data_6DNK # _model_server_result.job_id T4lgr-9lAkDOOPhY25yItw _model_server_result.datetime_utc '2025-08-31 03:10:52' _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 6dnk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6DNK # _exptl.entry_id 6DNK _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 90 _cell.angle_gamma 90 _cell.entry_id 6DNK _cell.length_a 110.414 _cell.length_b 110.414 _cell.length_c 35.863 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DNK _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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' 7_643 y+1,x-1,-z-2 0 1 0 1 0 0 0 0 -1 110.414 -110.414 -71.726 # _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 6DNK _atom_sites.fract_transf_matrix[1][1] 0.009057 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009057 _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] 0.027884 _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 1 401 401 1SY 1SY . C 3 HOH A 1 501 501 HOH HOH . C 3 HOH A 2 502 502 HOH HOH . C 3 HOH A 3 503 503 HOH HOH . C 3 HOH A 4 504 504 HOH HOH . C 3 HOH A 5 505 505 HOH HOH . C 3 HOH A 6 506 506 HOH HOH . C 3 HOH A 7 507 507 HOH HOH . C 3 HOH A 8 508 508 HOH HOH . C 3 HOH A 9 509 509 HOH HOH . C 3 HOH A 10 510 510 HOH HOH . C 3 HOH A 11 511 511 HOH HOH . C 3 HOH A 12 512 512 HOH HOH . C 3 HOH A 13 513 513 HOH HOH . C 3 HOH A 14 514 514 HOH HOH . C 3 HOH A 15 515 515 HOH HOH . C 3 HOH A 16 516 516 HOH HOH . C 3 HOH A 17 517 517 HOH HOH . C 3 HOH A 18 518 518 HOH HOH . C 3 HOH A 19 519 519 HOH HOH . C 3 HOH A 20 520 520 HOH HOH . C 3 HOH A 21 521 521 HOH HOH . C 3 HOH A 22 522 522 HOH HOH . C 3 HOH A 23 523 523 HOH HOH . C 3 HOH A 24 524 524 HOH HOH . C 3 HOH A 25 525 525 HOH HOH . C 3 HOH A 26 526 526 HOH HOH . C 3 HOH A 27 527 527 HOH HOH . C 3 HOH A 28 528 528 HOH HOH . C 3 HOH A 29 529 529 HOH HOH . C 3 HOH A 30 530 530 HOH HOH . C 3 HOH A 31 531 531 HOH HOH . C 3 HOH A 32 532 532 HOH HOH . C 3 HOH A 33 533 533 HOH HOH . C 3 HOH A 34 534 534 HOH HOH . C 3 HOH A 35 535 535 HOH HOH . C 3 HOH A 36 536 536 HOH HOH . C 3 HOH A 37 537 537 HOH HOH . C 3 HOH A 38 538 538 HOH HOH . C 3 HOH A 39 539 539 HOH HOH . C 3 HOH A 40 540 540 HOH HOH . C 3 HOH A 41 541 541 HOH HOH . C 3 HOH A 42 542 542 HOH HOH . C 3 HOH A 43 543 543 HOH HOH . C 3 HOH A 44 544 544 HOH HOH . C 3 HOH A 45 545 545 HOH HOH . C 3 HOH A 46 546 546 HOH HOH . C 3 HOH A 47 547 547 HOH HOH . C 3 HOH A 48 548 548 HOH HOH . C 3 HOH A 49 549 549 HOH HOH . C 3 HOH A 50 550 550 HOH HOH . C 3 HOH A 51 551 551 HOH HOH . C 3 HOH A 52 552 552 HOH HOH . C 3 HOH A 53 553 553 HOH HOH . C 3 HOH A 54 554 554 HOH HOH . C 3 HOH A 55 555 555 HOH HOH . C 3 HOH A 56 556 556 HOH HOH . C 3 HOH A 57 557 557 HOH HOH . C 3 HOH A 58 558 558 HOH HOH . C 3 HOH A 59 559 559 HOH HOH . C 3 HOH A 60 560 560 HOH HOH . C 3 HOH A 61 561 561 HOH HOH . C 3 HOH A 62 562 562 HOH HOH . C 3 HOH A 63 563 563 HOH HOH . C 3 HOH A 64 564 564 HOH HOH . C 3 HOH A 65 565 565 HOH HOH . C 3 HOH A 66 566 566 HOH HOH . C 3 HOH A 67 567 567 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 . A . B 2 124.043 20.856 -36.145 0.5 27.78 ? C2 1SY 401 A 1 HETATM 2 N N01 1SY . A . B 2 124.483 17.441 -37.103 0.5 31.16 ? N01 1SY 401 A 1 HETATM 3 C C6 1SY . A . B 2 124.747 18.747 -36.901 0.5 28.59 ? C6 1SY 401 A 1 HETATM 4 N N1 1SY . A . B 2 123.816 19.548 -36.357 0.5 28.77 ? N1 1SY 401 A 1 HETATM 5 N N3 1SY . A . B 2 125.169 21.458 -36.469 0.5 28.41 ? N3 1SY 401 A 1 HETATM 6 C C4 1SY . A . B 2 126.18 20.782 -37.03 0.5 27.74 ? C4 1SY 401 A 1 HETATM 7 C C5 1SY . A . B 2 126.026 19.358 -37.293 0.5 27.66 ? C5 1SY 401 A 1 HETATM 8 N N7 1SY . A . B 2 127.176 18.958 -37.863 0.5 28.84 ? N7 1SY 401 A 1 HETATM 9 C C8 1SY . A . B 2 128.004 20.026 -37.951 0.5 26.97 ? C8 1SY 401 A 1 HETATM 10 N N9 1SY . A . B 2 127.389 21.123 -37.462 0.5 26.92 ? N9 1SY 401 A 1 HETATM 11 C C1' 1SY . A . B 2 127.94 22.489 -37.434 0.5 23 ? C1' 1SY 401 A 1 HETATM 12 C C2' 1SY . A . B 2 128.491 22.782 -36.06 0.5 22.15 ? C2' 1SY 401 A 1 HETATM 13 O O2' 1SY . A . B 2 128.104 24.13 -35.773 0.5 20.27 ? O2' 1SY 401 A 1 HETATM 14 C C3' 1SY . A . B 2 130.021 22.576 -36.023 0.5 20.78 ? C3' 1SY 401 A 1 HETATM 15 C C4' 1SY . A . B 2 130.234 22.862 -37.52 0.5 21.45 ? C4' 1SY 401 A 1 HETATM 16 C C16 1SY . A . B 2 131.392 22.026 -38.091 0.5 19.86 ? C16 1SY 401 A 1 HETATM 17 O O17 1SY . A . B 2 131.111 20.655 -37.832 0.5 18.45 ? O17 1SY 401 A 1 HETATM 18 P P18 1SY . A . B 2 132.191 19.579 -38.344 0.5 19.17 ? P18 1SY 401 A 1 HETATM 19 O O19 1SY . A . B 2 131.465 18.297 -38.185 0.5 17.58 ? O19 1SY 401 A 1 HETATM 20 O O20 1SY . B . B 2 130.035 22.835 -34.585 0.5 27.85 ? O20 1SY 401 A 1 HETATM 21 C C21 1SY . B . B 2 130.208 22.308 -35.888 0.5 26.42 ? C21 1SY 401 A 1 HETATM 22 C C22 1SY . B . B 2 131.248 23.224 -36.494 0.5 26.27 ? C22 1SY 401 A 1 HETATM 23 O O23 1SY . B . B 2 131.306 24.597 -36.088 0.5 24.18 ? O23 1SY 401 A 1 HETATM 24 C C24 1SY . B . B 2 130.952 23.169 -37.988 0.5 27.04 ? C24 1SY 401 A 1 HETATM 25 C C25 1SY . B . B 2 131.814 22.136 -38.715 0.5 26.68 ? C25 1SY 401 A 1 HETATM 26 O O26 1SY . B . B 2 131.377 20.796 -38.484 0.5 26.05 ? O26 1SY 401 A 1 HETATM 27 P P27 1SY . B . B 2 132.687 19.68 -38.242 0.5 27.25 ? P27 1SY 401 A 1 HETATM 28 O O28 1SY . A . B 2 130.363 22.973 -34.712 0.5 20.17 ? O28 1SY 401 A 1 HETATM 29 O O28 1SY . B . B 2 132.033 18.154 -38.426 0.5 24.1 ? O28 1SY 401 A 1 HETATM 30 O O30 1SY . B . B 2 133.929 20.111 -39.266 0.5 23.03 ? O30 1SY 401 A 1 HETATM 31 O O31 1SY . B . B 2 129.546 22.869 -38.096 0.5 27.56 ? O31 1SY 401 A 1 HETATM 32 C C32 1SY . B . B 2 129.016 22.526 -36.804 0.5 28.97 ? C32 1SY 401 A 1 HETATM 33 N N33 1SY . B . B 2 128.182 21.315 -36.935 0.5 31.72 ? N33 1SY 401 A 1 HETATM 34 C C34 1SY . B . B 2 128.58 20.12 -37.432 0.5 30.69 ? C34 1SY 401 A 1 HETATM 35 N N35 1SY . B . B 2 127.536 19.249 -37.44 0.5 31.33 ? N35 1SY 401 A 1 HETATM 36 C C36 1SY . B . B 2 126.897 21.16 -36.653 0.5 31.18 ? C36 1SY 401 A 1 HETATM 37 C C37 1SY . B . B 2 126.465 19.9 -36.949 0.5 30.67 ? C37 1SY 401 A 1 HETATM 38 C C38 1SY . B . B 2 125.067 19.547 -36.684 0.5 29.44 ? C38 1SY 401 A 1 HETATM 39 N N39 1SY . B . B 2 124.283 20.507 -36.21 0.5 29.42 ? N39 1SY 401 A 1 HETATM 40 C C40 1SY . B . B 2 124.764 21.728 -35.895 0.5 29.31 ? C40 1SY 401 A 1 HETATM 41 N N41 1SY . B . B 2 123.891 22.646 -35.372 0.5 27.36 ? N41 1SY 401 A 1 HETATM 42 N N42 1SY . B . B 2 126.049 22.076 -36.115 0.5 31.29 ? N42 1SY 401 A 1 HETATM 43 O O43 1SY . B . B 2 124.607 18.325 -36.882 0.5 30.56 ? O43 1SY 401 A 1 HETATM 44 O O44 1SY . A . B 2 132.706 19.938 -39.687 0.5 19.44 ? O44 1SY 401 A 1 HETATM 45 O O4' 1SY . A . B 2 129.059 22.615 -38.287 0.5 21.37 ? O4' 1SY 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 484 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #