data_6YEA # _model_server_result.job_id Fxgu76r6Tq1P2JoYw8t4iw _model_server_result.datetime_utc '2024-11-28 19:16:03' _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 6yea # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6YEA # _exptl.entry_id 6YEA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.393 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',2'-difluoro-3',3'-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 6YEA _cell.length_a 110.948 _cell.length_b 110.948 _cell.length_c 35.586 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YEA _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 -17.793 # _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 H22 F2 N10 O11 P2' _chem_comp.formula_weight 678.393 _chem_comp.id OOE _chem_comp.mon_nstd_flag . _chem_comp.name "2',2'-difluoro-3',3'-cGAMP" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)- 3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-2-azan yl-1~{H}-purin-6-one' # 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 O4 P1 OOE doub 237 n n O22 P1 OOE sing 238 n n P1 O8 OOE sing 239 n n P1 O10 OOE sing 240 n n O5 C17 OOE sing 241 n n O5 C18 OOE sing 242 n n C14 N7 OOE doub 243 n y C14 N6 OOE sing 244 n y O8 C19 OOE sing 245 n n N7 C12 OOE sing 246 n y C19 C18 OOE sing 247 n n N6 C17 OOE sing 248 n n N6 C11 OOE sing 249 n y C17 C16 OOE sing 250 n n C12 C11 OOE doub 251 n y C12 C13 OOE sing 252 n n O9 C13 OOE doub 253 n n C11 N5 OOE sing 254 n n C18 C15 OOE sing 255 n n C13 N4 OOE sing 256 n n O10 C5 OOE sing 257 n n N5 C10 OOE doub 258 n n N4 C10 OOE sing 259 n n C10 N21 OOE sing 260 n n C16 C15 OOE sing 261 n n C16 F6 OOE sing 262 n n F9 C6 OOE sing 263 n n C5 C6 OOE sing 264 n n C5 C8 OOE sing 265 n n C15 O7 OOE sing 266 n n C6 C7 OOE sing 267 n n C N OOE doub 268 n y C N1 OOE sing 269 n y N C3 OOE sing 270 n y N1 C1 OOE doub 271 n y C3 N11 OOE sing 272 n n C3 C2 OOE doub 273 n y C1 C2 OOE sing 274 n y C1 N2 OOE sing 275 n y O7 P OOE sing 276 n n C8 C9 OOE sing 277 n n C8 O1 OOE sing 278 n n C2 N3 OOE sing 279 n y C7 N2 OOE sing 280 n n C7 O1 OOE sing 281 n n N2 C4 OOE sing 282 n y C9 O2 OOE sing 283 n n N3 C4 OOE doub 284 n y O2 P OOE sing 285 n n P O OOE doub 286 n n P O3 OOE sing 287 n n C H OOE sing 288 n n N11 H111 OOE sing 289 n n N11 H1 OOE sing 290 n n C14 H14 OOE sing 291 n n C15 H15 OOE sing 292 n n C16 H16 OOE sing 293 n n C17 H17 OOE sing 294 n n C18 H18 OOE sing 295 n n C19 H192 OOE sing 296 n n C19 H191 OOE sing 297 n n C4 H4 OOE sing 298 n n C5 H5 OOE sing 299 n n C6 H6 OOE sing 300 n n C7 H7 OOE sing 301 n n C8 H8 OOE sing 302 n n C9 H92 OOE sing 303 n n C9 H91 OOE sing 304 n n N21 HN22 OOE sing 305 n n N21 HN23 OOE sing 306 n n N4 HN4 OOE sing 307 n n O22 H2 OOE sing 308 n n O3 H3 OOE sing 309 n n # _atom_sites.entry_id 6YEA _atom_sites.fract_transf_matrix[1][1] 0.009013 _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] 0.009013 _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] 0.028101 _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 OOE A 1 401 1 OOE sdf . C 3 HOH A 1 501 5 HOH HOH . C 3 HOH A 2 502 1 HOH HOH . C 3 HOH A 3 503 6 HOH HOH . C 3 HOH A 4 504 11 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 N N OOE . . . B 2 -13.387 20.09 -8.448 0.5 54.23 ? N OOE 401 A 1 HETATM 2 C C OOE . . . B 2 -13.637 21.399 -8.659 0.5 52.39 ? C OOE 401 A 1 HETATM 3 O O OOE . . . B 2 -21.468 18.591 -6.325 0.5 40.25 ? O OOE 401 A 1 HETATM 4 N N11 OOE . . . B 2 -14.017 17.953 -7.665 0.5 52.02 ? N11 OOE 401 A 1 HETATM 5 C C1 OOE . . . B 2 -15.796 21.267 -7.72 0.5 42.75 ? C1 OOE 401 A 1 HETATM 6 C C10 OOE . . . B 2 -21.149 13.62 -9.387 0.5 52.21 ? C10 OOE 401 A 1 HETATM 7 C C11 OOE . . . B 2 -21.15 15.843 -10.189 0.5 42.73 ? C11 OOE 401 A 1 HETATM 8 C C12 OOE . . . B 2 -19.711 15.726 -10.446 0.5 43.46 ? C12 OOE 401 A 1 HETATM 9 C C13 OOE . . . B 2 -19.067 14.434 -10.112 0.5 49.09 ? C13 OOE 401 A 1 HETATM 10 C C14 OOE . . . B 2 -20.402 17.721 -11.024 0.5 45.82 ? C14 OOE 401 A 1 HETATM 11 C C15 OOE . . . B 2 -22.664 19.393 -8.827 0.5 39.41 ? C15 OOE 401 A 1 HETATM 12 C C16 OOE . . . B 2 -23.183 17.966 -9.017 0.5 40.75 ? C16 OOE 401 A 1 HETATM 13 C C17 OOE . . . B 2 -22.86 17.643 -10.476 0.5 43.7 ? C17 OOE 401 A 1 HETATM 14 C C18 OOE . . . B 2 -23.072 20.013 -10.171 0.5 41.27 ? C18 OOE 401 A 1 HETATM 15 C C19 OOE . . . B 2 -22.326 21.238 -10.677 0.5 39.83 ? C19 OOE 401 A 1 HETATM 16 C C2 OOE . . . B 2 -15.593 19.839 -7.46 0.5 43.46 ? C2 OOE 401 A 1 HETATM 17 C C3 OOE . . . B 2 -14.291 19.264 -7.868 0.5 49.2 ? C3 OOE 401 A 1 HETATM 18 C C4 OOE . . . B 2 -17.582 20.437 -6.77 0.5 45.63 ? C4 OOE 401 A 1 HETATM 19 C C5 OOE . . . B 2 -19.434 22.684 -8.959 0.5 39.53 ? C5 OOE 401 A 1 HETATM 20 C C6 OOE . . . B 2 -18.009 23.218 -8.801 0.5 42.37 ? C6 OOE 401 A 1 HETATM 21 C C7 OOE . . . B 2 -17.644 22.897 -7.351 0.5 44.09 ? C7 OOE 401 A 1 HETATM 22 C C8 OOE . . . B 2 -20.023 23.055 -7.591 0.5 39.13 ? C8 OOE 401 A 1 HETATM 23 C C9 OOE . . . B 2 -21.223 22.273 -7.081 0.5 39.26 ? C9 OOE 401 A 1 HETATM 24 F F6 OOE . . . B 2 -24.529 17.972 -8.802 0.5 39.82 ? F6 OOE 401 A 1 HETATM 25 F F9 OOE . . . B 2 -18.04 24.566 -9.003 0.5 40.39 ? F9 OOE 401 A 1 HETATM 26 N N1 OOE . . . B 2 -14.803 21.979 -8.311 0.5 47.13 ? N1 OOE 401 A 1 HETATM 27 N N2 OOE . . . B 2 -17.026 21.552 -7.277 0.5 44.24 ? N2 OOE 401 A 1 HETATM 28 N N21 OOE . . . B 2 -21.924 12.483 -8.817 0.5 44.32 ? N21 OOE 401 A 1 HETATM 29 N N3 OOE . . . B 2 -16.722 19.391 -6.877 0.5 46.09 ? N3 OOE 401 A 1 HETATM 30 N N4 OOE . . . B 2 -19.827 13.456 -9.6 0.5 53.48 ? N4 OOE 401 A 1 HETATM 31 N N5 OOE . . . B 2 -21.808 14.777 -9.669 0.5 47.32 ? N5 OOE 401 A 1 HETATM 32 N N6 OOE . . . B 2 -21.492 17.082 -10.565 0.5 43.26 ? N6 OOE 401 A 1 HETATM 33 N N7 OOE . . . B 2 -19.316 16.909 -10.955 0.5 46.14 ? N7 OOE 401 A 1 HETATM 34 O O1 OOE . . . B 2 -18.902 23.006 -6.662 0.5 37.92 ? O1 OOE 401 A 1 HETATM 35 O O10 OOE . . . B 2 -20.076 23.198 -10.104 0.5 43.5 ? O10 OOE 401 A 1 HETATM 36 O O2 OOE . . . B 2 -20.855 20.946 -6.803 0.5 37.37 ? O2 OOE 401 A 1 HETATM 37 O O22 OOE . . . B 2 -18.649 21.515 -11.46 0.5 39.25 ? O22 OOE 401 A 1 HETATM 38 O O3 OOE . . . B 2 -22.76 20.428 -5.235 0.5 38.45 ? O3 OOE 401 A 1 HETATM 39 O O4 OOE . . . B 2 -20.488 22.814 -12.541 0.5 38.37 ? O4 OOE 401 A 1 HETATM 40 O O5 OOE . . . B 2 -23.015 18.916 -11.13 0.5 37.94 ? O5 OOE 401 A 1 HETATM 41 O O7 OOE . . . B 2 -23.174 20.002 -7.663 0.5 46.46 ? O7 OOE 401 A 1 HETATM 42 O O8 OOE . . . B 2 -21.002 20.892 -10.993 0.5 38.21 ? O8 OOE 401 A 1 HETATM 43 O O9 OOE . . . B 2 -17.845 14.264 -10.303 0.5 52.44 ? O9 OOE 401 A 1 HETATM 44 P P OOE . . . B 2 -22.073 19.964 -6.484 0.5 37.28 ? P OOE 401 A 1 HETATM 45 P P1 OOE . . . B 2 -20.024 22.115 -11.299 0.5 37.11 ? P1 OOE 401 A 1 HETATM 46 H H OOE . . . B 2 -12.872 22.007 -9.127 0.5 63.02 ? H OOE 401 A 1 HETATM 47 H H111 OOE . . . B 2 -13.174 17.594 -7.932 0.5 62.57 ? H111 OOE 401 A 1 HETATM 48 H H14 OOE . . . B 2 -20.392 18.738 -11.396 0.5 55.13 ? H14 OOE 401 A 1 HETATM 49 H H15 OOE . . . B 2 -21.589 19.504 -8.629 0.5 47.44 ? H15 OOE 401 A 1 HETATM 50 H H16 OOE . . . B 2 -22.742 17.227 -8.333 0.5 49.06 ? H16 OOE 401 A 1 HETATM 51 H H17 OOE . . . B 2 -23.509 16.882 -10.932 0.5 52.6 ? H17 OOE 401 A 1 HETATM 52 H H18 OOE . . . B 2 -24.072 20.448 -10.031 0.5 49.67 ? H18 OOE 401 A 1 HETATM 53 H H192 OOE . . . B 2 -22.826 21.634 -11.563 0.5 47.95 ? H192 OOE 401 A 1 HETATM 54 H H191 OOE . . . B 2 -22.332 22.016 -9.911 0.5 47.95 ? H191 OOE 401 A 1 HETATM 55 H H4 OOE . . . B 2 -18.574 20.381 -6.338 0.5 54.91 ? H4 OOE 401 A 1 HETATM 56 H H5 OOE . . . B 2 -19.54 21.611 -9.169 0.5 47.59 ? H5 OOE 401 A 1 HETATM 57 H H6 OOE . . . B 2 -17.285 22.786 -9.507 0.5 50.99 ? H6 OOE 401 A 1 HETATM 58 H H7 OOE . . . B 2 -16.896 23.572 -6.913 0.5 53.06 ? H7 OOE 401 A 1 HETATM 59 H H8 OOE . . . B 2 -20.477 24.051 -7.691 0.5 47.11 ? H8 OOE 401 A 1 HETATM 60 H H92 OOE . . . B 2 -22.016 22.286 -7.832 0.5 47.26 ? H92 OOE 401 A 1 HETATM 61 H H91 OOE . . . B 2 -21.611 22.745 -6.176 0.5 47.26 ? H91 OOE 401 A 1 HETATM 62 H HN22 OOE . . . B 2 -21.863 11.671 -9.453 0.5 53.34 ? HN22 OOE 401 A 1 HETATM 63 H HN23 OOE . A . B 2 -22.913 12.76 -8.706 0.5 53.34 ? HN23 OOE 401 A 1 HETATM 64 H HN23 OOE . B . B 2 -21.533 12.227 -7.895 0.5 53.34 ? HN23 OOE 401 A 1 HETATM 65 H HN4 OOE . . . B 2 -19.386 12.545 -9.361 0.5 64.34 ? HN4 OOE 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 65 #