data_2V0N # _model_server_result.job_id RA8Hufialu7oR5sgRFifqw _model_server_result.datetime_utc '2024-11-13 16:23:43' _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 2v0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 2V0N # _exptl.entry_id 2V0N _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2V0N _cell.length_a 128.965 _cell.length_b 132.557 _cell.length_c 88.425 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 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,M,N,O,P,Q,R,S,T _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 O N N ? 4 P 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 9 A ASP 10 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 A OD2 ASP 9 A ASP 10 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc3 A OD1 ASP 52 A ASP 53 1_555 C BE BEF . A BEF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? metalc ? metalc4 A OD2 ASP 52 A ASP 53 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc5 A O MET 54 A MET 55 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc6 A OD1 ASP 326 A ASP 327 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc7 A OD2 ASP 326 A ASP 327 1_555 I MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc8 A O ILE 327 A ILE 328 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc9 A OE2 GLU 369 A GLU 370 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc10 A OE1 GLU 369 A GLU 370 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc11 A OE2 GLU 369 A GLU 370 1_555 I MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 C F2 BEF . A BEF 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc13 D MG MG . A MG 502 1_555 S O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc14 G O2B GAV . A GAV 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc15 G O3G GAV . A GAV 600 1_555 H MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc16 B OD1 ASP 9 B ASP 10 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc17 B OD1 ASP 52 B ASP 53 1_555 M BE BEF . B BEF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.584 ? metalc ? metalc18 B OD2 ASP 52 B ASP 53 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc19 B O MET 54 B MET 55 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc20 B OD1 ASP 326 B ASP 327 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc21 B O ILE 327 B ILE 328 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc22 B OE1 GLU 369 B GLU 370 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc23 B OE2 GLU 369 B GLU 370 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc24 M F2 BEF . B BEF 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc25 N MG MG . B MG 502 1_555 T O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc26 Q O2B GAV . B GAV 600 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc27 Q O3G GAV . B GAV 600 1_555 R MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? # _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 73 n n O1P P1 C2E doub 74 n n O5' P1 C2E sing 75 n n C5' O5' C2E sing 76 n n C4' O4' C2E sing 77 n n C4' C5' C2E sing 78 n n C3' C4' C2E sing 79 n n O3' P11 C2E sing 80 n n O3' C3' C2E sing 81 n n C2' C3' C2E sing 82 n n C2' C1' C2E sing 83 n n O2' C2' C2E sing 84 n n C1' O4' C2E sing 85 n n C1' N9 C2E sing 86 n n N9 C4 C2E sing 87 n y N9 C8 C2E sing 88 n y C8 N7 C2E doub 89 n y C5 N7 C2E sing 90 n y C5 C6 C2E sing 91 n n C6 O6 C2E doub 92 n n N1 C6 C2E sing 93 n n C2 N1 C2E sing 94 n n N2 C2 C2E sing 95 n n N3 C2 C2E doub 96 n n N3 C4 C2E sing 97 n n C4 C5 C2E doub 98 n y P11 O21 C2E sing 99 n n P11 O5A C2E sing 100 n n O11 P11 C2E doub 101 n n C5A O5A C2E sing 102 n n C5A C4A C2E sing 103 n n C4A O4A C2E sing 104 n n C4A C3A C2E sing 105 n n O4A C1A C2E sing 106 n n C3A C2A C2E sing 107 n n O3A C3A C2E sing 108 n n O3A P1 C2E sing 109 n n C2A O2A C2E sing 110 n n C1A C2A C2E sing 111 n n C1A N91 C2E sing 112 n n N91 C41 C2E sing 113 n y C81 N71 C2E doub 114 n y C81 N91 C2E sing 115 n y N71 C51 C2E sing 116 n y C51 C41 C2E doub 117 n y C51 C61 C2E sing 118 n n C61 O61 C2E doub 119 n n C61 N11 C2E sing 120 n n C21 N11 C2E sing 121 n n C21 N21 C2E sing 122 n n N31 C21 C2E doub 123 n n C41 N31 C2E sing 124 n n O2P HO2P C2E sing 125 n n C5' "H5'1" C2E sing 126 n n C5' "H5'2" C2E sing 127 n n C4' H4' C2E sing 128 n n C3' H3' C2E sing 129 n n C2' H2' C2E sing 130 n n O2' HO2' C2E sing 131 n n C1' H1' C2E sing 132 n n C8 H8 C2E sing 133 n n N1 HN1 C2E sing 134 n n N2 HN21 C2E sing 135 n n N2 HN22 C2E sing 136 n n O21 HO21 C2E sing 137 n n C5A H511 C2E sing 138 n n C5A H512 C2E sing 139 n n C4A H4A C2E sing 140 n n C3A H3A C2E sing 141 n n C2A H2A C2E sing 142 n n O2A HO2A C2E sing 143 n n C1A H1A C2E sing 144 n n C81 H81 C2E sing 145 n n N11 HN11 C2E sing 146 n n N21 HN24 C2E sing 147 n n N21 HN23 C2E sing 148 n n # _atom_sites.entry_id 2V0N _atom_sites.fract_transf_matrix[1][1] 0.007754 _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] 0.007544 _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] 0.011309 _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 BEF A 1 501 501 BEF BEF . D 3 MG A 1 502 502 MG MG . E 4 C2E A 1 503 503 C2E C2E . F 4 C2E A 1 505 505 C2E C2E . G 5 GAV A 1 600 600 GAV GAV . H 3 MG A 1 601 601 MG MG . I 3 MG A 1 602 602 MG MG . J 6 SO4 A 1 1470 1470 SO4 SO4 . K 6 SO4 A 1 1471 1471 SO4 SO4 . L 7 CL A 1 1472 1472 CL CL . M 2 BEF B 1 501 501 BEF BEF . N 3 MG B 1 502 502 MG MG . O 4 C2E B 1 503 503 C2E C2E . P 4 C2E B 1 505 505 C2E C2E . Q 5 GAV B 1 600 600 GAV GAV . R 3 MG B 1 601 601 MG MG . S 8 HOH A 1 2001 2001 HOH HOH . S 8 HOH A 2 2002 2002 HOH HOH . S 8 HOH A 3 2003 2003 HOH HOH . S 8 HOH A 4 2004 2004 HOH HOH . S 8 HOH A 5 2005 2005 HOH HOH . S 8 HOH A 6 2006 2006 HOH HOH . S 8 HOH A 7 2007 2007 HOH HOH . S 8 HOH A 8 2008 2008 HOH HOH . T 8 HOH B 1 2001 2001 HOH HOH . T 8 HOH B 2 2002 2002 HOH HOH . T 8 HOH B 3 2003 2003 HOH HOH . T 8 HOH B 4 2004 2004 HOH HOH . T 8 HOH B 5 2005 2005 HOH HOH . T 8 HOH B 6 2006 2006 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 . . . E 4 76.91 63.988 70.313 1 40.61 ? P1 C2E 503 A 1 HETATM 2 O O2P C2E . . . E 4 76.901 62.523 70.6 1 40.36 ? O2P C2E 503 A 1 HETATM 3 O O1P C2E . . . E 4 76.654 64.885 71.497 1 45.03 ? O1P C2E 503 A 1 HETATM 4 O O5' C2E . . . E 4 78.365 64.479 69.858 1 39.79 ? O5' C2E 503 A 1 HETATM 5 C C5' C2E . . . E 4 78.645 65.59 68.993 1 39.8 ? C5' C2E 503 A 1 HETATM 6 C C4' C2E . . . E 4 79.711 64.947 68.142 1 41.97 ? C4' C2E 503 A 1 HETATM 7 O O4' C2E . . . E 4 81.029 65.308 68.546 1 37.31 ? O4' C2E 503 A 1 HETATM 8 C C3' C2E . . . E 4 79.663 64.92 66.608 1 42.03 ? C3' C2E 503 A 1 HETATM 9 O O3' C2E . . . E 4 78.842 65.917 65.982 1 42.07 ? O3' C2E 503 A 1 HETATM 10 C C2' C2E . . . E 4 81.15 64.968 66.276 1 42.75 ? C2' C2E 503 A 1 HETATM 11 O O2' C2E . . . E 4 81.548 66.264 65.856 1 44.75 ? O2' C2E 503 A 1 HETATM 12 C C1' C2E . . . E 4 81.867 64.664 67.583 1 41.78 ? C1' C2E 503 A 1 HETATM 13 N N9 C2E . . . E 4 81.986 63.189 67.801 1 42.51 ? N9 C2E 503 A 1 HETATM 14 C C8 C2E . . . E 4 81.36 62.452 68.752 1 42.97 ? C8 C2E 503 A 1 HETATM 15 N N7 C2E . . . E 4 81.693 61.155 68.648 1 42.34 ? N7 C2E 503 A 1 HETATM 16 C C5 C2E . . . E 4 82.562 61.073 67.627 1 43.21 ? C5 C2E 503 A 1 HETATM 17 C C6 C2E . . . E 4 83.243 59.999 67.089 1 43.41 ? C6 C2E 503 A 1 HETATM 18 O O6 C2E . . . E 4 83.127 58.843 67.555 1 43.38 ? O6 C2E 503 A 1 HETATM 19 N N1 C2E . . . E 4 84.036 60.212 66.054 1 42.92 ? N1 C2E 503 A 1 HETATM 20 C C2 C2E . . . E 4 84.198 61.427 65.553 1 41.97 ? C2 C2E 503 A 1 HETATM 21 N N2 C2E . . . E 4 85.032 61.533 64.511 1 43.17 ? N2 C2E 503 A 1 HETATM 22 N N3 C2E . . . E 4 83.566 62.511 66.052 1 41.17 ? N3 C2E 503 A 1 HETATM 23 C C4 C2E . . . E 4 82.738 62.346 67.095 1 41.71 ? C4 C2E 503 A 1 HETATM 24 P P11 C2E . . . E 4 78.047 65.259 64.738 1 44.17 ? P11 C2E 503 A 1 HETATM 25 O O21 C2E . . . E 4 79 64.373 63.959 1 41.73 ? O21 C2E 503 A 1 HETATM 26 O O11 C2E . . . E 4 77.244 66.347 64.026 1 42.36 ? O11 C2E 503 A 1 HETATM 27 O O5A C2E . . . E 4 76.885 64.33 65.301 1 42.91 ? O5A C2E 503 A 1 HETATM 28 C C5A C2E . . . E 4 75.906 65.016 66.072 1 42.01 ? C5A C2E 503 A 1 HETATM 29 C C4A C2E . . . E 4 75.092 64.058 66.918 1 41.39 ? C4A C2E 503 A 1 HETATM 30 O O4A C2E . . . E 4 74.396 63.072 66.141 1 43.1 ? O4A C2E 503 A 1 HETATM 31 C C3A C2E . . . E 4 75.802 63.39 68.105 1 42.22 ? C3A C2E 503 A 1 HETATM 32 O O3A C2E . . . E 4 75.805 64.348 69.175 1 41.61 ? O3A C2E 503 A 1 HETATM 33 C C2A C2E . . . E 4 74.883 62.184 68.261 1 40.65 ? C2A C2E 503 A 1 HETATM 34 O O2A C2E . . . E 4 73.777 62.553 69.05 1 41.81 ? O2A C2E 503 A 1 HETATM 35 C C1A C2E . . . E 4 74.333 61.86 66.892 1 41.25 ? C1A C2E 503 A 1 HETATM 36 N N91 C2E . . . E 4 75.165 60.889 66.17 1 41.3 ? N91 C2E 503 A 1 HETATM 37 C C81 C2E . . . E 4 76.156 61.179 65.313 1 42.9 ? C81 C2E 503 A 1 HETATM 38 N N71 C2E . . . E 4 76.674 60.035 64.823 1 43.94 ? N71 C2E 503 A 1 HETATM 39 C C51 C2E . . . E 4 75.986 59.01 65.377 1 44.38 ? C51 C2E 503 A 1 HETATM 40 C C61 C2E . . . E 4 76.047 57.612 65.269 1 43.76 ? C61 C2E 503 A 1 HETATM 41 O O61 C2E . . . E 4 76.863 56.991 64.541 1 41.59 ? O61 C2E 503 A 1 HETATM 42 N N11 C2E . . . E 4 75.206 56.885 65.981 1 42.63 ? N11 C2E 503 A 1 HETATM 43 C C21 C2E . . . E 4 74.324 57.444 66.773 1 41.19 ? C21 C2E 503 A 1 HETATM 44 N N21 C2E . . . E 4 73.504 56.652 67.448 1 43.56 ? N21 C2E 503 A 1 HETATM 45 N N31 C2E . . . E 4 74.22 58.767 66.916 1 42.03 ? N31 C2E 503 A 1 HETATM 46 C C41 C2E . . . E 4 75.045 59.572 66.226 1 42.45 ? C41 C2E 503 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 46 #