data_4DN0 # _model_server_result.job_id tNAgsjIxbk5NgP4v8Zf2ow _model_server_result.datetime_utc '2024-12-21 14:27:13' _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 4dn0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4DN0 # _exptl.entry_id 4DN0 _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 4DN0 _cell.length_a 41.776 _cell.length_b 82.043 _cell.length_c 91.808 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DN0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 ? 2 B N N ? 2 C N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OE1 _struct_conn.ptnr1_label_comp_id GLU _struct_conn.ptnr1_label_seq_id 214 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id GLU _struct_conn.ptnr1_auth_seq_id 348 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id NA _struct_conn.ptnr2_label_comp_id NA _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NA _struct_conn.ptnr2_auth_seq_id 504 _struct_conn.ptnr2_symmetry 1_555 _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 2.828 _struct_conn.pdbx_value_order ? # _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 4DN0 _atom_sites.fract_transf_matrix[1][1] 0.023937 _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] 0.012189 _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] 0.010892 _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 1 501 1 C2E C2E . C 2 C2E A 1 502 2 C2E C2E . D 3 SO4 A 1 503 1 SO4 SO4 . E 4 NA A 1 504 1 NA NA . F 4 NA A 1 505 2 NA NA . G 5 HOH A 1 601 1 HOH HOH . G 5 HOH A 2 602 2 HOH HOH . G 5 HOH A 3 603 3 HOH HOH . G 5 HOH A 4 604 4 HOH HOH . G 5 HOH A 5 605 5 HOH HOH . G 5 HOH A 6 606 6 HOH HOH . G 5 HOH A 7 607 7 HOH HOH . G 5 HOH A 8 608 8 HOH HOH . G 5 HOH A 9 609 9 HOH HOH . G 5 HOH A 10 610 10 HOH HOH . G 5 HOH A 11 611 11 HOH HOH . G 5 HOH A 12 612 12 HOH HOH . G 5 HOH A 13 613 13 HOH HOH . G 5 HOH A 14 614 14 HOH HOH . G 5 HOH A 15 615 15 HOH HOH . G 5 HOH A 16 616 16 HOH HOH . G 5 HOH A 17 617 17 HOH HOH . G 5 HOH A 18 618 18 HOH HOH . G 5 HOH A 19 619 19 HOH HOH . G 5 HOH A 20 620 20 HOH HOH . G 5 HOH A 21 621 21 HOH HOH . G 5 HOH A 22 622 22 HOH HOH . G 5 HOH A 23 623 23 HOH HOH . G 5 HOH A 24 624 24 HOH HOH . G 5 HOH A 25 625 25 HOH HOH . G 5 HOH A 26 626 26 HOH HOH . G 5 HOH A 27 627 27 HOH HOH . G 5 HOH A 28 628 28 HOH HOH . G 5 HOH A 29 629 29 HOH HOH . G 5 HOH A 30 630 30 HOH HOH . G 5 HOH A 31 631 31 HOH HOH . G 5 HOH A 32 632 32 HOH HOH . G 5 HOH A 33 633 33 HOH HOH . G 5 HOH A 34 634 34 HOH HOH . G 5 HOH A 35 635 35 HOH HOH . G 5 HOH A 36 636 36 HOH HOH . G 5 HOH A 37 637 37 HOH HOH . G 5 HOH A 38 638 38 HOH HOH . G 5 HOH A 39 639 39 HOH HOH . G 5 HOH A 40 640 40 HOH HOH . G 5 HOH A 41 641 41 HOH HOH . G 5 HOH A 42 642 42 HOH HOH . G 5 HOH A 43 643 43 HOH HOH . G 5 HOH A 44 644 44 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 7.217 6.496 -8.211 1 63.18 ? P1 C2E 501 A 1 HETATM 2 O O2P C2E . . . B 2 5.92 7.083 -7.796 1 49.46 ? O2P C2E 501 A 1 HETATM 3 O O1P C2E . . . B 2 7.89 7.555 -9.07 1 62.03 ? O1P C2E 501 A 1 HETATM 4 O O5' C2E . . . B 2 8.27 6.254 -7.058 1 53.01 ? O5' C2E 501 A 1 HETATM 5 C C5' C2E . . . B 2 9.428 5.612 -7.308 1 53.57 ? C5' C2E 501 A 1 HETATM 6 C C4' C2E . . . B 2 10.105 5.099 -6.148 1 57.33 ? C4' C2E 501 A 1 HETATM 7 O O4' C2E . . . B 2 10.084 6.077 -5.157 1 56.04 ? O4' C2E 501 A 1 HETATM 8 C C3' C2E . . . B 2 9.322 3.957 -5.538 1 56.17 ? C3' C2E 501 A 1 HETATM 9 O O3' C2E . . . B 2 9.705 2.705 -6.063 1 60.86 ? O3' C2E 501 A 1 HETATM 10 C C2' C2E . . . B 2 9.634 4.014 -4.203 1 53.38 ? C2' C2E 501 A 1 HETATM 11 O O2' C2E . . . B 2 10.85 3.31 -3.886 1 51.41 ? O2' C2E 501 A 1 HETATM 12 C C1' C2E . . . B 2 9.814 5.425 -3.941 1 54.01 ? C1' C2E 501 A 1 HETATM 13 N N9 C2E . . . B 2 8.611 6.024 -3.4 1 50.08 ? N9 C2E 501 A 1 HETATM 14 C C8 C2E . . . B 2 7.742 6.823 -4.03 1 49.49 ? C8 C2E 501 A 1 HETATM 15 N N7 C2E . . . B 2 6.756 7.151 -3.174 1 47.14 ? N7 C2E 501 A 1 HETATM 16 C C5 C2E . . . B 2 7.007 6.551 -1.993 1 42.72 ? C5 C2E 501 A 1 HETATM 17 C C6 C2E . . . B 2 6.375 6.514 -0.753 1 41.28 ? C6 C2E 501 A 1 HETATM 18 O O6 C2E . . . B 2 5.242 7.191 -0.542 1 45.46 ? O6 C2E 501 A 1 HETATM 19 N N1 C2E . . . B 2 6.919 5.799 0.233 1 42.61 ? N1 C2E 501 A 1 HETATM 20 C C2 C2E . . . B 2 8.053 5.122 0.039 1 37.59 ? C2 C2E 501 A 1 HETATM 21 N N2 C2E . . . B 2 8.59 4.37 1.15 1 32.53 ? N2 C2E 501 A 1 HETATM 22 N N3 C2E . . . B 2 8.703 5.115 -1.135 1 39.04 ? N3 C2E 501 A 1 HETATM 23 C C4 C2E . . . B 2 8.183 5.826 -2.148 1 42.65 ? C4 C2E 501 A 1 HETATM 24 P P11 C2E . . . B 2 8.596 1.568 -6.08 1 65.53 ? P11 C2E 501 A 1 HETATM 25 O O21 C2E . . . B 2 8.183 1.059 -4.723 1 66.6 ? O21 C2E 501 A 1 HETATM 26 O O11 C2E . . . B 2 9.276 0.426 -6.713 1 64.43 ? O11 C2E 501 A 1 HETATM 27 O O5A C2E . . . B 2 7.376 1.969 -6.987 1 52.78 ? O5A C2E 501 A 1 HETATM 28 C C5A C2E . . . B 2 7.646 2.305 -8.354 1 56.46 ? C5A C2E 501 A 1 HETATM 29 C C4A C2E . . . B 2 6.607 2.92 -9.105 1 60.61 ? C4A C2E 501 A 1 HETATM 30 O O4A C2E . . . B 2 5.35 2.129 -8.988 1 59.36 ? O4A C2E 501 A 1 HETATM 31 C C3A C2E . . . B 2 6.264 4.233 -8.533 1 64.24 ? C3A C2E 501 A 1 HETATM 32 O O3A C2E . . . B 2 7.038 5.232 -9.067 1 66.51 ? O3A C2E 501 A 1 HETATM 33 C C2A C2E . . . B 2 4.873 4.412 -8.955 1 67.24 ? C2A C2E 501 A 1 HETATM 34 O O2A C2E . . . B 2 4.824 4.87 -10.25 1 73.23 ? O2A C2E 501 A 1 HETATM 35 C C1A C2E . . . B 2 4.298 3.043 -8.863 1 61.47 ? C1A C2E 501 A 1 HETATM 36 N N91 C2E . . . B 2 3.565 2.791 -7.578 1 56.95 ? N91 C2E 501 A 1 HETATM 37 C C81 C2E . . . B 2 3.971 2.024 -6.569 1 54.4 ? C81 C2E 501 A 1 HETATM 38 N N71 C2E . . . B 2 3.045 2.069 -5.581 1 52 ? N71 C2E 501 A 1 HETATM 39 C C51 C2E . . . B 2 2.056 2.875 -5.969 1 47.43 ? C51 C2E 501 A 1 HETATM 40 C C61 C2E . . . B 2 0.861 3.3 -5.401 1 48.55 ? C61 C2E 501 A 1 HETATM 41 O O61 C2E . . . B 2 0.467 2.84 -4.09 1 46.91 ? O61 C2E 501 A 1 HETATM 42 N N11 C2E . . . B 2 0.083 4.146 -6.089 1 52.84 ? N11 C2E 501 A 1 HETATM 43 C C21 C2E . . . B 2 0.433 4.574 -7.307 1 56.44 ? C21 C2E 501 A 1 HETATM 44 N N21 C2E . . . B 2 -0.389 5.445 -8.001 1 61.23 ? N21 C2E 501 A 1 HETATM 45 N N31 C2E . . . B 2 1.573 4.173 -7.877 1 55.64 ? N31 C2E 501 A 1 HETATM 46 C C41 C2E . . . B 2 2.389 3.337 -7.238 1 52.74 ? C41 C2E 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 46 #