data_3I5A # _model_server_result.job_id lOv5JMH4ucaRfP3hthWx1g _model_server_result.datetime_utc '2025-02-27 07:06:30' _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 3i5a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":335}' # _entry.id 3I5A # _exptl.entry_id 3I5A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 2 _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 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 3I5A _cell.length_a 111.7 _cell.length_b 181.2 _cell.length_c 39.55 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I5A _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C 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 OD1 ASP 24 A ASP 24 1_555 D SR SR . A SR 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc2 A OD1 ASP 68 A ASP 68 1_555 D SR SR . A SR 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc3 A O VAL 70 A VAL 70 1_555 D SR SR . A SR 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? # _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 3I5A _atom_sites.fract_transf_matrix[1][1] 0.008953 _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] 0.005519 _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] 0.025284 _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 C2E A 1 335 3 C2E C2E . C 2 C2E A 1 336 4 C2E C2E . D 3 SR A 1 337 1 SR SR . E 4 HOH A 1 338 1 HOH HOH . E 4 HOH A 2 339 2 HOH HOH . E 4 HOH A 3 340 3 HOH HOH . E 4 HOH A 4 341 4 HOH HOH . E 4 HOH A 5 342 5 HOH HOH . E 4 HOH A 6 343 7 HOH HOH . E 4 HOH A 7 344 8 HOH HOH . E 4 HOH A 8 345 10 HOH HOH . E 4 HOH A 9 346 11 HOH HOH . E 4 HOH A 10 347 13 HOH HOH . E 4 HOH A 11 348 14 HOH HOH . E 4 HOH A 12 349 15 HOH HOH . E 4 HOH A 13 350 17 HOH HOH . E 4 HOH A 14 351 19 HOH HOH . E 4 HOH A 15 352 22 HOH HOH . E 4 HOH A 16 353 23 HOH HOH . E 4 HOH A 17 354 24 HOH HOH . E 4 HOH A 18 355 25 HOH HOH . E 4 HOH A 19 356 32 HOH HOH . E 4 HOH A 20 357 33 HOH HOH . E 4 HOH A 21 358 35 HOH HOH . E 4 HOH A 22 359 38 HOH HOH . E 4 HOH A 23 360 39 HOH HOH . E 4 HOH A 24 361 42 HOH HOH . E 4 HOH A 25 362 43 HOH HOH . E 4 HOH A 26 363 45 HOH HOH . E 4 HOH A 27 364 50 HOH HOH . E 4 HOH A 28 365 60 HOH HOH . E 4 HOH A 29 366 71 HOH HOH . E 4 HOH A 30 367 75 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 . . . B 2 35.935 -9.579 16.241 1 41.63 ? P1 C2E 335 A 1 HETATM 2 O O2P C2E . . . B 2 36.194 -10.742 17.064 1 52.79 ? O2P C2E 335 A 1 HETATM 3 O O1P C2E . . . B 2 34.587 -8.775 16.737 1 42.72 ? O1P C2E 335 A 1 HETATM 4 O O5' C2E . . . B 2 35.223 -10.244 14.744 1 50.79 ? O5' C2E 335 A 1 HETATM 5 C C5' C2E . . . B 2 36.055 -9.944 13.728 1 46.17 ? C5' C2E 335 A 1 HETATM 6 C C4' C2E . . . B 2 35.584 -10.564 12.394 1 38.77 ? C4' C2E 335 A 1 HETATM 7 O O4' C2E . . . B 2 34.325 -11.321 12.437 1 38.25 ? O4' C2E 335 A 1 HETATM 8 C C3' C2E . . . B 2 35.376 -9.366 11.547 1 35.19 ? C3' C2E 335 A 1 HETATM 9 O O3' C2E . . . B 2 36.659 -9.119 11.016 1 42.67 ? O3' C2E 335 A 1 HETATM 10 C C2' C2E . . . B 2 34.251 -9.783 10.568 1 39.21 ? C2' C2E 335 A 1 HETATM 11 O O2' C2E . . . B 2 34.605 -10.291 9.294 1 37.59 ? O2' C2E 335 A 1 HETATM 12 C C1' C2E . . . B 2 33.396 -10.614 11.566 1 36.84 ? C1' C2E 335 A 1 HETATM 13 N N9 C2E . . . B 2 32.531 -9.708 12.318 1 33.87 ? N9 C2E 335 A 1 HETATM 14 C C8 C2E . . . B 2 32.448 -9.484 13.726 1 34.46 ? C8 C2E 335 A 1 HETATM 15 N N7 C2E . . . B 2 31.232 -8.677 13.937 1 30.37 ? N7 C2E 335 A 1 HETATM 16 C C5 C2E . . . B 2 30.604 -8.442 12.648 1 24.18 ? C5 C2E 335 A 1 HETATM 17 C C6 C2E . . . B 2 29.428 -7.763 12.274 1 29.99 ? C6 C2E 335 A 1 HETATM 18 O O6 C2E . . . B 2 28.603 -7.166 13.249 1 30.88 ? O6 C2E 335 A 1 HETATM 19 N N1 C2E . . . B 2 29.067 -7.696 10.882 1 31.07 ? N1 C2E 335 A 1 HETATM 20 C C2 C2E . . . B 2 29.843 -8.284 9.922 1 30.91 ? C2 C2E 335 A 1 HETATM 21 N N2 C2E . . . B 2 29.48 -8.229 8.507 1 32.06 ? N2 C2E 335 A 1 HETATM 22 N N3 C2E . . . B 2 31.028 -8.96 10.306 1 28.22 ? N3 C2E 335 A 1 HETATM 23 C C4 C2E . . . B 2 31.382 -9.024 11.675 1 28.2 ? C4 C2E 335 A 1 HETATM 24 P P11 C2E . . . B 2 37.471 -7.959 11.409 1 48.09 ? P11 C2E 335 A 1 HETATM 25 O O21 C2E . . . B 2 36.562 -6.747 10.724 1 30.93 ? O21 C2E 335 A 1 HETATM 26 O O11 C2E . . . B 2 38.691 -8.192 10.646 1 41.83 ? O11 C2E 335 A 1 HETATM 27 O O5A C2E . . . B 2 38.094 -7.104 12.773 1 37.5 ? O5A C2E 335 A 1 HETATM 28 C C5A C2E . . . B 2 38.483 -7.969 13.973 1 38.67 ? C5A C2E 335 A 1 HETATM 29 C C4A C2E . . . B 2 38.623 -7.075 15.218 1 40.33 ? C4A C2E 335 A 1 HETATM 30 O O4A C2E . . . B 2 38.707 -5.638 15.009 1 39.46 ? O4A C2E 335 A 1 HETATM 31 C C3A C2E . . . B 2 37.144 -7.226 16.022 1 35.87 ? C3A C2E 335 A 1 HETATM 32 O O3A C2E . . . B 2 37.063 -8.503 16.75 1 36.97 ? O3A C2E 335 A 1 HETATM 33 C C2A C2E . . . B 2 37.249 -5.96 16.912 1 35.31 ? C2A C2E 335 A 1 HETATM 34 O O2A C2E . . . B 2 37.836 -6.073 18.187 1 44.04 ? O2A C2E 335 A 1 HETATM 35 C C1A C2E . . . B 2 37.849 -4.956 15.931 1 33.96 ? C1A C2E 335 A 1 HETATM 36 N N91 C2E . . . B 2 36.749 -4.24 15.206 1 36.97 ? N91 C2E 335 A 1 HETATM 37 C C81 C2E . . . B 2 36.39 -4.304 13.783 1 35.82 ? C81 C2E 335 A 1 HETATM 38 N N71 C2E . . . B 2 35.345 -3.288 13.568 1 28.33 ? N71 C2E 335 A 1 HETATM 39 C C51 C2E . . . B 2 34.859 -2.876 14.876 1 30.39 ? C51 C2E 335 A 1 HETATM 40 C C61 C2E . . . B 2 33.789 -2.079 15.253 1 35.09 ? C61 C2E 335 A 1 HETATM 41 O O61 C2E . . . B 2 32.957 -1.514 14.266 1 36.71 ? O61 C2E 335 A 1 HETATM 42 N N11 C2E . . . B 2 33.53 -1.822 16.666 1 38.33 ? N11 C2E 335 A 1 HETATM 43 C C21 C2E . . . B 2 34.348 -2.364 17.634 1 34.55 ? C21 C2E 335 A 1 HETATM 44 N N21 C2E . . . B 2 34.088 -2.107 19.045 1 41.24 ? N21 C2E 335 A 1 HETATM 45 N N31 C2E . . . B 2 35.458 -3.184 17.251 1 38.84 ? N31 C2E 335 A 1 HETATM 46 C C41 C2E . . . B 2 35.698 -3.432 15.884 1 37.45 ? C41 C2E 335 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 46 #