data_6YDZ # _model_server_result.job_id gWOQiLejx23PsxtLK3ILKQ _model_server_result.datetime_utc '2024-11-28 18:08:44' _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 6ydz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6YDZ # _exptl.entry_id 6YDZ _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 "2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" _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 6YDZ _cell.length_a 110.962 _cell.length_b 110.962 _cell.length_c 35.409 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YDZ _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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -17.7045 # _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 4BW _chem_comp.mon_nstd_flag . _chem_comp.name "2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "3',3' cGAMP;c-GMP-AMP;c[G(3',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 NAA CBA 4BW sing 1 n n CBA NAS 4BW doub 2 n n CBA NAT 4BW sing 3 n n NAS CBG 4BW sing 4 n n NAT CBC 4BW sing 5 n n OAG CBI 4BW sing 6 n n CBG NBQ 4BW sing 7 n y CBG CBE 4BW doub 8 n y CBC CBE 4BW sing 9 n n CBC OAC 4BW doub 10 n n OAI PBS 4BW doub 11 n n CBI CBO 4BW sing 12 n n CBI CBM 4BW sing 13 n n CBO NBQ 4BW sing 14 n n CBO OAX 4BW sing 15 n n NBQ CAL 4BW sing 16 n y CBE NAR 4BW sing 17 n y OAE PBS 4BW sing 18 n n OAX CBK 4BW sing 19 n n PBS OAZ 4BW sing 20 n n PBS O5' 4BW sing 21 n n OAZ CBM 4BW sing 22 n n CBM CBK 4BW sing 23 n n CAL NAR 4BW doub 24 n y CBK CAN 4BW sing 25 n n N6 C6 4BW sing 26 n n N7 C8 4BW doub 27 n y N7 C5 4BW sing 28 n y O5' C5' 4BW sing 29 n n C8 N9 4BW sing 30 n y C6 C5 4BW doub 31 n y C6 N1 4BW sing 32 n y C5 C4 4BW sing 33 n y CAN OAV 4BW sing 34 n n C5' C4' 4BW sing 35 n n OAV PBR 4BW sing 36 n n N9 C4 4BW sing 37 n y N9 C1' 4BW sing 38 n n N1 C2 4BW doub 39 n y C4 N3 4BW doub 40 n y O4' C4' 4BW sing 41 n n O4' C1' 4BW sing 42 n n C4' C3' 4BW sing 43 n n C3' C2' 4BW sing 44 n n C3' O3' 4BW sing 45 n n C1' C2' 4BW sing 46 n n C2 N3 4BW sing 47 n y PBR OAD 4BW doub 48 n n PBR O3' 4BW sing 49 n n PBR OAH 4BW sing 50 n n C2' O2' 4BW sing 51 n n NAT H1 4BW sing 52 n n NAA H2 4BW sing 53 n n NAA H3 4BW sing 54 n n CAL H4 4BW sing 55 n n CBO H5 4BW sing 56 n n CBI H6 4BW sing 57 n n OAG H7 4BW sing 58 n n CBK H8 4BW sing 59 n n CAN H9 4BW sing 60 n n CAN H10 4BW sing 61 n n OAH H11 4BW sing 62 n n CBM H12 4BW sing 63 n n OAE H13 4BW sing 64 n n C5' H14 4BW sing 65 n n C5' H15 4BW sing 66 n n C4' H16 4BW sing 67 n n C3' H17 4BW sing 68 n n C2' H18 4BW sing 69 n n O2' H19 4BW sing 70 n n C1' H20 4BW sing 71 n n C8 H21 4BW sing 72 n n C2 H22 4BW sing 73 n n N6 H23 4BW sing 74 n n N6 H24 4BW sing 75 n n # _atom_sites.entry_id 6YDZ _atom_sites.fract_transf_matrix[1][1] 0.009012 _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] 0.009012 _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] 0.028241 _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 4BW A 1 401 1 4BW sdf . C 3 HOH A 1 501 5 HOH HOH . C 3 HOH A 2 502 6 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 O OAC 4BW . . . B 2 -14.703 17.782 -7.261 0.5 54.57 ? OAC 4BW 401 A 1 HETATM 2 C CBC 4BW . . . B 2 -14.872 19 -7.49 0.5 51.16 ? CBC 4BW 401 A 1 HETATM 3 N NAT 4BW . . . B 2 -13.909 19.737 -8.061 0.5 54.14 ? NAT 4BW 401 A 1 HETATM 4 C CBA 4BW . . . B 2 -14.076 21.05 -8.318 0.5 51.99 ? CBA 4BW 401 A 1 HETATM 5 N NAA 4BW . . . B 2 -12.973 21.82 -8.95 0.5 46.8 ? NAA 4BW 401 A 1 HETATM 6 N NAS 4BW . . . B 2 -15.208 21.726 -8.024 0.5 49.38 ? NAS 4BW 401 A 1 HETATM 7 C CBG 4BW . . . B 2 -16.248 21.098 -7.449 0.5 48.65 ? CBG 4BW 401 A 1 HETATM 8 C CBE 4BW . . . B 2 -16.144 19.671 -7.138 0.5 50 ? CBE 4BW 401 A 1 HETATM 9 N NAR 4BW . . . B 2 -17.318 19.326 -6.578 0.5 54.97 ? NAR 4BW 401 A 1 HETATM 10 C CAL 4BW . . . B 2 -18.104 20.438 -6.534 0.5 52.08 ? CAL 4BW 401 A 1 HETATM 11 N NBQ 4BW . . . B 2 -17.45 21.492 -7.052 0.5 47.45 ? NBQ 4BW 401 A 1 HETATM 12 C CBO 4BW . . . B 2 -17.934 22.875 -7.205 0.5 45.73 ? CBO 4BW 401 A 1 HETATM 13 C CBI 4BW . . . B 2 -18.166 23.105 -8.703 0.5 48.42 ? CBI 4BW 401 A 1 HETATM 14 O OAG 4BW . . . B 2 -17.952 24.458 -9.067 0.5 46.88 ? OAG 4BW 401 A 1 HETATM 15 O OAX 4BW . . . B 2 -19.2 23.073 -6.56 0.5 47.82 ? OAX 4BW 401 A 1 HETATM 16 C CBK 4BW . . . B 2 -20.241 23.247 -7.541 0.5 47.87 ? CBK 4BW 401 A 1 HETATM 17 C CAN 4BW . . . B 2 -21.511 22.557 -7.109 0.5 47.9 ? CAN 4BW 401 A 1 HETATM 18 O OAV 4BW . . . B 2 -21.238 21.209 -6.772 0.5 46.4 ? OAV 4BW 401 A 1 HETATM 19 P PBR 4BW . . . B 2 -22.469 20.224 -6.461 0.5 51.52 ? PBR 4BW 401 A 1 HETATM 20 O O3' 4BW . . . B 2 -23.377 20.088 -7.787 0.5 51.27 ? O3' 4BW 401 A 1 HETATM 21 O OAH 4BW . . . B 2 -21.922 18.87 -6.071 0.5 47.85 ? OAH 4BW 401 A 1 HETATM 22 O OAD 4BW . . . B 2 -23.312 20.811 -5.353 0.5 49.78 ? OAD 4BW 401 A 1 HETATM 23 C CBM 4BW . . . B 2 -19.647 22.717 -8.853 0.5 49.74 ? CBM 4BW 401 A 1 HETATM 24 O OAZ 4BW . . . B 2 -20.205 23.241 -10.025 0.5 51.35 ? OAZ 4BW 401 A 1 HETATM 25 P PBS 4BW . . . B 2 -20.259 22.243 -11.292 0.5 50.84 ? PBS 4BW 401 A 1 HETATM 26 O OAI 4BW . . . B 2 -20.849 22.987 -12.468 0.5 49.74 ? OAI 4BW 401 A 1 HETATM 27 O OAE 4BW . . . B 2 -18.869 21.746 -11.612 0.5 49.08 ? OAE 4BW 401 A 1 HETATM 28 O O5' 4BW . . . B 2 -21.195 20.983 -10.941 0.5 46.34 ? O5' 4BW 401 A 1 HETATM 29 C C5' 4BW . . . B 2 -22.581 21.197 -10.745 0.5 47.65 ? C5' 4BW 401 A 1 HETATM 30 C C4' 4BW . . . B 2 -23.253 19.935 -10.263 0.5 47.85 ? C4' 4BW 401 A 1 HETATM 31 O O4' 4BW . . . B 2 -23.02 18.819 -11.146 0.5 47.57 ? O4' 4BW 401 A 1 HETATM 32 C C3' 4BW . . . B 2 -22.781 19.454 -8.883 0.5 50 ? C3' 4BW 401 A 1 HETATM 33 C C2' 4BW . . . B 2 -23.134 17.961 -8.932 0.5 50.27 ? C2' 4BW 401 A 1 HETATM 34 O O2' 4BW . . . B 2 -24.499 17.766 -8.599 0.5 48.61 ? O2' 4BW 401 A 1 HETATM 35 C C1' 4BW . . . B 2 -22.876 17.602 -10.396 0.5 45.73 ? C1' 4BW 401 A 1 HETATM 36 N N9 4BW . . . B 2 -21.509 17.059 -10.492 0.5 47.69 ? N9 4BW 401 A 1 HETATM 37 C C8 4BW . . . B 2 -20.44 17.694 -11 0.5 52.13 ? C8 4BW 401 A 1 HETATM 38 N N7 4BW . . . B 2 -19.338 16.902 -10.922 0.5 53.99 ? N7 4BW 401 A 1 HETATM 39 C C5 4BW . . . B 2 -19.705 15.742 -10.348 0.5 49.3 ? C5 4BW 401 A 1 HETATM 40 C C4 4BW . . . B 2 -21.139 15.853 -10.062 0.5 48.49 ? C4 4BW 401 A 1 HETATM 41 N N3 4BW . . . B 2 -21.773 14.811 -9.476 0.5 50.07 ? N3 4BW 401 A 1 HETATM 42 C C2 4BW . . . B 2 -21.11 13.685 -9.156 0.5 52.56 ? C2 4BW 401 A 1 HETATM 43 N N1 4BW . . . B 2 -19.794 13.519 -9.388 0.5 55.04 ? N1 4BW 401 A 1 HETATM 44 C C6 4BW . . . B 2 -19.037 14.478 -9.968 0.5 52 ? C6 4BW 401 A 1 HETATM 45 N N6 4BW . . . B 2 -17.714 14.29 -10.194 0.5 55.49 ? N6 4BW 401 A 1 HETATM 46 H H1 4BW . . . B 2 -13.008 19.283 -8.315 0.5 64.97 ? H1 4BW 401 A 1 HETATM 47 H H2 4BW . . . B 2 -12.545 21.253 -9.699 0.5 56.16 ? H2 4BW 401 A 1 HETATM 48 H H3 4BW . . . B 2 -13.348 22.695 -9.351 0.5 56.16 ? H3 4BW 401 A 1 HETATM 49 H H4 4BW . . . B 2 -19.108 20.467 -6.132 0.5 62.49 ? H4 4BW 401 A 1 HETATM 50 H H5 4BW . . . B 2 -17.19 23.593 -6.833 0.5 54.88 ? H5 4BW 401 A 1 HETATM 51 H H6 4BW . . . B 2 -17.544 22.431 -9.307 0.5 58.1 ? H6 4BW 401 A 1 HETATM 52 H H7 4BW . . . B 2 -18.523 25.035 -8.543 0.5 56.25 ? H7 4BW 401 A 1 HETATM 53 H H8 4BW . . . B 2 -20.456 24.318 -7.663 0.5 57.44 ? H8 4BW 401 A 1 HETATM 54 H H9 4BW . . . B 2 -22.245 22.595 -7.916 0.5 57.48 ? H9 4BW 401 A 1 HETATM 55 H H10 4BW . . . B 2 -21.932 23.073 -6.243 0.5 57.48 ? H10 4BW 401 A 1 HETATM 56 H H12 4BW . . . B 2 -19.725 21.621 -8.859 0.5 59.69 ? H12 4BW 401 A 1 HETATM 57 H H14 4BW . . . B 2 -22.729 21.994 -10.014 0.5 57.18 ? H14 4BW 401 A 1 HETATM 58 H H15 4BW . . . B 2 -23.036 21.515 -11.685 0.5 57.18 ? H15 4BW 401 A 1 HETATM 59 H H16 4BW . . . B 2 -24.333 20.128 -10.204 0.5 57.41 ? H16 4BW 401 A 1 HETATM 60 H H17 4BW . . . B 2 -21.688 19.557 -8.827 0.5 60 ? H17 4BW 401 A 1 HETATM 61 H H18 4BW . . . B 2 -22.47 17.392 -8.267 0.5 60.32 ? H18 4BW 401 A 1 HETATM 62 H H19 4BW . . . B 2 -24.783 16.892 -8.901 0.5 58.33 ? H19 4BW 401 A 1 HETATM 63 H H20 4BW . . . B 2 -23.609 16.855 -10.732 0.5 54.88 ? H20 4BW 401 A 1 HETATM 64 H H21 4BW . . . B 2 -20.455 18.692 -11.419 0.5 62.56 ? H21 4BW 401 A 1 HETATM 65 H H22 4BW . . . B 2 -21.658 12.877 -8.687 0.5 63.07 ? H22 4BW 401 A 1 HETATM 66 H H23 4BW . . . B 2 -17.197 14.979 -10.604 0.5 66.58 ? H23 4BW 401 A 1 HETATM 67 H HN23 4BW . . . B 2 -12.28 22.045 -8.22 0.5 56.16 ? HN23 4BW 401 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 67 #