data_4URS # _model_server_result.job_id fBV-x5qGv5nKah6sK-DDtw _model_server_result.datetime_utc '2024-11-16 17:51:36' _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 4urs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1249}' # _entry.id 4URS # _exptl.entry_id 4URS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 95.48 _cell.angle_beta 100.23 _cell.angle_gamma 107.78 _cell.entry_id 4URS _cell.length_a 37.15 _cell.length_b 37.14 _cell.length_c 62.28 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4URS _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 J N N # _chem_comp.formula 'C20 H24 N10 O14 P2' _chem_comp.formula_weight 690.411 _chem_comp.id C2E _chem_comp.mon_nstd_flag . _chem_comp.name "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'c-di-GMP;Cyclic diguanosine monophosphate' # 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 P1 O2P C2E sing 70 n n O1P P1 C2E doub 71 n n O5' P1 C2E sing 72 n n C5' O5' C2E sing 73 n n C4' O4' C2E sing 74 n n C4' C5' C2E sing 75 n n C3' C4' C2E sing 76 n n O3' P11 C2E sing 77 n n O3' C3' C2E sing 78 n n C2' C3' C2E sing 79 n n C2' C1' C2E sing 80 n n O2' C2' C2E sing 81 n n C1' O4' C2E sing 82 n n C1' N9 C2E sing 83 n n N9 C4 C2E sing 84 n y N9 C8 C2E sing 85 n y C8 N7 C2E doub 86 n y C5 N7 C2E sing 87 n y C5 C6 C2E sing 88 n n C6 O6 C2E doub 89 n n N1 C6 C2E sing 90 n n C2 N1 C2E sing 91 n n N2 C2 C2E sing 92 n n N3 C2 C2E doub 93 n n N3 C4 C2E sing 94 n n C4 C5 C2E doub 95 n y P11 O21 C2E sing 96 n n P11 O5A C2E sing 97 n n O11 P11 C2E doub 98 n n C5A O5A C2E sing 99 n n C5A C4A C2E sing 100 n n C4A O4A C2E sing 101 n n C4A C3A C2E sing 102 n n O4A C1A C2E sing 103 n n C3A C2A C2E sing 104 n n O3A C3A C2E sing 105 n n O3A P1 C2E sing 106 n n C2A O2A C2E sing 107 n n C1A C2A C2E sing 108 n n C1A N91 C2E sing 109 n n N91 C41 C2E sing 110 n y C81 N71 C2E doub 111 n y C81 N91 C2E sing 112 n y N71 C51 C2E sing 113 n y C51 C41 C2E doub 114 n y C51 C61 C2E sing 115 n n C61 O61 C2E doub 116 n n C61 N11 C2E sing 117 n n C21 N11 C2E sing 118 n n C21 N21 C2E sing 119 n n N31 C21 C2E doub 120 n n C41 N31 C2E sing 121 n n O2P HO2P C2E sing 122 n n C5' "H5'1" C2E sing 123 n n C5' "H5'2" C2E sing 124 n n C4' H4' C2E sing 125 n n C3' H3' C2E sing 126 n n C2' H2' C2E sing 127 n n O2' HO2' C2E sing 128 n n C1' H1' C2E sing 129 n n C8 H8 C2E sing 130 n n N1 HN1 C2E sing 131 n n N2 HN21 C2E sing 132 n n N2 HN22 C2E sing 133 n n O21 HO21 C2E sing 134 n n C5A H511 C2E sing 135 n n C5A H512 C2E sing 136 n n C4A H4A C2E sing 137 n n C3A H3A C2E sing 138 n n C2A H2A C2E sing 139 n n O2A HO2A C2E sing 140 n n C1A H1A C2E sing 141 n n C81 H81 C2E sing 142 n n N11 HN11 C2E sing 143 n n N21 HN24 C2E sing 144 n n N21 HN23 C2E sing 145 n n # _atom_sites.entry_id 4URS _atom_sites.fract_transf_matrix[1][1] 0.026918 _atom_sites.fract_transf_matrix[1][2] 0.008632 _atom_sites.fract_transf_matrix[1][3] 0.006318 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028276 _atom_sites.fract_transf_matrix[2][3] 0.004577 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016528 _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 GOL A 1 1249 1249 GOL GOL . D 3 MES A 1 1250 1250 MES MES . E 4 C2E A 1 1251 1251 C2E C2E . F 4 C2E A 1 1252 1252 C2E C2E . G 4 C2E B 1 1249 1249 C2E C2E . H 2 GOL B 1 1250 1250 GOL GOL . I 2 GOL B 1 1251 1251 GOL GOL . J 4 C2E B 1 1252 1252 C2E C2E . K 5 HOH A 1 2001 2001 HOH HOH . K 5 HOH A 2 2002 2002 HOH HOH . K 5 HOH A 3 2003 2003 HOH HOH . K 5 HOH A 4 2004 2004 HOH HOH . K 5 HOH A 5 2005 2005 HOH HOH . K 5 HOH A 6 2006 2006 HOH HOH . K 5 HOH A 7 2007 2007 HOH HOH . K 5 HOH A 8 2008 2008 HOH HOH . K 5 HOH A 9 2009 2009 HOH HOH . K 5 HOH A 10 2010 2010 HOH HOH . K 5 HOH A 11 2011 2011 HOH HOH . K 5 HOH A 12 2012 2012 HOH HOH . K 5 HOH A 13 2013 2013 HOH HOH . K 5 HOH A 14 2014 2014 HOH HOH . K 5 HOH A 15 2015 2015 HOH HOH . K 5 HOH A 16 2016 2016 HOH HOH . K 5 HOH A 17 2017 2017 HOH HOH . K 5 HOH A 18 2018 2018 HOH HOH . K 5 HOH A 19 2019 2019 HOH HOH . K 5 HOH A 20 2020 2020 HOH HOH . K 5 HOH A 21 2021 2021 HOH HOH . K 5 HOH A 22 2022 2022 HOH HOH . K 5 HOH A 23 2023 2023 HOH HOH . K 5 HOH A 24 2024 2024 HOH HOH . K 5 HOH A 25 2025 2025 HOH HOH . K 5 HOH A 26 2026 2026 HOH HOH . K 5 HOH A 27 2027 2027 HOH HOH . K 5 HOH A 28 2028 2028 HOH HOH . K 5 HOH A 29 2029 2029 HOH HOH . K 5 HOH A 30 2030 2030 HOH HOH . K 5 HOH A 31 2031 2031 HOH HOH . K 5 HOH A 32 2032 2032 HOH HOH . K 5 HOH A 33 2033 2033 HOH HOH . K 5 HOH A 34 2034 2034 HOH HOH . K 5 HOH A 35 2035 2035 HOH HOH . K 5 HOH A 36 2036 2036 HOH HOH . K 5 HOH A 37 2037 2037 HOH HOH . K 5 HOH A 38 2038 2038 HOH HOH . K 5 HOH A 39 2039 2039 HOH HOH . K 5 HOH A 40 2040 2040 HOH HOH . K 5 HOH A 41 2041 2041 HOH HOH . K 5 HOH A 42 2042 2042 HOH HOH . K 5 HOH A 43 2043 2043 HOH HOH . K 5 HOH A 44 2044 2044 HOH HOH . K 5 HOH A 45 2045 2045 HOH HOH . K 5 HOH A 46 2046 2046 HOH HOH . K 5 HOH A 47 2047 2047 HOH HOH . K 5 HOH A 48 2048 2048 HOH HOH . K 5 HOH A 49 2049 2049 HOH HOH . K 5 HOH A 50 2050 2050 HOH HOH . K 5 HOH A 51 2051 2051 HOH HOH . K 5 HOH A 52 2052 2052 HOH HOH . K 5 HOH A 53 2053 2053 HOH HOH . K 5 HOH A 54 2054 2054 HOH HOH . K 5 HOH A 55 2055 2055 HOH HOH . K 5 HOH A 56 2056 2056 HOH HOH . K 5 HOH A 57 2057 2057 HOH HOH . K 5 HOH A 58 2058 2058 HOH HOH . K 5 HOH A 59 2059 2059 HOH HOH . K 5 HOH A 60 2060 2060 HOH HOH . K 5 HOH A 61 2061 2061 HOH HOH . K 5 HOH A 62 2062 2062 HOH HOH . L 5 HOH B 1 2001 2001 HOH HOH . L 5 HOH B 2 2002 2002 HOH HOH . L 5 HOH B 3 2003 2003 HOH HOH . L 5 HOH B 4 2004 2004 HOH HOH . L 5 HOH B 5 2005 2005 HOH HOH . L 5 HOH B 6 2006 2006 HOH HOH . L 5 HOH B 7 2007 2007 HOH HOH . L 5 HOH B 8 2008 2008 HOH HOH . L 5 HOH B 9 2009 2009 HOH HOH . L 5 HOH B 10 2010 2010 HOH HOH . L 5 HOH B 11 2011 2011 HOH HOH . L 5 HOH B 12 2012 2012 HOH HOH . L 5 HOH B 13 2013 2013 HOH HOH . L 5 HOH B 14 2014 2014 HOH HOH . L 5 HOH B 15 2015 2015 HOH HOH . L 5 HOH B 16 2016 2016 HOH HOH . L 5 HOH B 17 2017 2017 HOH HOH . L 5 HOH B 18 2018 2018 HOH HOH . L 5 HOH B 19 2019 2019 HOH HOH . L 5 HOH B 20 2020 2020 HOH HOH . L 5 HOH B 21 2021 2021 HOH HOH . L 5 HOH B 22 2022 2022 HOH HOH . L 5 HOH B 23 2023 2023 HOH HOH . L 5 HOH B 24 2024 2024 HOH HOH . L 5 HOH B 25 2025 2025 HOH HOH . L 5 HOH B 26 2026 2026 HOH HOH . L 5 HOH B 27 2027 2027 HOH HOH . L 5 HOH B 28 2028 2028 HOH HOH . L 5 HOH B 29 2029 2029 HOH HOH . L 5 HOH B 30 2030 2030 HOH HOH . L 5 HOH B 31 2031 2031 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 P P1 C2E . . . G 4 3.096 -24.123 -30.044 1 50.54 ? P1 C2E 1249 B 1 HETATM 2 O O2P C2E . . . G 4 3.33 -25.542 -30.441 1 47.54 ? O2P C2E 1249 B 1 HETATM 3 O O1P C2E . . . G 4 3.366 -23.042 -31.036 1 50.46 ? O1P C2E 1249 B 1 HETATM 4 O O5' C2E . . . G 4 3.872 -23.786 -28.621 1 47.52 ? O5' C2E 1249 B 1 HETATM 5 C C5' C2E . . . G 4 3.762 -24.699 -27.497 1 44.36 ? C5' C2E 1249 B 1 HETATM 6 C C4' C2E . . . G 4 4.257 -24.123 -26.136 1 43.93 ? C4' C2E 1249 B 1 HETATM 7 O O4' C2E . . . G 4 5.656 -23.644 -26.136 1 43.68 ? O4' C2E 1249 B 1 HETATM 8 C C3' C2E . . . G 4 3.41 -22.967 -25.626 1 43.84 ? C3' C2E 1249 B 1 HETATM 9 O O3' C2E . . . G 4 2.23 -23.473 -24.964 1 45.18 ? O3' C2E 1249 B 1 HETATM 10 C C2' C2E . . . G 4 4.372 -22.319 -24.603 1 41 ? C2' C2E 1249 B 1 HETATM 11 O O2' C2E . . . G 4 4.442 -23.073 -23.365 1 33.27 ? O2' C2E 1249 B 1 HETATM 12 C C1' C2E . . . G 4 5.704 -22.396 -25.366 1 43.51 ? C1' C2E 1249 B 1 HETATM 13 N N9 C2E . . . G 4 5.923 -21.17 -26.249 1 43.44 ? N9 C2E 1249 B 1 HETATM 14 C C8 C2E . . . G 4 5.748 -21.122 -27.571 1 40.19 ? C8 C2E 1249 B 1 HETATM 15 N N7 C2E . . . G 4 6.04 -19.901 -28.011 1 41.36 ? N7 C2E 1249 B 1 HETATM 16 C C5 C2E . . . G 4 6.356 -19.152 -26.953 1 43.82 ? C5 C2E 1249 B 1 HETATM 17 C C6 C2E . . . G 4 6.714 -17.856 -26.818 1 42.54 ? C6 C2E 1249 B 1 HETATM 18 O O6 C2E . . . G 4 6.749 -17.049 -27.919 1 38.82 ? O6 C2E 1249 B 1 HETATM 19 N N1 C2E . . . G 4 7.009 -17.368 -25.61 1 42.83 ? N1 C2E 1249 B 1 HETATM 20 C C2 C2E . . . G 4 6.91 -18.145 -24.516 1 40.21 ? C2 C2E 1249 B 1 HETATM 21 N N2 C2E . . . G 4 7.204 -17.617 -23.33 1 39.15 ? N2 C2E 1249 B 1 HETATM 22 N N3 C2E . . . G 4 6.568 -19.443 -24.641 1 38.81 ? N3 C2E 1249 B 1 HETATM 23 C C4 C2E . . . G 4 6.279 -19.942 -25.856 1 42.57 ? C4 C2E 1249 B 1 HETATM 24 P P11 C2E . . . G 4 0.91 -22.576 -24.752 1 47.46 ? P11 C2E 1249 B 1 HETATM 25 O O21 C2E . . . G 4 1.275 -21.149 -24.615 1 47.5 ? O21 C2E 1249 B 1 HETATM 26 O O11 C2E . . . G 4 0.15 -23.214 -23.642 1 48.73 ? O11 C2E 1249 B 1 HETATM 27 O O5A C2E . . . G 4 0.09 -22.608 -26.171 1 49.33 ? O5A C2E 1249 B 1 HETATM 28 C C5A C2E . . . G 4 -0.081 -23.76 -27.036 1 51.24 ? C5A C2E 1249 B 1 HETATM 29 C C4A C2E . . . G 4 -0.385 -23.326 -28.501 1 52.4 ? C4A C2E 1249 B 1 HETATM 30 O O4A C2E . . . G 4 -1.29 -22.2 -28.637 1 51.4 ? O4A C2E 1249 B 1 HETATM 31 C C3A C2E . . . G 4 0.865 -22.909 -29.231 1 52.91 ? C3A C2E 1249 B 1 HETATM 32 O O3A C2E . . . G 4 1.536 -24.093 -29.637 1 53.19 ? O3A C2E 1249 B 1 HETATM 33 C C2A C2E . . . G 4 0.321 -22.148 -30.435 1 51.84 ? C2A C2E 1249 B 1 HETATM 34 O O2A C2E . . . G 4 -0.051 -23.017 -31.491 1 55.39 ? O2A C2E 1249 B 1 HETATM 35 C C1A C2E . . . G 4 -0.901 -21.458 -29.895 1 50.39 ? C1A C2E 1249 B 1 HETATM 36 N N91 C2E . . . G 4 -0.548 -20.03 -29.657 1 49.48 ? N91 C2E 1249 B 1 HETATM 37 C C81 C2E . . . G 4 -0.146 -19.639 -28.466 1 48.51 ? C81 C2E 1249 B 1 HETATM 38 N N71 C2E . . . G 4 0.166 -18.362 -28.497 1 50.18 ? N71 C2E 1249 B 1 HETATM 39 C C51 C2E . . . G 4 -0.028 -17.936 -29.731 1 52.63 ? C51 C2E 1249 B 1 HETATM 40 C C61 C2E . . . G 4 0.145 -16.737 -30.29 1 53.83 ? C61 C2E 1249 B 1 HETATM 41 O O61 C2E . . . G 4 0.536 -15.725 -29.474 1 55.67 ? O61 C2E 1249 B 1 HETATM 42 N N11 C2E . . . G 4 -0.118 -16.546 -31.585 1 52.67 ? N11 C2E 1249 B 1 HETATM 43 C C21 C2E . . . G 4 -0.526 -17.582 -32.339 1 52.45 ? C21 C2E 1249 B 1 HETATM 44 N N21 C2E . . . G 4 -0.798 -17.389 -33.627 1 52.21 ? N21 C2E 1249 B 1 HETATM 45 N N31 C2E . . . G 4 -0.701 -18.793 -31.777 1 52.19 ? N31 C2E 1249 B 1 HETATM 46 C C41 C2E . . . G 4 -0.444 -18.974 -30.467 1 51.44 ? C41 C2E 1249 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #