data_1W25 # _model_server_result.job_id lMaNOWwbA0oJqt6f5YeKTw _model_server_result.datetime_utc '2024-11-25 07:24:20' _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 1w25 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":505}' # _entry.id 1W25 # _exptl.entry_id 1W25 _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 5 _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 1W25 _cell.length_a 135.87 _cell.length_b 135.87 _cell.length_c 169.247 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1W25 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # _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 I N N ? 4 J 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 8 A ASP 9 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc2 A OD1 ASP 9 A ASP 10 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc3 A OD2 ASP 52 A ASP 53 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc4 A O MET 54 A MET 55 1_555 D MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 B OD1 ASP 8 B ASP 9 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc6 B OD1 ASP 9 B ASP 10 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc7 B OD2 ASP 52 B ASP 53 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc8 B O MET 54 B MET 55 1_555 H MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? # _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 1W25 _atom_sites.fract_transf_matrix[1][1] 0.00736 _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] 0.00736 _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] 0.005909 _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 ZN A 1 499 499 ZN ZN . D 3 MG A 1 500 500 MG MG . E 4 C2E A 1 501 501 C2E C2E . F 4 C2E A 1 503 503 C2E C2E . G 4 C2E A 1 505 505 C2E C2E . H 3 MG B 1 500 500 MG MG . I 4 C2E B 1 503 503 C2E C2E . J 4 C2E B 1 505 505 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 . 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 . # 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 . . . J 4 97.486 62.38 60.571 1 19.87 ? P1 C2E 505 B 1 HETATM 2 O O2P C2E . . . J 4 98.045 63.747 60.297 1 13.5 ? O2P C2E 505 B 1 HETATM 3 O O1P C2E . . . J 4 96.061 62.459 61.074 1 19.42 ? O1P C2E 505 B 1 HETATM 4 O O5' C2E . . . J 4 97.474 61.495 59.227 1 16.1 ? O5' C2E 505 B 1 HETATM 5 C C5' C2E . . . J 4 96.776 60.26 59.256 1 19.14 ? C5' C2E 505 B 1 HETATM 6 C C4' C2E . . . J 4 97.197 59.401 58.073 1 21.49 ? C4' C2E 505 B 1 HETATM 7 O O4' C2E . . . J 4 96.711 60.019 56.874 1 24.05 ? O4' C2E 505 B 1 HETATM 8 C C3' C2E . . . J 4 98.709 59.192 57.923 1 19.69 ? C3' C2E 505 B 1 HETATM 9 O O3' C2E . . . J 4 99.046 57.995 58.637 1 19.97 ? O3' C2E 505 B 1 HETATM 10 C C2' C2E . . . J 4 98.836 59.089 56.416 1 22.38 ? C2' C2E 505 B 1 HETATM 11 O O2' C2E . . . J 4 98.671 57.726 55.985 1 21.82 ? O2' C2E 505 B 1 HETATM 12 C C1' C2E . . . J 4 97.687 59.91 55.843 1 20.92 ? C1' C2E 505 B 1 HETATM 13 N N9 C2E . . . J 4 98.083 61.278 55.455 1 20.72 ? N9 C2E 505 B 1 HETATM 14 C C8 C2E . . . J 4 97.67 62.432 56.03 1 21.88 ? C8 C2E 505 B 1 HETATM 15 N N7 C2E . . . J 4 98.217 63.526 55.418 1 20.58 ? N7 C2E 505 B 1 HETATM 16 C C5 C2E . . . J 4 98.983 63.059 54.423 1 20.62 ? C5 C2E 505 B 1 HETATM 17 C C6 C2E . . . J 4 99.841 63.646 53.382 1 20.87 ? C6 C2E 505 B 1 HETATM 18 O O6 C2E . . . J 4 99.961 64.883 53.305 1 22.51 ? O6 C2E 505 B 1 HETATM 19 N N1 C2E . . . J 4 100.477 62.816 52.538 1 22.24 ? N1 C2E 505 B 1 HETATM 20 C C2 C2E . . . J 4 100.343 61.478 52.614 1 19.72 ? C2 C2E 505 B 1 HETATM 21 N N2 C2E . . . J 4 101.003 60.684 51.741 1 19.16 ? N2 C2E 505 B 1 HETATM 22 N N3 C2E . . . J 4 99.572 60.878 53.547 1 20.79 ? N3 C2E 505 B 1 HETATM 23 C C4 C2E . . . J 4 98.883 61.59 54.451 1 20.52 ? C4 C2E 505 B 1 HETATM 24 P P11 C2E . . . J 4 100.606 57.973 59.015 1 17.36 ? P11 C2E 505 B 1 HETATM 25 O O21 C2E . . . J 4 101.425 58.043 57.768 1 21.75 ? O21 C2E 505 B 1 HETATM 26 O O11 C2E . . . J 4 100.916 56.676 59.727 1 16.43 ? O11 C2E 505 B 1 HETATM 27 O O5A C2E . . . J 4 100.94 59.198 59.991 1 20.77 ? O5A C2E 505 B 1 HETATM 28 C C5A C2E . . . J 4 100.316 59.167 61.267 1 20.83 ? C5A C2E 505 B 1 HETATM 29 C C4A C2E . . . J 4 100.462 60.498 61.956 1 21.74 ? C4A C2E 505 B 1 HETATM 30 O O4A C2E . . . J 4 101.841 60.847 62.046 1 24.49 ? O4A C2E 505 B 1 HETATM 31 C C3A C2E . . . J 4 99.753 61.638 61.25 1 22.75 ? C3A C2E 505 B 1 HETATM 32 O O3A C2E . . . J 4 98.38 61.661 61.674 1 20.51 ? O3A C2E 505 B 1 HETATM 33 C C2A C2E . . . J 4 100.578 62.807 61.749 1 22.14 ? C2A C2E 505 B 1 HETATM 34 O O2A C2E . . . J 4 100.101 63.23 63.023 1 23.19 ? O2A C2E 505 B 1 HETATM 35 C C1A C2E . . . J 4 101.986 62.257 61.914 1 21.84 ? C1A C2E 505 B 1 HETATM 36 N N91 C2E . . . J 4 102.793 62.553 60.712 1 22.16 ? N91 C2E 505 B 1 HETATM 37 C C81 C2E . . . J 4 103.238 61.685 59.781 1 22.87 ? C81 C2E 505 B 1 HETATM 38 N N71 C2E . . . J 4 103.937 62.333 58.815 1 22.17 ? N71 C2E 505 B 1 HETATM 39 C C51 C2E . . . J 4 103.946 63.633 59.128 1 21.71 ? C51 C2E 505 B 1 HETATM 40 C C61 C2E . . . J 4 104.497 64.871 58.549 1 22.25 ? C61 C2E 505 B 1 HETATM 41 O O61 C2E . . . J 4 105.156 64.872 57.495 1 21.78 ? O61 C2E 505 B 1 HETATM 42 N N11 C2E . . . J 4 104.269 66.011 59.202 1 23.16 ? N11 C2E 505 B 1 HETATM 43 C C21 C2E . . . J 4 103.557 66.068 60.344 1 22.38 ? C21 C2E 505 B 1 HETATM 44 N N21 C2E . . . J 4 103.371 67.263 60.942 1 22.25 ? N21 C2E 505 B 1 HETATM 45 N N31 C2E . . . J 4 103.025 64.974 60.935 1 21.65 ? N31 C2E 505 B 1 HETATM 46 C C41 C2E . . . J 4 103.191 63.763 60.377 1 21.3 ? C41 C2E 505 B 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #