 1 HETATM 44 O O44 1SY . . . E 2 5.968 101.811 129.819 1 56.22 ? O44 1SY 1101 B 1 HETATM 45 O O4' 1SY . . . E 2 10.928 102.765 130.757 1 50.93 ? O4' 1SY 1101 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 45 #