data_6YEA
#
_model_server_result.job_id            jAdwIuuEAaXTYNB1Z5p4RA 
_model_server_result.datetime_utc      '2024-10-15 18:31:46' 
_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              17 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           301 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           65 
#