data_3TVK # _model_server_result.job_id l5E-t8T31I5MBZHbezFNHQ _model_server_result.datetime_utc '2024-11-25 15:55:49' _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 3tvk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 3TVK # _exptl.entry_id 3TVK _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 3 _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 3TVK _cell.length_a 79.623 _cell.length_b 79.623 _cell.length_c 51.207 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TVK _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _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 ? 2 D 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 covale ? covale1 B P1 C2E . A C2E 501 1_555 B O3' C2E . A C2E 501 4_665 ? ? ? ? ? ? ? ? ? ? ? ? 1.653 ? metalc ? metalc1 A OD2 ASP 73 A ASP 198 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc2 C O1P C2E . A C2E 502 1_555 E MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc3 E MG MG . A MG 504 1_555 G O HOH . A HOH 678 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc4 E MG MG . A MG 504 1_555 G O HOH . A HOH 680 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc5 E MG MG . A MG 504 1_555 G O HOH . A HOH 685 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc6 E MG MG . A MG 504 1_555 G O HOH . A HOH 723 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _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 3TVK _atom_sites.fract_transf_matrix[1][1] 0.012559 _atom_sites.fract_transf_matrix[1][2] 0.007251 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014502 _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] 0.019529 _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 1 501 501 C2E C2E . C 2 C2E A 1 502 503 C2E C2E . D 2 C2E A 1 503 505 C2E C2E . E 3 MG A 1 504 601 MG MG . F 4 TAR A 1 505 800 TAR TAR . 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 . G 5 HOH A 45 645 45 HOH HOH . G 5 HOH A 46 646 46 HOH HOH . G 5 HOH A 47 647 47 HOH HOH . G 5 HOH A 48 648 48 HOH HOH . G 5 HOH A 49 649 49 HOH HOH . G 5 HOH A 50 650 50 HOH HOH . G 5 HOH A 51 651 51 HOH HOH . G 5 HOH A 52 652 52 HOH HOH . G 5 HOH A 53 653 53 HOH HOH . G 5 HOH A 54 654 54 HOH HOH . G 5 HOH A 55 655 55 HOH HOH . G 5 HOH A 56 656 56 HOH HOH . G 5 HOH A 57 657 57 HOH HOH . G 5 HOH A 58 658 58 HOH HOH . G 5 HOH A 59 659 59 HOH HOH . G 5 HOH A 60 660 60 HOH HOH . G 5 HOH A 61 661 61 HOH HOH . G 5 HOH A 62 662 62 HOH HOH . G 5 HOH A 63 663 63 HOH HOH . G 5 HOH A 64 664 64 HOH HOH . G 5 HOH A 65 665 65 HOH HOH . G 5 HOH A 66 666 66 HOH HOH . G 5 HOH A 67 667 67 HOH HOH . G 5 HOH A 68 668 68 HOH HOH . G 5 HOH A 69 669 69 HOH HOH . G 5 HOH A 70 670 70 HOH HOH . G 5 HOH A 71 671 71 HOH HOH . G 5 HOH A 72 672 72 HOH HOH . G 5 HOH A 73 673 73 HOH HOH . G 5 HOH A 74 674 74 HOH HOH . G 5 HOH A 75 675 75 HOH HOH . G 5 HOH A 76 676 76 HOH HOH . G 5 HOH A 77 677 77 HOH HOH . G 5 HOH A 78 678 78 HOH HOH . G 5 HOH A 79 679 79 HOH HOH . G 5 HOH A 80 680 80 HOH HOH . G 5 HOH A 81 681 81 HOH HOH . G 5 HOH A 82 682 82 HOH HOH . G 5 HOH A 83 683 83 HOH HOH . G 5 HOH A 84 684 84 HOH HOH . G 5 HOH A 85 685 85 HOH HOH . G 5 HOH A 86 686 86 HOH HOH . G 5 HOH A 87 687 87 HOH HOH . G 5 HOH A 88 688 88 HOH HOH . G 5 HOH A 89 689 89 HOH HOH . G 5 HOH A 90 690 90 HOH HOH . G 5 HOH A 91 691 91 HOH HOH . G 5 HOH A 92 692 92 HOH HOH . G 5 HOH A 93 693 93 HOH HOH . G 5 HOH A 94 694 94 HOH HOH . G 5 HOH A 95 695 95 HOH HOH . G 5 HOH A 96 696 96 HOH HOH . G 5 HOH A 97 697 97 HOH HOH . G 5 HOH A 98 698 98 HOH HOH . G 5 HOH A 99 699 99 HOH HOH . G 5 HOH A 100 700 100 HOH HOH . G 5 HOH A 101 701 101 HOH HOH . G 5 HOH A 102 702 102 HOH HOH . G 5 HOH A 103 703 103 HOH HOH . G 5 HOH A 104 704 104 HOH HOH . G 5 HOH A 105 705 105 HOH HOH . G 5 HOH A 106 706 106 HOH HOH . G 5 HOH A 107 707 107 HOH HOH . G 5 HOH A 108 708 108 HOH HOH . G 5 HOH A 109 709 109 HOH HOH . G 5 HOH A 110 710 110 HOH HOH . G 5 HOH A 111 711 111 HOH HOH . G 5 HOH A 112 712 112 HOH HOH . G 5 HOH A 113 713 113 HOH HOH . G 5 HOH A 114 714 114 HOH HOH . G 5 HOH A 115 715 115 HOH HOH . G 5 HOH A 116 716 116 HOH HOH . G 5 HOH A 117 717 117 HOH HOH . G 5 HOH A 118 718 118 HOH HOH . G 5 HOH A 119 719 119 HOH HOH . G 5 HOH A 120 720 120 HOH HOH . G 5 HOH A 121 721 121 HOH HOH . G 5 HOH A 122 722 122 HOH HOH . G 5 HOH A 123 723 123 HOH HOH . G 5 HOH A 124 724 124 HOH HOH . G 5 HOH A 125 725 125 HOH HOH . G 5 HOH A 126 726 139 HOH HOH . G 5 HOH A 127 727 140 HOH HOH . G 5 HOH A 128 728 126 HOH HOH . G 5 HOH A 129 729 127 HOH HOH . G 5 HOH A 130 730 128 HOH HOH . G 5 HOH A 131 731 129 HOH HOH . G 5 HOH A 132 732 130 HOH HOH . G 5 HOH A 133 733 131 HOH HOH . G 5 HOH A 134 734 132 HOH HOH . G 5 HOH A 135 735 133 HOH HOH . G 5 HOH A 136 736 134 HOH HOH . G 5 HOH A 137 737 135 HOH HOH . G 5 HOH A 138 738 136 HOH HOH . G 5 HOH A 139 739 137 HOH HOH . G 5 HOH A 140 740 138 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 18.471 32.139 44.69 1 24.77 ? P1 C2E 501 A 1 HETATM 2 O O2P C2E . . . B 2 18.464 31.471 45.994 1 18.91 ? O2P C2E 501 A 1 HETATM 3 O O1P C2E . . . B 2 17.724 31.528 43.558 1 32.27 ? O1P C2E 501 A 1 HETATM 4 O O5' C2E . . . B 2 18.068 33.632 44.822 1 22.32 ? O5' C2E 501 A 1 HETATM 5 C C5' C2E . . . B 2 17.818 34.437 43.683 1 20.55 ? C5' C2E 501 A 1 HETATM 6 C C4' C2E . . . B 2 17.588 35.877 44.072 1 23.58 ? C4' C2E 501 A 1 HETATM 7 O O4' C2E . . . B 2 16.408 35.936 44.93 1 23.23 ? O4' C2E 501 A 1 HETATM 8 C C3' C2E . . . B 2 18.733 36.368 44.953 1 23.49 ? C3' C2E 501 A 1 HETATM 9 O O3' C2E . . . B 2 19.783 36.927 44.147 1 25.88 ? O3' C2E 501 A 1 HETATM 10 C C2' C2E . . . B 2 18.071 37.465 45.757 1 20.44 ? C2' C2E 501 A 1 HETATM 11 O O2' C2E . . . B 2 17.906 38.656 44.977 1 24.07 ? O2' C2E 501 A 1 HETATM 12 C C1' C2E . . . B 2 16.678 36.878 46.009 1 17.82 ? C1' C2E 501 A 1 HETATM 13 N N9 C2E . . . B 2 16.422 36.14 47.276 1 17.75 ? N9 C2E 501 A 1 HETATM 14 C C8 C2E . . . B 2 16.565 34.837 47.512 1 19.94 ? C8 C2E 501 A 1 HETATM 15 N N7 C2E . . . B 2 16.199 34.577 48.767 1 17.79 ? N7 C2E 501 A 1 HETATM 16 C C5 C2E . . . B 2 15.792 35.718 49.322 1 17.44 ? C5 C2E 501 A 1 HETATM 17 C C6 C2E . . . B 2 15.302 36.045 50.577 1 21.73 ? C6 C2E 501 A 1 HETATM 18 O O6 C2E . . . B 2 15.156 35.19 51.456 1 23.69 ? O6 C2E 501 A 1 HETATM 19 N N1 C2E . . . B 2 14.97 37.38 50.826 1 21.71 ? N1 C2E 501 A 1 HETATM 20 C C2 C2E . . . B 2 15.135 38.346 49.816 1 15.33 ? C2 C2E 501 A 1 HETATM 21 N N2 C2E . . . B 2 14.825 39.605 50.066 1 17.25 ? N2 C2E 501 A 1 HETATM 22 N N3 C2E . . . B 2 15.618 37.995 48.616 1 16.75 ? N3 C2E 501 A 1 HETATM 23 C C4 C2E . . . B 2 15.928 36.713 48.364 1 16.67 ? C4 C2E 501 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #