data_4KSY # _model_server_result.job_id OxAMv_GayHb6yE8sNj4cTQ _model_server_result.datetime_utc '2024-11-25 23:17:18' _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 4ksy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 4KSY # _exptl.entry_id 4KSY _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 96.97 _cell.angle_gamma 90 _cell.entry_id 4KSY _cell.length_a 89.522 _cell.length_b 77.927 _cell.length_c 35.974 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KSY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _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_654 -x+1,y,-z-1 -1 0 0 0 1 0 0 0 -1 93.887432 0 -35.708146 # _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 4KSY _atom_sites.fract_transf_matrix[1][1] 0.01117 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001367 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012833 _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] 0.028005 _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 A 1 500 500 1SY CGA . C 3 HOH A 1 601 1 HOH HOH . C 3 HOH A 2 602 2 HOH HOH . C 3 HOH A 3 603 3 HOH HOH . C 3 HOH A 4 604 4 HOH HOH . C 3 HOH A 5 605 5 HOH HOH . C 3 HOH A 6 606 6 HOH HOH . C 3 HOH A 7 607 7 HOH HOH . C 3 HOH A 8 608 8 HOH HOH . C 3 HOH A 9 609 9 HOH HOH . C 3 HOH A 10 610 10 HOH HOH . C 3 HOH A 11 611 11 HOH HOH . C 3 HOH A 12 612 12 HOH HOH . C 3 HOH A 13 613 13 HOH HOH . C 3 HOH A 14 614 14 HOH HOH . C 3 HOH A 15 615 15 HOH HOH . C 3 HOH A 16 616 16 HOH HOH . C 3 HOH A 17 617 17 HOH HOH . C 3 HOH A 18 618 18 HOH HOH . C 3 HOH A 19 619 19 HOH HOH . C 3 HOH A 20 620 20 HOH HOH . C 3 HOH A 21 621 21 HOH HOH . C 3 HOH A 22 622 22 HOH HOH . C 3 HOH A 23 623 23 HOH HOH . C 3 HOH A 24 624 24 HOH HOH . C 3 HOH A 25 625 25 HOH HOH . C 3 HOH A 26 626 26 HOH HOH . C 3 HOH A 27 627 27 HOH HOH . C 3 HOH A 28 628 28 HOH HOH . C 3 HOH A 29 629 29 HOH HOH . C 3 HOH A 30 630 30 HOH HOH . C 3 HOH A 31 631 31 HOH HOH . C 3 HOH A 32 632 32 HOH HOH . C 3 HOH A 33 633 33 HOH HOH . C 3 HOH A 34 634 34 HOH HOH . C 3 HOH A 35 635 35 HOH HOH . C 3 HOH A 36 636 36 HOH HOH . C 3 HOH A 37 637 37 HOH HOH . C 3 HOH A 38 638 38 HOH HOH . C 3 HOH A 39 639 39 HOH HOH . C 3 HOH A 40 640 41 HOH HOH . C 3 HOH A 41 641 42 HOH HOH . C 3 HOH A 42 642 43 HOH HOH . C 3 HOH A 43 643 44 HOH HOH . C 3 HOH A 44 644 45 HOH HOH . C 3 HOH A 45 645 46 HOH HOH . C 3 HOH A 46 646 47 HOH HOH . C 3 HOH A 47 647 48 HOH HOH . C 3 HOH A 48 648 49 HOH HOH . C 3 HOH A 49 649 50 HOH HOH . C 3 HOH A 50 650 51 HOH HOH . C 3 HOH A 51 651 52 HOH HOH . C 3 HOH A 52 652 53 HOH HOH . C 3 HOH A 53 653 54 HOH HOH . C 3 HOH A 54 654 55 HOH HOH . C 3 HOH A 55 655 56 HOH HOH . C 3 HOH A 56 656 57 HOH HOH . C 3 HOH A 57 657 58 HOH HOH . C 3 HOH A 58 658 59 HOH HOH . C 3 HOH A 59 659 60 HOH HOH . C 3 HOH A 60 660 61 HOH HOH . C 3 HOH A 61 661 62 HOH HOH . C 3 HOH A 62 662 63 HOH HOH . C 3 HOH A 63 663 64 HOH HOH . C 3 HOH A 64 664 65 HOH HOH . C 3 HOH A 65 665 67 HOH HOH . C 3 HOH A 66 666 68 HOH HOH . C 3 HOH A 67 667 69 HOH HOH . C 3 HOH A 68 668 70 HOH HOH . C 3 HOH A 69 669 71 HOH HOH . C 3 HOH A 70 670 72 HOH HOH . C 3 HOH A 71 671 73 HOH HOH . C 3 HOH A 72 672 74 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 52.285 8.645 -17.445 0.5 26.56 ? C2 1SY 500 A 1 HETATM 2 N N01 1SY . . . B 2 49.671 10.964 -18.686 0.5 29.27 ? N01 1SY 500 A 1 HETATM 3 C C6 1SY . . . B 2 50.424 9.721 -18.417 0.5 24.78 ? C6 1SY 500 A 1 HETATM 4 N N1 1SY . . . B 2 51.572 9.746 -17.722 0.5 24.19 ? N1 1SY 500 A 1 HETATM 5 N N3 1SY . . . B 2 51.861 7.466 -17.865 0.5 25.79 ? N3 1SY 500 A 1 HETATM 6 C C4 1SY . . . B 2 50.707 7.322 -18.571 0.5 23.61 ? C4 1SY 500 A 1 HETATM 7 C C5 1SY . . . B 2 49.932 8.463 -18.884 0.5 23.55 ? C5 1SY 500 A 1 HETATM 8 N N7 1SY . . . B 2 48.846 8.028 -19.599 0.5 20.84 ? N7 1SY 500 A 1 HETATM 9 C C8 1SY . . . B 2 48.904 6.68 -19.752 0.5 24.84 ? C8 1SY 500 A 1 HETATM 10 N N9 1SY . . . B 2 50.021 6.278 -19.141 0.5 22.84 ? N9 1SY 500 A 1 HETATM 11 C C1' 1SY . . . B 2 50.682 5.019 -18.928 0.5 20.94 ? C1' 1SY 500 A 1 HETATM 12 C C2' 1SY . . . B 2 50.38 4.522 -17.603 0.5 19.99 ? C2' 1SY 500 A 1 HETATM 13 O O2' 1SY . . . B 2 51.44 3.63 -17.229 0.5 22.3 ? O2' 1SY 500 A 1 HETATM 14 C C3' 1SY . . . B 2 49.138 3.764 -17.764 0.5 20.34 ? C3' 1SY 500 A 1 HETATM 15 C C4' 1SY . . . B 2 49.37 3.094 -19.052 0.5 23.2 ? C4' 1SY 500 A 1 HETATM 16 C C16 1SY . . . B 2 48.077 2.813 -19.76 0.5 23.73 ? C16 1SY 500 A 1 HETATM 17 O O17 1SY . . . B 2 47.351 4.005 -19.842 0.5 21.49 ? O17 1SY 500 A 1 HETATM 18 P P18 1SY . . . B 2 45.831 3.976 -20.336 0.5 20.3 ? P18 1SY 500 A 1 HETATM 19 O O19 1SY . . . B 2 45.21 5.359 -20.429 0.5 20.21 ? O19 1SY 500 A 1 HETATM 20 O O20 1SY . . . B 2 44.941 3.03 -19.356 0.5 24.84 ? O20 1SY 500 A 1 HETATM 21 C C21 1SY . . . B 2 45.238 3.102 -17.973 0.5 20.66 ? C21 1SY 500 A 1 HETATM 22 C C22 1SY . . . B 2 45.225 1.757 -17.318 0.5 22.74 ? C22 1SY 500 A 1 HETATM 23 O O23 1SY . . . B 2 44.203 0.94 -17.865 0.5 23.1 ? O23 1SY 500 A 1 HETATM 24 C C24 1SY . . . B 2 44.873 2.031 -15.933 0.5 17.89 ? C24 1SY 500 A 1 HETATM 25 C C25 1SY . . . B 2 46.069 2.169 -15.026 0.5 22.33 ? C25 1SY 500 A 1 HETATM 26 O O26 1SY . . . B 2 46.821 3.329 -15.275 0.5 21.55 ? O26 1SY 500 A 1 HETATM 27 P P27 1SY . . . B 2 48.421 3.298 -15.237 0.5 22.23 ? P27 1SY 500 A 1 HETATM 28 O O28 1SY . . . B 2 49.055 2.793 -16.676 0.5 21.23 ? O28 1SY 500 A 1 HETATM 29 O O29 1SY . . . B 2 48.935 4.647 -14.857 0.5 20.69 ? O29 1SY 500 A 1 HETATM 30 O O30 1SY . . . B 2 48.867 2.315 -14.223 0.5 22.58 ? O30 1SY 500 A 1 HETATM 31 O O31 1SY . . . B 2 44.051 3.225 -15.94 0.5 22.05 ? O31 1SY 500 A 1 HETATM 32 C C32 1SY . . . B 2 44.157 3.838 -17.254 0.5 22.06 ? C32 1SY 500 A 1 HETATM 33 N N33 1SY . . . B 2 44.435 5.171 -17.082 0.5 24.74 ? N33 1SY 500 A 1 HETATM 34 C C34 1SY . . . B 2 45.479 5.722 -16.498 0.5 24.66 ? C34 1SY 500 A 1 HETATM 35 N N35 1SY . . . B 2 45.348 7.054 -16.528 0.5 26.4 ? N35 1SY 500 A 1 HETATM 36 C C36 1SY . . . B 2 43.59 6.164 -17.482 0.5 23.52 ? C36 1SY 500 A 1 HETATM 37 C C37 1SY . . . B 2 44.175 7.37 -17.126 0.5 23.65 ? C37 1SY 500 A 1 HETATM 38 C C38 1SY . . . B 2 43.486 8.666 -17.444 0.5 25.61 ? C38 1SY 500 A 1 HETATM 39 N N39 1SY . . . B 2 42.231 8.64 -18.103 0.5 22.85 ? N39 1SY 500 A 1 HETATM 40 C C40 1SY . . . B 2 41.638 7.385 -18.456 0.5 27.01 ? C40 1SY 500 A 1 HETATM 41 N N41 1SY . . . B 2 40.375 7.354 -19.117 0.5 27.09 ? N41 1SY 500 A 1 HETATM 42 N N42 1SY . . . B 2 42.319 6.133 -18.156 0.5 23.08 ? N42 1SY 500 A 1 HETATM 43 O O43 1SY . . . B 2 44.002 9.763 -17.139 0.5 25.04 ? O43 1SY 500 A 1 HETATM 44 O O44 1SY . . . B 2 45.826 3.332 -21.655 0.5 20.64 ? O44 1SY 500 A 1 HETATM 45 O O4' 1SY . . . B 2 50.154 4.044 -19.82 0.5 23.4 ? O4' 1SY 500 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #