data_4ETZ # _model_server_result.job_id 22AfwlpzZzPnuA6gekxqOQ _model_server_result.datetime_utc '2024-11-05 00:36:11' _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 4etz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 4ETZ # _exptl.entry_id 4ETZ _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 95.45 _cell.angle_gamma 90 _cell.entry_id 4ETZ _cell.length_a 70.32 _cell.length_b 41.31 _cell.length_c 110.85 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ETZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 D N N # _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 4ETZ _atom_sites.fract_transf_matrix[1][1] 0.014221 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001357 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024207 _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] 0.009062 _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 1 501 501 C2E C2E . D 2 C2E B 1 501 501 C2E C2E . E 3 HOH A 1 601 1 HOH HOH . E 3 HOH A 2 602 2 HOH HOH . E 3 HOH A 3 603 3 HOH HOH . E 3 HOH A 4 604 4 HOH HOH . E 3 HOH A 5 605 7 HOH HOH . E 3 HOH A 6 606 8 HOH HOH . E 3 HOH A 7 607 10 HOH HOH . E 3 HOH A 8 608 11 HOH HOH . E 3 HOH A 9 609 12 HOH HOH . E 3 HOH A 10 610 13 HOH HOH . E 3 HOH A 11 611 14 HOH HOH . E 3 HOH A 12 612 16 HOH HOH . E 3 HOH A 13 613 17 HOH HOH . E 3 HOH A 14 614 18 HOH HOH . E 3 HOH A 15 615 20 HOH HOH . E 3 HOH A 16 616 21 HOH HOH . E 3 HOH A 17 617 22 HOH HOH . E 3 HOH A 18 618 23 HOH HOH . E 3 HOH A 19 619 24 HOH HOH . E 3 HOH A 20 620 25 HOH HOH . E 3 HOH A 21 621 27 HOH HOH . E 3 HOH A 22 622 28 HOH HOH . E 3 HOH A 23 623 30 HOH HOH . E 3 HOH A 24 624 31 HOH HOH . E 3 HOH A 25 625 32 HOH HOH . E 3 HOH A 26 626 34 HOH HOH . E 3 HOH A 27 627 35 HOH HOH . E 3 HOH A 28 628 36 HOH HOH . E 3 HOH A 29 629 37 HOH HOH . E 3 HOH A 30 630 38 HOH HOH . E 3 HOH A 31 631 39 HOH HOH . E 3 HOH A 32 632 41 HOH HOH . E 3 HOH A 33 633 42 HOH HOH . E 3 HOH A 34 634 48 HOH HOH . E 3 HOH A 35 635 49 HOH HOH . E 3 HOH A 36 636 50 HOH HOH . E 3 HOH A 37 637 51 HOH HOH . E 3 HOH A 38 638 52 HOH HOH . E 3 HOH A 39 639 53 HOH HOH . E 3 HOH A 40 640 54 HOH HOH . E 3 HOH A 41 641 56 HOH HOH . E 3 HOH A 42 642 60 HOH HOH . E 3 HOH A 43 643 63 HOH HOH . E 3 HOH A 44 644 66 HOH HOH . E 3 HOH A 45 645 67 HOH HOH . E 3 HOH A 46 646 73 HOH HOH . E 3 HOH A 47 647 74 HOH HOH . E 3 HOH A 48 648 75 HOH HOH . E 3 HOH A 49 649 76 HOH HOH . E 3 HOH A 50 650 77 HOH HOH . E 3 HOH A 51 651 78 HOH HOH . E 3 HOH A 52 652 80 HOH HOH . E 3 HOH A 53 653 81 HOH HOH . E 3 HOH A 54 654 83 HOH HOH . E 3 HOH A 55 655 84 HOH HOH . E 3 HOH A 56 656 85 HOH HOH . E 3 HOH A 57 657 87 HOH HOH . E 3 HOH A 58 658 88 HOH HOH . E 3 HOH A 59 659 89 HOH HOH . E 3 HOH A 60 660 91 HOH HOH . E 3 HOH A 61 661 92 HOH HOH . E 3 HOH A 62 662 93 HOH HOH . E 3 HOH A 63 663 94 HOH HOH . E 3 HOH A 64 664 95 HOH HOH . E 3 HOH A 65 665 98 HOH HOH . E 3 HOH A 66 666 99 HOH HOH . E 3 HOH A 67 667 100 HOH HOH . E 3 HOH A 68 668 102 HOH HOH . E 3 HOH A 69 669 103 HOH HOH . E 3 HOH A 70 670 105 HOH HOH . E 3 HOH A 71 671 106 HOH HOH . E 3 HOH A 72 672 107 HOH HOH . E 3 HOH A 73 673 108 HOH HOH . E 3 HOH A 74 674 109 HOH HOH . E 3 HOH A 75 675 110 HOH HOH . E 3 HOH A 76 676 112 HOH HOH . E 3 HOH A 77 677 114 HOH HOH . E 3 HOH A 78 678 115 HOH HOH . E 3 HOH A 79 679 116 HOH HOH . E 3 HOH A 80 680 117 HOH HOH . E 3 HOH A 81 681 118 HOH HOH . E 3 HOH A 82 682 120 HOH HOH . E 3 HOH A 83 683 121 HOH HOH . E 3 HOH A 84 684 122 HOH HOH . E 3 HOH A 85 685 125 HOH HOH . E 3 HOH A 86 686 126 HOH HOH . E 3 HOH A 87 687 127 HOH HOH . E 3 HOH A 88 688 128 HOH HOH . E 3 HOH A 89 689 129 HOH HOH . E 3 HOH A 90 690 130 HOH HOH . E 3 HOH A 91 691 131 HOH HOH . E 3 HOH A 92 692 132 HOH HOH . E 3 HOH A 93 693 133 HOH HOH . E 3 HOH A 94 694 134 HOH HOH . E 3 HOH A 95 695 135 HOH HOH . E 3 HOH A 96 696 136 HOH HOH . E 3 HOH A 97 697 138 HOH HOH . E 3 HOH A 98 698 140 HOH HOH . F 3 HOH B 1 601 5 HOH HOH . F 3 HOH B 2 602 6 HOH HOH . F 3 HOH B 3 603 9 HOH HOH . F 3 HOH B 4 604 15 HOH HOH . F 3 HOH B 5 605 19 HOH HOH . F 3 HOH B 6 606 26 HOH HOH . F 3 HOH B 7 607 29 HOH HOH . F 3 HOH B 8 608 33 HOH HOH . F 3 HOH B 9 609 40 HOH HOH . F 3 HOH B 10 610 43 HOH HOH . F 3 HOH B 11 611 44 HOH HOH . F 3 HOH B 12 612 45 HOH HOH . F 3 HOH B 13 613 46 HOH HOH . F 3 HOH B 14 614 47 HOH HOH . F 3 HOH B 15 615 55 HOH HOH . F 3 HOH B 16 616 57 HOH HOH . F 3 HOH B 17 617 58 HOH HOH . F 3 HOH B 18 618 59 HOH HOH . F 3 HOH B 19 619 61 HOH HOH . F 3 HOH B 20 620 62 HOH HOH . F 3 HOH B 21 621 64 HOH HOH . F 3 HOH B 22 622 65 HOH HOH . F 3 HOH B 23 623 68 HOH HOH . F 3 HOH B 24 624 69 HOH HOH . F 3 HOH B 25 625 70 HOH HOH . F 3 HOH B 26 626 71 HOH HOH . F 3 HOH B 27 627 72 HOH HOH . F 3 HOH B 28 628 79 HOH HOH . F 3 HOH B 29 629 82 HOH HOH . F 3 HOH B 30 630 86 HOH HOH . F 3 HOH B 31 631 90 HOH HOH . F 3 HOH B 32 632 96 HOH HOH . F 3 HOH B 33 633 97 HOH HOH . F 3 HOH B 34 634 101 HOH HOH . F 3 HOH B 35 635 104 HOH HOH . F 3 HOH B 36 636 111 HOH HOH . F 3 HOH B 37 637 113 HOH HOH . F 3 HOH B 38 638 119 HOH HOH . F 3 HOH B 39 639 123 HOH HOH . F 3 HOH B 40 640 124 HOH HOH . F 3 HOH B 41 641 137 HOH HOH . F 3 HOH B 42 642 139 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 . . . C 2 14.322 -1.977 -7.388 1 43.15 ? P1 C2E 501 A 1 HETATM 2 O O2P C2E . . . C 2 13.32 -1.567 -8.448 1 44.44 ? O2P C2E 501 A 1 HETATM 3 O O1P C2E . . . C 2 13.996 -3.172 -6.524 1 43.43 ? O1P C2E 501 A 1 HETATM 4 O O5' C2E . . . C 2 14.663 -0.809 -6.383 1 42.81 ? O5' C2E 501 A 1 HETATM 5 C C5' C2E . . . C 2 15.026 0.513 -6.803 1 44.1 ? C5' C2E 501 A 1 HETATM 6 C C4' C2E . . . C 2 15.494 1.33 -5.599 1 41.81 ? C4' C2E 501 A 1 HETATM 7 O O4' C2E . . . C 2 14.45 1.388 -4.64 1 40.36 ? O4' C2E 501 A 1 HETATM 8 C C3' C2E . . . C 2 16.64 0.697 -4.806 1 41.94 ? C3' C2E 501 A 1 HETATM 9 O O3' C2E . . . C 2 17.936 0.983 -5.305 1 42.35 ? O3' C2E 501 A 1 HETATM 10 C C2' C2E . . . C 2 16.48 1.21 -3.396 1 41.38 ? C2' C2E 501 A 1 HETATM 11 O O2' C2E . . . C 2 17.177 2.445 -3.215 1 44.02 ? O2' C2E 501 A 1 HETATM 12 C C1' C2E . . . C 2 14.981 1.384 -3.291 1 39.51 ? C1' C2E 501 A 1 HETATM 13 N N9 C2E . . . C 2 14.409 0.184 -2.611 1 36.64 ? N9 C2E 501 A 1 HETATM 14 C C8 C2E . . . C 2 13.657 -0.729 -3.236 1 33.25 ? C8 C2E 501 A 1 HETATM 15 N N7 C2E . . . C 2 13.225 -1.687 -2.414 1 33.37 ? N7 C2E 501 A 1 HETATM 16 C C5 C2E . . . C 2 13.737 -1.406 -1.19 1 34.32 ? C5 C2E 501 A 1 HETATM 17 C C6 C2E . . . C 2 13.695 -2.016 0.157 1 33.87 ? C6 C2E 501 A 1 HETATM 18 O O6 C2E . . . C 2 13.007 -3.163 0.429 1 37.23 ? O6 C2E 501 A 1 HETATM 19 N N1 C2E . . . C 2 14.363 -1.382 1.158 1 34.68 ? N1 C2E 501 A 1 HETATM 20 C C2 C2E . . . C 2 15.096 -0.236 0.977 1 32.87 ? C2 C2E 501 A 1 HETATM 21 N N2 C2E . . . C 2 15.726 0.3 2.041 1 34.97 ? N2 C2E 501 A 1 HETATM 22 N N3 C2E . . . C 2 15.165 0.385 -0.225 1 32.54 ? N3 C2E 501 A 1 HETATM 23 C C4 C2E . . . C 2 14.525 -0.156 -1.321 1 35.38 ? C4 C2E 501 A 1 HETATM 24 P P11 C2E . . . C 2 19.122 -0.092 -5.119 1 40.88 ? P11 C2E 501 A 1 HETATM 25 O O21 C2E . . . C 2 20.362 0.577 -5.655 1 45.11 ? O21 C2E 501 A 1 HETATM 26 O O11 C2E . . . C 2 19.167 -0.589 -3.695 1 40.39 ? O11 C2E 501 A 1 HETATM 27 O O5A C2E . . . C 2 18.692 -1.256 -6.108 1 40.16 ? O5A C2E 501 A 1 HETATM 28 C C5A C2E . . . C 2 18.684 -1.069 -7.508 1 42.77 ? C5A C2E 501 A 1 HETATM 29 C C4A C2E . . . C 2 18.161 -2.354 -8.098 1 42.54 ? C4A C2E 501 A 1 HETATM 30 O O4A C2E . . . C 2 19.031 -3.401 -7.676 1 45.17 ? O4A C2E 501 A 1 HETATM 31 C C3A C2E . . . C 2 16.827 -2.77 -7.524 1 42.94 ? C3A C2E 501 A 1 HETATM 32 O O3A C2E . . . C 2 15.706 -2.216 -8.183 1 46.01 ? O3A C2E 501 A 1 HETATM 33 C C2A C2E . . . C 2 16.826 -4.267 -7.683 1 43.14 ? C2A C2E 501 A 1 HETATM 34 O O2A C2E . . . C 2 16.485 -4.673 -8.999 1 43.34 ? O2A C2E 501 A 1 HETATM 35 C C1A C2E . . . C 2 18.276 -4.604 -7.454 1 42.91 ? C1A C2E 501 A 1 HETATM 36 N N91 C2E . . . C 2 18.413 -4.994 -6.041 1 40.78 ? N91 C2E 501 A 1 HETATM 37 C C81 C2E . . . C 2 18.918 -4.208 -5.069 1 40.87 ? C81 C2E 501 A 1 HETATM 38 N N71 C2E . . . C 2 18.91 -4.86 -3.877 1 40.48 ? N71 C2E 501 A 1 HETATM 39 C C51 C2E . . . C 2 18.365 -6.069 -4.101 1 39.7 ? C51 C2E 501 A 1 HETATM 40 C C61 C2E . . . C 2 18.07 -7.239 -3.264 1 40.5 ? C61 C2E 501 A 1 HETATM 41 O O61 C2E . . . C 2 18.385 -7.179 -1.959 1 43.9 ? O61 C2E 501 A 1 HETATM 42 N N11 C2E . . . C 2 17.484 -8.311 -3.8 1 42.36 ? N11 C2E 501 A 1 HETATM 43 C C21 C2E . . . C 2 17.191 -8.339 -5.131 1 44.01 ? C21 C2E 501 A 1 HETATM 44 N N21 C2E . . . C 2 16.616 -9.452 -5.643 1 46.2 ? N21 C2E 501 A 1 HETATM 45 N N31 C2E . . . C 2 17.452 -7.289 -5.955 1 42.99 ? N31 C2E 501 A 1 HETATM 46 C C41 C2E . . . C 2 18.029 -6.155 -5.507 1 40.27 ? C41 C2E 501 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #