data_6HQ5 # _model_server_result.job_id -PjGWPwU0YsHWu0lORtHSA _model_server_result.datetime_utc '2024-10-25 20:27:13' _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 6hq5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":801}' # _entry.id 6HQ5 # _exptl.entry_id 6HQ5 _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 120 _cell.entry_id 6HQ5 _cell.length_a 83.857 _cell.length_b 83.857 _cell.length_c 138.454 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HQ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _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 ? 2 C N N ? 2 G 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 OE2 GLU 174 A GLU 178 1_555 E CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc2 A OD1 ASN 241 A ASN 245 1_555 E CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc3 A OE2 GLU 273 A GLU 277 1_555 E CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc4 A OD2 ASP 302 A ASP 306 1_555 E CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc5 A OD1 ASP 302 A ASP 306 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc6 A OD1 ASP 303 A ASP 307 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc7 A OD1 ASP 325 A ASP 329 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc8 A OE1 GLU 359 A GLU 363 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc9 A OE2 GLU 359 A GLU 363 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc10 C O11 C2E . A C2E 801 1_555 E CA CA . A CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc11 C O21 C2E . A C2E 801 1_555 F CA CA . A CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc12 E CA CA . A CA 803 1_555 K O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc13 B OE2 GLU 174 B GLU 178 1_555 I CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc14 B OD1 ASN 241 B ASN 245 1_555 I CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc15 B OE2 GLU 273 B GLU 277 1_555 I CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc16 B OD2 ASP 302 B ASP 306 1_555 I CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc17 B OD1 ASP 302 B ASP 306 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc18 B OD1 ASP 303 B ASP 307 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc19 B OD1 ASP 325 B ASP 329 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc20 B OE1 GLU 359 B GLU 363 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc21 B OE2 GLU 359 B GLU 363 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc22 G O11 C2E . B C2E 801 1_555 I CA CA . B CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc23 G O21 C2E . B C2E 801 1_555 J CA CA . B CA 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc24 I CA CA . B CA 803 1_555 L O HOH . B HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? # _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 6HQ5 _atom_sites.fract_transf_matrix[1][1] 0.011925 _atom_sites.fract_transf_matrix[1][2] 0.006885 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01377 _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] 0.007223 _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 C2E A 1 801 801 C2E C2E . D 3 CMP A 1 802 901 CMP CMP . E 4 CA A 1 803 802 CA CA . F 4 CA A 1 804 803 CA CA . G 2 C2E B 1 801 801 C2E C2E . H 3 CMP B 1 802 901 CMP CMP . I 4 CA B 1 803 802 CA CA . J 4 CA B 1 804 803 CA CA . K 5 HOH A 1 901 1 HOH HOH . L 5 HOH B 1 901 2 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 2 71.538 -12.298 -7.108 1 79.21 ? P1 C2E 801 B 1 HETATM 2 O O2P C2E . . . G 2 72.292 -12.54 -5.857 1 77.28 ? O2P C2E 801 B 1 HETATM 3 O O1P C2E . . . G 2 70.284 -13.058 -7.365 1 78.82 ? O1P C2E 801 B 1 HETATM 4 O O5' C2E . . . G 2 72.522 -12.567 -8.333 1 72.02 ? O5' C2E 801 B 1 HETATM 5 C C5' C2E . . . G 2 73.798 -11.942 -8.344 1 72.13 ? C5' C2E 801 B 1 HETATM 6 C C4' C2E . . . G 2 74.517 -12.277 -9.635 1 70.05 ? C4' C2E 801 B 1 HETATM 7 O O4' C2E . . . G 2 74.622 -13.7 -9.774 1 70.38 ? O4' C2E 801 B 1 HETATM 8 C C3' C2E . . . G 2 73.691 -11.865 -10.821 1 70.78 ? C3' C2E 801 B 1 HETATM 9 O O3' C2E . . . G 2 73.751 -10.418 -10.983 1 73.26 ? O3' C2E 801 B 1 HETATM 10 C C2' C2E . . . G 2 74.397 -12.652 -11.905 1 67.8 ? C2' C2E 801 B 1 HETATM 11 O O2' C2E . . . G 2 75.596 -11.997 -12.285 1 65.21 ? O2' C2E 801 B 1 HETATM 12 C C1' C2E . . . G 2 74.73 -13.966 -11.193 1 69.71 ? C1' C2E 801 B 1 HETATM 13 N N9 C2E . . . G 2 73.75 -15.021 -11.49 1 72.71 ? N9 C2E 801 B 1 HETATM 14 C C8 C2E . . . G 2 72.656 -15.273 -10.77 1 77.49 ? C8 C2E 801 B 1 HETATM 15 N N7 C2E . . . G 2 72.009 -16.287 -11.337 1 76.74 ? N7 C2E 801 B 1 HETATM 16 C C5 C2E . . . G 2 72.702 -16.662 -12.407 1 74.69 ? C5 C2E 801 B 1 HETATM 17 C C6 C2E . . . G 2 72.468 -17.624 -13.299 1 74.35 ? C6 C2E 801 B 1 HETATM 18 O O6 C2E . . . G 2 71.476 -18.339 -13.201 1 73.42 ? O6 C2E 801 B 1 HETATM 19 N N1 C2E . . . G 2 73.365 -17.827 -14.354 1 73.03 ? N1 C2E 801 B 1 HETATM 20 C C2 C2E . . . G 2 74.487 -17.001 -14.432 1 72.83 ? C2 C2E 801 B 1 HETATM 21 N N2 C2E . . . G 2 75.355 -17.175 -15.423 1 77.12 ? N2 C2E 801 B 1 HETATM 22 N N3 C2E . . . G 2 74.671 -16.039 -13.505 1 71.02 ? N3 C2E 801 B 1 HETATM 23 C C4 C2E . . . G 2 73.786 -15.877 -12.506 1 73.09 ? C4 C2E 801 B 1 HETATM 24 P P11 C2E . . . G 2 72.955 -9.592 -12.158 1 80.11 ? P11 C2E 801 B 1 HETATM 25 O O21 C2E . . . G 2 73.82 -8.456 -12.564 1 81.08 ? O21 C2E 801 B 1 HETATM 26 O O11 C2E . . . G 2 72.4 -10.496 -13.204 1 63.12 ? O11 C2E 801 B 1 HETATM 27 O O5A C2E . . . G 2 71.758 -8.905 -11.332 1 77.04 ? O5A C2E 801 B 1 HETATM 28 C C5A C2E . . . G 2 70.854 -9.633 -10.516 1 75.16 ? C5A C2E 801 B 1 HETATM 29 C C4A C2E . . . G 2 71.068 -9.223 -9.071 1 76.44 ? C4A C2E 801 B 1 HETATM 30 O O4A C2E . . . G 2 70.517 -7.9 -8.813 1 77.08 ? O4A C2E 801 B 1 HETATM 31 C C3A C2E . . . G 2 70.319 -10.185 -8.172 1 78.52 ? C3A C2E 801 B 1 HETATM 32 O O3A C2E . . . G 2 71.239 -10.714 -7.189 1 78.87 ? O3A C2E 801 B 1 HETATM 33 C C2A C2E . . . G 2 69.244 -9.329 -7.527 1 80.55 ? C2A C2E 801 B 1 HETATM 34 O O2A C2E . . . G 2 68.962 -9.785 -6.186 1 81.78 ? O2A C2E 801 B 1 HETATM 35 C C1A C2E . . . G 2 69.901 -7.966 -7.51 1 80.98 ? C1A C2E 801 B 1 HETATM 36 N N91 C2E . . . G 2 68.907 -6.86 -7.306 1 86.71 ? N91 C2E 801 B 1 HETATM 37 C C81 C2E . . . G 2 67.901 -6.557 -8.119 1 85.43 ? C81 C2E 801 B 1 HETATM 38 N N71 C2E . . . G 2 67.251 -5.521 -7.604 1 85.28 ? N71 C2E 801 B 1 HETATM 39 C C51 C2E . . . G 2 67.846 -5.172 -6.468 1 90.88 ? C51 C2E 801 B 1 HETATM 40 C C61 C2E . . . G 2 67.581 -4.2 -5.582 1 95.68 ? C61 C2E 801 B 1 HETATM 41 O O61 C2E . . . G 2 66.639 -3.421 -5.734 1 87.61 ? O61 C2E 801 B 1 HETATM 42 N N11 C2E . . . G 2 68.396 -4.065 -4.453 1 98.4 ? N11 C2E 801 B 1 HETATM 43 C C21 C2E . . . G 2 69.465 -4.954 -4.294 1 98.08 ? C21 C2E 801 B 1 HETATM 44 N N21 C2E . . . G 2 70.259 -4.865 -3.237 1 103.71 ? N21 C2E 801 B 1 HETATM 45 N N31 C2E . . . G 2 69.68 -5.9 -5.216 1 90.84 ? N31 C2E 801 B 1 HETATM 46 C C41 C2E . . . G 2 68.877 -6.007 -6.286 1 88.05 ? C41 C2E 801 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 46 #