data_8T5L # _model_server_result.job_id 41kFIQXLhAJTNo2N04QdbQ _model_server_result.datetime_utc '2024-10-15 18:22:41' _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 8t5l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 8T5L # _exptl.entry_id 8T5L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 674.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description cGAMP _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.13 _cell.angle_gamma 90 _cell.entry_id 8T5L _cell.length_a 88.33 _cell.length_b 79.23 _cell.length_c 36.59 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8T5L _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 84.422748 0 36.380785 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H24 N10 O13 P2' _chem_comp.formula_weight 674.411 _chem_comp.id 1SY _chem_comp.mon_nstd_flag . _chem_comp.name cGAMP _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2',3' cGAMP;c-GMP-AMP;c[G(2',5')pA(3',5')p]" # 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 O44 P18 1SY doub 1 n n O19 P18 1SY sing 2 n n P18 O17 1SY sing 3 n n P18 O20 1SY sing 4 n n O17 C16 1SY sing 5 n n O4' C4' 1SY sing 6 n n O4' C1' 1SY sing 7 n n C16 C4' 1SY sing 8 n n C8 N7 1SY doub 9 n y C8 N9 1SY sing 10 n y N7 C5 1SY sing 11 n y O20 C21 1SY sing 12 n n N9 C1' 1SY sing 13 n n N9 C4 1SY sing 14 n y N41 C40 1SY sing 15 n n C4' C3' 1SY sing 16 n n C1' C2' 1SY sing 17 n n C5 C4 1SY doub 18 n y C5 C6 1SY sing 19 n y N01 C6 1SY sing 20 n n C4 N3 1SY sing 21 n y C40 N42 1SY sing 22 n n C40 N39 1SY doub 23 n n C6 N1 1SY doub 24 n y N42 C36 1SY sing 25 n n N39 C38 1SY sing 26 n n C21 C22 1SY sing 27 n n C21 C32 1SY sing 28 n n O23 C22 1SY sing 29 n n N3 C2 1SY doub 30 n y C3' C2' 1SY sing 31 n n C3' O28 1SY sing 32 n n N1 C2 1SY sing 33 n y C2' O2' 1SY sing 34 n n C36 C37 1SY doub 35 n y C36 N33 1SY sing 36 n y C38 O43 1SY doub 37 n n C38 C37 1SY sing 38 n n C22 C24 1SY sing 39 n n C32 N33 1SY sing 40 n n C32 O31 1SY sing 41 n n C37 N35 1SY sing 42 n y N33 C34 1SY sing 43 n y O28 P27 1SY sing 44 n n N35 C34 1SY doub 45 n y O31 C24 1SY sing 46 n n C24 C25 1SY sing 47 n n O26 P27 1SY sing 48 n n O26 C25 1SY sing 49 n n P27 O29 1SY doub 50 n n P27 O30 1SY sing 51 n n C2 H1 1SY sing 52 n n N01 H2 1SY sing 53 n n N01 H3 1SY sing 54 n n C8 H4 1SY sing 55 n n C1' H5 1SY sing 56 n n C2' H6 1SY sing 57 n n O2' H7 1SY sing 58 n n C3' H8 1SY sing 59 n n C4' H9 1SY sing 60 n n C16 H10 1SY sing 61 n n C16 H11 1SY sing 62 n n O19 H12 1SY sing 63 n n C21 H13 1SY sing 64 n n C22 H14 1SY sing 65 n n O23 H15 1SY sing 66 n n C24 H16 1SY sing 67 n n C25 H17 1SY sing 68 n n C25 H18 1SY sing 69 n n O30 H19 1SY sing 70 n n C32 H20 1SY sing 71 n n C34 H21 1SY sing 72 n n N41 H22 1SY sing 73 n n N41 H23 1SY sing 74 n n N42 H24 1SY sing 75 n n # _atom_sites.entry_id 8T5L _atom_sites.fract_transf_matrix[1][1] 0.011321 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001216 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012621 _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] 0.027487 _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 1SY B 1 500 500 1SY 1SY . C 3 HOH B 1 601 134 HOH HOH . C 3 HOH B 2 602 164 HOH HOH . C 3 HOH B 3 603 84 HOH HOH . C 3 HOH B 4 604 114 HOH HOH . C 3 HOH B 5 605 47 HOH HOH . C 3 HOH B 6 606 45 HOH HOH . C 3 HOH B 7 607 53 HOH HOH . C 3 HOH B 8 608 138 HOH HOH . C 3 HOH B 9 609 28 HOH HOH . C 3 HOH B 10 610 139 HOH HOH . C 3 HOH B 11 611 35 HOH HOH . C 3 HOH B 12 612 171 HOH HOH . C 3 HOH B 13 613 3 HOH HOH . C 3 HOH B 14 614 32 HOH HOH . C 3 HOH B 15 615 168 HOH HOH . C 3 HOH B 16 616 20 HOH HOH . C 3 HOH B 17 617 37 HOH HOH . C 3 HOH B 18 618 1 HOH HOH . C 3 HOH B 19 619 22 HOH HOH . C 3 HOH B 20 620 25 HOH HOH . C 3 HOH B 21 621 78 HOH HOH . C 3 HOH B 22 622 9 HOH HOH . C 3 HOH B 23 623 83 HOH HOH . C 3 HOH B 24 624 108 HOH HOH . C 3 HOH B 25 625 27 HOH HOH . C 3 HOH B 26 626 26 HOH HOH . C 3 HOH B 27 627 36 HOH HOH . C 3 HOH B 28 628 160 HOH HOH . C 3 HOH B 29 629 19 HOH HOH . C 3 HOH B 30 630 155 HOH HOH . C 3 HOH B 31 631 65 HOH HOH . C 3 HOH B 32 632 8 HOH HOH . C 3 HOH B 33 633 159 HOH HOH . C 3 HOH B 34 634 5 HOH HOH . C 3 HOH B 35 635 23 HOH HOH . C 3 HOH B 36 636 12 HOH HOH . C 3 HOH B 37 637 57 HOH HOH . C 3 HOH B 38 638 29 HOH HOH . C 3 HOH B 39 639 33 HOH HOH . C 3 HOH B 40 640 133 HOH HOH . C 3 HOH B 41 641 85 HOH HOH . C 3 HOH B 42 642 68 HOH HOH . C 3 HOH B 43 643 38 HOH HOH . C 3 HOH B 44 644 110 HOH HOH . C 3 HOH B 45 645 11 HOH HOH . C 3 HOH B 46 646 71 HOH HOH . C 3 HOH B 47 647 67 HOH HOH . C 3 HOH B 48 648 120 HOH HOH . C 3 HOH B 49 649 109 HOH HOH . C 3 HOH B 50 650 15 HOH HOH . C 3 HOH B 51 651 157 HOH HOH . C 3 HOH B 52 652 88 HOH HOH . C 3 HOH B 53 653 93 HOH HOH . C 3 HOH B 54 654 59 HOH HOH . C 3 HOH B 55 655 111 HOH HOH . C 3 HOH B 56 656 51 HOH HOH . C 3 HOH B 57 657 4 HOH HOH . C 3 HOH B 58 658 16 HOH HOH . C 3 HOH B 59 659 30 HOH HOH . C 3 HOH B 60 660 17 HOH HOH . C 3 HOH B 61 661 107 HOH HOH . C 3 HOH B 62 662 87 HOH HOH . C 3 HOH B 63 663 48 HOH HOH . C 3 HOH B 64 664 102 HOH HOH . C 3 HOH B 65 665 49 HOH HOH . C 3 HOH B 66 666 10 HOH HOH . C 3 HOH B 67 667 75 HOH HOH . C 3 HOH B 68 668 41 HOH HOH . C 3 HOH B 69 669 76 HOH HOH . C 3 HOH B 70 670 54 HOH HOH . C 3 HOH B 71 671 163 HOH HOH . C 3 HOH B 72 672 116 HOH HOH . C 3 HOH B 73 673 86 HOH HOH . C 3 HOH B 74 674 13 HOH HOH . C 3 HOH B 75 675 31 HOH HOH . C 3 HOH B 76 676 117 HOH HOH . C 3 HOH B 77 677 7 HOH HOH . C 3 HOH B 78 678 2 HOH HOH . C 3 HOH B 79 679 113 HOH HOH . C 3 HOH B 80 680 148 HOH HOH . C 3 HOH B 81 681 95 HOH HOH . C 3 HOH B 82 682 21 HOH HOH . C 3 HOH B 83 683 90 HOH HOH . C 3 HOH B 84 684 42 HOH HOH . C 3 HOH B 85 685 128 HOH HOH . C 3 HOH B 86 686 112 HOH HOH . C 3 HOH B 87 687 14 HOH HOH . C 3 HOH B 88 688 72 HOH HOH . C 3 HOH B 89 689 56 HOH HOH . C 3 HOH B 90 690 70 HOH HOH . C 3 HOH B 91 691 79 HOH HOH . C 3 HOH B 92 692 60 HOH HOH . C 3 HOH B 93 693 99 HOH HOH . C 3 HOH B 94 694 166 HOH HOH . C 3 HOH B 95 695 18 HOH HOH . C 3 HOH B 96 696 143 HOH HOH . C 3 HOH B 97 697 6 HOH HOH . C 3 HOH B 98 698 97 HOH HOH . C 3 HOH B 99 699 167 HOH HOH . C 3 HOH B 100 700 170 HOH HOH . C 3 HOH B 101 701 135 HOH HOH . C 3 HOH B 102 702 106 HOH HOH . C 3 HOH B 103 703 140 HOH HOH . C 3 HOH B 104 704 50 HOH HOH . C 3 HOH B 105 705 63 HOH HOH . C 3 HOH B 106 706 73 HOH HOH . C 3 HOH B 107 707 46 HOH HOH . C 3 HOH B 108 708 40 HOH HOH . C 3 HOH B 109 709 58 HOH HOH . C 3 HOH B 110 710 162 HOH HOH . C 3 HOH B 111 711 34 HOH HOH . C 3 HOH B 112 712 169 HOH HOH . C 3 HOH B 113 713 158 HOH HOH . C 3 HOH B 114 714 149 HOH HOH . C 3 HOH B 115 715 165 HOH HOH . C 3 HOH B 116 716 126 HOH HOH . C 3 HOH B 117 717 104 HOH HOH . C 3 HOH B 118 718 61 HOH HOH . C 3 HOH B 119 719 64 HOH HOH . C 3 HOH B 120 720 161 HOH HOH . C 3 HOH B 121 721 81 HOH HOH . C 3 HOH B 122 722 136 HOH HOH . C 3 HOH B 123 723 80 HOH HOH . C 3 HOH B 124 724 82 HOH HOH . C 3 HOH B 125 725 122 HOH HOH . C 3 HOH B 126 726 147 HOH HOH . C 3 HOH B 127 727 129 HOH HOH . C 3 HOH B 128 728 115 HOH HOH . C 3 HOH B 129 729 145 HOH HOH . C 3 HOH B 130 730 89 HOH HOH . C 3 HOH B 131 731 74 HOH HOH . C 3 HOH B 132 732 44 HOH HOH . C 3 HOH B 133 733 118 HOH HOH . C 3 HOH B 134 734 150 HOH HOH . C 3 HOH B 135 735 39 HOH HOH . C 3 HOH B 136 736 52 HOH HOH . C 3 HOH B 137 737 24 HOH HOH . C 3 HOH B 138 738 105 HOH HOH . C 3 HOH B 139 739 154 HOH HOH . C 3 HOH B 140 740 131 HOH HOH . C 3 HOH B 141 741 144 HOH HOH . C 3 HOH B 142 742 100 HOH HOH . C 3 HOH B 143 743 142 HOH HOH . C 3 HOH B 144 744 137 HOH HOH . C 3 HOH B 145 745 103 HOH HOH . C 3 HOH B 146 746 96 HOH HOH . C 3 HOH B 147 747 98 HOH HOH . C 3 HOH B 148 748 62 HOH HOH . C 3 HOH B 149 749 91 HOH HOH . C 3 HOH B 150 750 69 HOH HOH . C 3 HOH B 151 751 130 HOH HOH . C 3 HOH B 152 752 66 HOH HOH . C 3 HOH B 153 753 152 HOH HOH . C 3 HOH B 154 754 123 HOH HOH . C 3 HOH B 155 755 43 HOH HOH . C 3 HOH B 156 756 156 HOH HOH . C 3 HOH B 157 757 119 HOH HOH . C 3 HOH B 158 758 92 HOH HOH . C 3 HOH B 159 759 153 HOH HOH . C 3 HOH B 160 760 55 HOH HOH . C 3 HOH B 161 761 132 HOH HOH . C 3 HOH B 162 762 121 HOH HOH . C 3 HOH B 163 763 146 HOH HOH . C 3 HOH B 164 764 124 HOH HOH . C 3 HOH B 165 765 101 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 C C2 1SY . . . B 2 47.193 -3.43 18.66 0.5 22.3 ? C2 1SY 500 B 1 HETATM 2 N N01 1SY . . . B 2 44.759 -1.273 17.291 0.5 23.05 ? N01 1SY 500 B 1 HETATM 3 C C6 1SY . . . B 2 45.374 -2.571 17.494 0.5 23.85 ? C6 1SY 500 B 1 HETATM 4 N N1 1SY . . . B 2 46.418 -2.393 18.283 0.5 23.87 ? N1 1SY 500 B 1 HETATM 5 N N3 1SY . . . B 2 46.91 -4.661 18.222 0.5 20.96 ? N3 1SY 500 B 1 HETATM 6 C C4 1SY . . . B 2 45.852 -4.847 17.418 0.5 23.45 ? C4 1SY 500 B 1 HETATM 7 C C5 1SY . . . B 2 45.073 -3.834 17.041 0.5 22.65 ? C5 1SY 500 B 1 HETATM 8 N N7 1SY . . . B 2 44.11 -4.324 16.247 0.5 23.05 ? N7 1SY 500 B 1 HETATM 9 C C8 1SY . . . B 2 44.289 -5.642 16.13 0.5 21.77 ? C8 1SY 500 B 1 HETATM 10 N N9 1SY . . . B 2 45.372 -5.945 16.856 0.5 21.91 ? N9 1SY 500 B 1 HETATM 11 C C1' 1SY . . . B 2 45.961 -7.205 17.057 0.5 21.69 ? C1' 1SY 500 B 1 HETATM 12 C C2' 1SY . . . B 2 45.629 -7.66 18.462 0.5 21.08 ? C2' 1SY 500 B 1 HETATM 13 O O2' 1SY . . . B 2 46.671 -8.476 18.946 0.5 22.76 ? O2' 1SY 500 B 1 HETATM 14 C C3' 1SY . . . B 2 44.368 -8.404 18.265 0.5 20.93 ? C3' 1SY 500 B 1 HETATM 15 C C4' 1SY . . . B 2 44.632 -9.071 16.996 0.5 21.79 ? C4' 1SY 500 B 1 HETATM 16 C C16 1SY . . . B 2 43.315 -9.431 16.268 0.5 21.27 ? C16 1SY 500 B 1 HETATM 17 O O17 1SY . . . B 2 42.615 -8.194 16.079 0.5 21.54 ? O17 1SY 500 B 1 HETATM 18 P P18 1SY . . . B 2 40.988 -8.234 15.661 0.5 17.9 ? P18 1SY 500 B 1 HETATM 19 O O19 1SY . . . B 2 40.45 -6.873 15.337 0.5 21.76 -1 O19 1SY 500 B 1 HETATM 20 O O20 1SY . . . B 2 40.018 -9.153 16.667 0.5 19.47 ? O20 1SY 500 B 1 HETATM 21 C C21 1SY . . . B 2 40.354 -8.964 18.069 0.5 21.09 ? C21 1SY 500 B 1 HETATM 22 C C22 1SY . . . B 2 40.507 -10.268 18.758 0.5 22.66 ? C22 1SY 500 B 1 HETATM 23 O O23 1SY . . . B 2 39.554 -11.209 18.3 0.5 22 ? O23 1SY 500 B 1 HETATM 24 C C24 1SY . . . B 2 40.157 -9.995 20.204 0.5 23.02 ? C24 1SY 500 B 1 HETATM 25 C C25 1SY . . . B 2 41.365 -9.758 20.996 0.5 19.8 ? C25 1SY 500 B 1 HETATM 26 O O26 1SY . . . B 2 42.034 -8.631 20.507 0.5 21.68 ? O26 1SY 500 B 1 HETATM 27 P P27 1SY . . . B 2 43.65 -8.781 20.749 0.5 20.76 ? P27 1SY 500 B 1 HETATM 28 O O28 1SY . . . B 2 44.162 -9.392 19.297 0.5 19.82 ? O28 1SY 500 B 1 HETATM 29 O O29 1SY . . . B 2 44.138 -7.379 20.932 0.5 20.84 -1 O29 1SY 500 B 1 HETATM 30 O O30 1SY . . . B 2 44.068 -9.628 21.927 0.5 23.07 ? O30 1SY 500 B 1 HETATM 31 O O31 1SY . . . B 2 39.298 -8.825 20.195 0.5 20.4 ? O31 1SY 500 B 1 HETATM 32 C C32 1SY . . . B 2 39.229 -8.401 18.82 0.5 21.01 ? C32 1SY 500 B 1 HETATM 33 N N33 1SY . . . B 2 39.214 -6.953 18.819 0.5 22.44 ? N33 1SY 500 B 1 HETATM 34 C C34 1SY . . . B 2 40.34 -6.521 19.421 0.5 22.77 ? C34 1SY 500 B 1 HETATM 35 N N35 1SY . . . B 2 40.3 -5.17 19.425 0.5 22.19 ? N35 1SY 500 B 1 HETATM 36 C C36 1SY . . . B 2 38.493 -5.922 18.472 0.5 22.99 ? C36 1SY 500 B 1 HETATM 37 C C37 1SY . . . B 2 39.166 -4.796 18.841 0.5 23.52 ? C37 1SY 500 B 1 HETATM 38 C C38 1SY . . . B 2 38.545 -3.43 18.54 0.5 23.27 ? C38 1SY 500 B 1 HETATM 39 N N39 1SY . . . B 2 37.279 -3.379 17.884 0.5 22.23 ? N39 1SY 500 B 1 HETATM 40 C C40 1SY . . . B 2 36.593 -4.587 17.511 0.5 22.8 ? C40 1SY 500 B 1 HETATM 41 N N41 1SY . . . B 2 35.315 -4.571 16.844 0.5 23.98 ? N41 1SY 500 B 1 HETATM 42 N N42 1SY . . . B 2 37.175 -5.878 17.791 0.5 23.16 ? N42 1SY 500 B 1 HETATM 43 O O43 1SY . . . B 2 39.108 -2.427 18.849 0.5 23.94 ? O43 1SY 500 B 1 HETATM 44 O O44 1SY . . . B 2 40.994 -9.001 14.366 0.5 22.66 ? O44 1SY 500 B 1 HETATM 45 O O4' 1SY . . . B 2 45.365 -8.153 16.163 0.5 19.61 ? O4' 1SY 500 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #