data_8SMG # _model_server_result.job_id 7V6EN_Na6zSSsj-KsVTfJg _model_server_result.datetime_utc '2024-11-15 08:53:45' _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 8smg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":101}' # _entry.id 8SMG # _exptl.entry_id 8SMG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 541.3 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione _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 120 _cell.entry_id 8SMG _cell.length_a 108.064 _cell.length_b 108.064 _cell.length_c 72.357 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SMG _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall 'P 6c 2c' _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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' 10_554 -y,-x,-z-1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 0 0 -36.1785 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H21 N5 O13 P2' _chem_comp.formula_weight 541.3 _chem_comp.id MF6 _chem_comp.mon_nstd_flag . _chem_comp.name (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "1'-2' gcADPR" # 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 O22 C21 MF6 sing 224 n n C23 C21 MF6 sing 225 n n C23 O35 MF6 sing 226 n n C23 C24 MF6 sing 227 n n C21 C12 MF6 sing 228 n n O35 C11 MF6 sing 229 n n C11 C12 MF6 sing 230 n n C11 N10 MF6 sing 231 n n C24 O25 MF6 sing 232 n n O13 C12 MF6 sing 233 n n O13 C14 MF6 sing 234 n n C14 O15 MF6 sing 235 n n C14 C19 MF6 sing 236 n n C09 N10 MF6 sing 237 n y C09 N08 MF6 doub 238 n y N10 C06 MF6 sing 239 n y O20 C19 MF6 sing 240 n n O15 C16 MF6 sing 241 n n C19 C17 MF6 sing 242 n n O25 P26 MF6 sing 243 n n N08 C07 MF6 sing 244 n y C06 C07 MF6 doub 245 n y C06 N05 MF6 sing 246 n y O34 P26 MF6 doub 247 n n C16 C17 MF6 sing 248 n n C16 C32 MF6 sing 249 n n C17 O18 MF6 sing 250 n n P26 O28 MF6 sing 251 n n P26 O27 MF6 sing 252 n n O28 P29 MF6 sing 253 n n C07 C02 MF6 sing 254 n y N05 C04 MF6 doub 255 n y O31 C32 MF6 sing 256 n n O31 P29 MF6 sing 257 n n O33 P29 MF6 doub 258 n n P29 O30 MF6 sing 259 n n C02 N01 MF6 sing 260 n n C02 N03 MF6 doub 261 n y C04 N03 MF6 sing 262 n y C17 H1 MF6 sing 263 n n C21 H2 MF6 sing 264 n n C24 H3 MF6 sing 265 n n C24 H4 MF6 sing 266 n n C04 H5 MF6 sing 267 n n C09 H6 MF6 sing 268 n n C11 H7 MF6 sing 269 n n C12 H8 MF6 sing 270 n n C14 H9 MF6 sing 271 n n C16 H10 MF6 sing 272 n n C19 H11 MF6 sing 273 n n C23 H12 MF6 sing 274 n n C32 H13 MF6 sing 275 n n C32 H14 MF6 sing 276 n n N01 H15 MF6 sing 277 n n N01 H16 MF6 sing 278 n n O18 H17 MF6 sing 279 n n O20 H18 MF6 sing 280 n n O22 H19 MF6 sing 281 n n O27 H20 MF6 sing 282 n n O30 H21 MF6 sing 283 n n # _atom_sites.entry_id 8SMG _atom_sites.fract_transf_matrix[1][1] 0.009254 _atom_sites.fract_transf_matrix[1][2] 0.005343 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010685 _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] 0.01382 _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 C 2 MF6 B 1 101 101 MF6 LIG . D 3 HOH A 1 101 11 HOH HOH . D 3 HOH A 2 102 20 HOH HOH . D 3 HOH A 3 103 4 HOH HOH . D 3 HOH A 4 104 1 HOH HOH . D 3 HOH A 5 105 27 HOH HOH . D 3 HOH A 6 106 9 HOH HOH . D 3 HOH A 7 107 14 HOH HOH . D 3 HOH A 8 108 19 HOH HOH . D 3 HOH A 9 109 13 HOH HOH . D 3 HOH A 10 110 12 HOH HOH . D 3 HOH A 11 111 26 HOH HOH . D 3 HOH A 12 112 7 HOH HOH . D 3 HOH A 13 113 17 HOH HOH . D 3 HOH A 14 114 18 HOH HOH . D 3 HOH A 15 115 10 HOH HOH . D 3 HOH A 16 116 21 HOH HOH . E 3 HOH B 1 201 25 HOH HOH . E 3 HOH B 2 202 2 HOH HOH . E 3 HOH B 3 203 23 HOH HOH . E 3 HOH B 4 204 6 HOH HOH . E 3 HOH B 5 205 16 HOH HOH . E 3 HOH B 6 206 5 HOH HOH . E 3 HOH B 7 207 8 HOH HOH . E 3 HOH B 8 208 22 HOH HOH . E 3 HOH B 9 209 15 HOH HOH . E 3 HOH B 10 210 3 HOH HOH . E 3 HOH B 11 211 24 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 C17 MF6 . . . C 2 -31.005 7.727 -17.758 1 45.53 ? C17 MF6 101 B 1 HETATM 2 C C21 MF6 . . . C 2 -32.476 8.882 -22.408 1 59.1 ? C21 MF6 101 B 1 HETATM 3 C C24 MF6 . . . C 2 -34.114 7.626 -23.757 1 57.62 ? C24 MF6 101 B 1 HETATM 4 C C02 MF6 . . . C 2 -37.809 9.873 -17.846 1 60.7 ? C02 MF6 101 B 1 HETATM 5 C C04 MF6 . . . C 2 -36.713 11.89 -18.143 1 54.46 ? C04 MF6 101 B 1 HETATM 6 C C06 MF6 . . . C 2 -36.025 10.053 -19.431 1 56.37 ? C06 MF6 101 B 1 HETATM 7 C C07 MF6 . . . C 2 -36.973 9.273 -18.832 1 61.55 ? C07 MF6 101 B 1 HETATM 8 C C09 MF6 . . . C 2 -35.875 8.053 -20.278 1 66.9 ? C09 MF6 101 B 1 HETATM 9 C C11 MF6 . . . C 2 -34.277 9.708 -21.172 1 51.51 ? C11 MF6 101 B 1 HETATM 10 C C12 MF6 . . . C 2 -33.057 8.842 -21.057 1 42.61 ? C12 MF6 101 B 1 HETATM 11 C C14 MF6 . . . C 2 -31.039 8.593 -19.912 1 54.3 ? C14 MF6 101 B 1 HETATM 12 C C16 MF6 . . . C 2 -30.966 6.591 -18.734 1 48.13 ? C16 MF6 101 B 1 HETATM 13 C C19 MF6 . . . C 2 -30.472 8.837 -18.543 1 51.59 ? C19 MF6 101 B 1 HETATM 14 C C23 MF6 . . . C 2 -33.663 8.979 -23.314 1 62.41 ? C23 MF6 101 B 1 HETATM 15 C C32 MF6 . . . C 2 -31.903 5.501 -18.3 1 49.99 ? C32 MF6 101 B 1 HETATM 16 N N01 MF6 . . . C 2 -38.836 9.096 -17.175 1 61.56 ? N01 MF6 101 B 1 HETATM 17 N N03 MF6 . . . C 2 -37.642 11.154 -17.547 1 58.97 ? N03 MF6 101 B 1 HETATM 18 N N05 MF6 . . . C 2 -35.926 11.359 -19.06 1 53.25 ? N05 MF6 101 B 1 HETATM 19 N N08 MF6 . . . C 2 -36.863 8.032 -19.375 1 65.28 ? N08 MF6 101 B 1 HETATM 20 N N10 MF6 . . . C 2 -35.352 9.278 -20.32 1 51.02 ? N10 MF6 101 B 1 HETATM 21 O O13 MF6 . . . C 2 -32.155 9.374 -20.08 1 53.37 ? O13 MF6 101 B 1 HETATM 22 O O15 MF6 . . . C 2 -31.361 7.178 -19.985 1 58.29 ? O15 MF6 101 B 1 HETATM 23 O O18 MF6 . . . C 2 -30.19 7.461 -16.622 1 46.97 ? O18 MF6 101 B 1 HETATM 24 O O20 MF6 . . . C 2 -29.045 8.782 -18.58 1 50.92 ? O20 MF6 101 B 1 HETATM 25 O O22 MF6 . . . C 2 -31.672 10.047 -22.596 1 52.94 ? O22 MF6 101 B 1 HETATM 26 O O25 MF6 . . . C 2 -34.55 6.909 -22.641 1 63.66 ? O25 MF6 101 B 1 HETATM 27 O O27 MF6 . . . C 2 -35.696 4.711 -23.549 1 74.96 -1 O27 MF6 101 B 1 HETATM 28 O O28 MF6 . . . C 2 -34.554 4.558 -21.2 1 70.09 ? O28 MF6 101 B 1 HETATM 29 O O30 MF6 . . . C 2 -33.144 2.941 -19.685 1 78.21 -1 O30 MF6 101 B 1 HETATM 30 O O31 MF6 . . . C 2 -33.056 5.521 -19.089 1 79.73 ? O31 MF6 101 B 1 HETATM 31 O O33 MF6 . . . C 2 -32.035 4.495 -21.114 1 97.18 ? O33 MF6 101 B 1 HETATM 32 O O34 MF6 . . . C 2 -33.325 4.875 -23.422 1 46.05 ? O34 MF6 101 B 1 HETATM 33 O O35 MF6 . . . C 2 -34.702 9.642 -22.539 1 54.73 ? O35 MF6 101 B 1 HETATM 34 P P26 MF6 . . . C 2 -34.584 5.264 -22.691 1 55.15 ? P26 MF6 101 B 1 HETATM 35 P P29 MF6 . . . C 2 -33.247 4.345 -20.225 1 67.29 ? P29 MF6 101 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #