data_3EEI # _model_server_result.job_id u2mnc-BY9YamrIupkWKBJA _model_server_result.datetime_utc '2024-11-05 04:07:45' _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 3eei # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":234}' # _entry.id 3EEI # _exptl.entry_id 3EEI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.377 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.22 _cell.angle_gamma 90 _cell.entry_id 3EEI _cell.length_a 128.359 _cell.length_b 40.897 _cell.length_c 83.612 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EEI _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C12 H19 N5 O2 S' _chem_comp.formula_weight 297.377 _chem_comp.id MTM _chem_comp.mon_nstd_flag . _chem_comp.name (3S,4R)-2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-[(METHYLSULFANYL)METHYL]PYRROLIDINE-3,4-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (1S)-1-(9-DEAZAADENIN-9-YL)-1,4,5-TRIDEOXY-1,4-IMINO-5-METHYLTHIO-D-RIBITOL # 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 CS S5' MTM sing 237 n n CS HCS1 MTM sing 238 n n CS HCS2 MTM sing 239 n n CS HCS3 MTM sing 240 n n S5' C5' MTM sing 241 n n C5' C4' MTM sing 242 n n C5' "H5'1" MTM sing 243 n n C5' "H5'2" MTM sing 244 n n C4' N4' MTM sing 245 n n C4' C3' MTM sing 246 n n C4' H4' MTM sing 247 n n N4' C1' MTM sing 248 n n N4' HN4 MTM sing 249 n n C2' O2' MTM sing 250 n n C2' C3' MTM sing 251 n n C2' C1' MTM sing 252 n n C2' H2' MTM sing 253 n n O2' "HO'2" MTM sing 254 n n C3' O3' MTM sing 255 n n C3' H3' MTM sing 256 n n O3' H3T MTM sing 257 n n C1' C9 MTM sing 258 n n C1' H1' MTM sing 259 n n C9 C8 MTM doub 260 n y C9 C4 MTM sing 261 n y C8 N7 MTM sing 262 n y C8 H8 MTM sing 263 n n N7 C5 MTM sing 264 n y N7 H7 MTM sing 265 n n C5 C6 MTM sing 266 n n C5 C4 MTM doub 267 n y C6 N6 MTM sing 268 n n C6 N1 MTM sing 269 n n C6 H6 MTM sing 270 n n N6 H61 MTM sing 271 n n N6 H62 MTM sing 272 n n N1 C2 MTM sing 273 n n N1 HN1 MTM sing 274 n n C2 N3 MTM doub 275 n n C2 H2 MTM sing 276 n n N3 C4 MTM sing 277 n n # _atom_sites.entry_id 3EEI _atom_sites.fract_transf_matrix[1][1] 0.007791 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002716 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024452 _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] 0.012666 _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 MTM A 1 234 1 MTM MTM . D 2 MTM B 1 234 1 MTM MTM . E 3 HOH A 1 235 1 HOH HOH . E 3 HOH A 2 236 2 HOH HOH . E 3 HOH A 3 237 4 HOH HOH . E 3 HOH A 4 238 5 HOH HOH . E 3 HOH A 5 239 6 HOH HOH . E 3 HOH A 6 240 7 HOH HOH . E 3 HOH A 7 241 8 HOH HOH . E 3 HOH A 8 242 9 HOH HOH . E 3 HOH A 9 243 10 HOH HOH . E 3 HOH A 10 244 11 HOH HOH . E 3 HOH A 11 245 13 HOH HOH . E 3 HOH A 12 246 14 HOH HOH . E 3 HOH A 13 247 16 HOH HOH . E 3 HOH A 14 248 17 HOH HOH . E 3 HOH A 15 249 21 HOH HOH . E 3 HOH A 16 250 28 HOH HOH . E 3 HOH A 17 251 29 HOH HOH . E 3 HOH A 18 252 30 HOH HOH . E 3 HOH A 19 253 35 HOH HOH . E 3 HOH A 20 254 37 HOH HOH . E 3 HOH A 21 255 42 HOH HOH . E 3 HOH A 22 256 43 HOH HOH . E 3 HOH A 23 257 44 HOH HOH . E 3 HOH A 24 258 45 HOH HOH . E 3 HOH A 25 259 46 HOH HOH . E 3 HOH A 26 260 49 HOH HOH . E 3 HOH A 27 261 50 HOH HOH . E 3 HOH A 28 262 53 HOH HOH . E 3 HOH A 29 263 54 HOH HOH . E 3 HOH A 30 264 55 HOH HOH . E 3 HOH A 31 265 58 HOH HOH . E 3 HOH A 32 266 61 HOH HOH . E 3 HOH A 33 267 62 HOH HOH . E 3 HOH A 34 268 63 HOH HOH . E 3 HOH A 35 269 64 HOH HOH . E 3 HOH A 36 270 66 HOH HOH . E 3 HOH A 37 271 70 HOH HOH . E 3 HOH A 38 272 72 HOH HOH . E 3 HOH A 39 273 73 HOH HOH . E 3 HOH A 40 274 77 HOH HOH . E 3 HOH A 41 275 78 HOH HOH . E 3 HOH A 42 276 80 HOH HOH . E 3 HOH A 43 277 81 HOH HOH . E 3 HOH A 44 278 82 HOH HOH . E 3 HOH A 45 279 83 HOH HOH . E 3 HOH A 46 280 86 HOH HOH . E 3 HOH A 47 281 91 HOH HOH . E 3 HOH A 48 282 92 HOH HOH . E 3 HOH A 49 283 93 HOH HOH . E 3 HOH A 50 284 94 HOH HOH . E 3 HOH A 51 285 96 HOH HOH . E 3 HOH A 52 286 97 HOH HOH . E 3 HOH A 53 287 98 HOH HOH . E 3 HOH A 54 288 99 HOH HOH . E 3 HOH A 55 289 100 HOH HOH . E 3 HOH A 56 290 106 HOH HOH . E 3 HOH A 57 291 108 HOH HOH . E 3 HOH A 58 292 109 HOH HOH . E 3 HOH A 59 293 110 HOH HOH . E 3 HOH A 60 294 118 HOH HOH . E 3 HOH A 61 295 119 HOH HOH . E 3 HOH A 62 296 120 HOH HOH . E 3 HOH A 63 297 121 HOH HOH . E 3 HOH A 64 298 122 HOH HOH . E 3 HOH A 65 299 123 HOH HOH . E 3 HOH A 66 300 124 HOH HOH . E 3 HOH A 67 301 125 HOH HOH . E 3 HOH A 68 302 126 HOH HOH . F 3 HOH B 1 235 3 HOH HOH . F 3 HOH B 2 236 12 HOH HOH . F 3 HOH B 3 237 15 HOH HOH . F 3 HOH B 4 238 18 HOH HOH . F 3 HOH B 5 239 19 HOH HOH . F 3 HOH B 6 240 20 HOH HOH . F 3 HOH B 7 241 22 HOH HOH . F 3 HOH B 8 242 23 HOH HOH . F 3 HOH B 9 243 24 HOH HOH . F 3 HOH B 10 244 25 HOH HOH . F 3 HOH B 11 245 26 HOH HOH . F 3 HOH B 12 246 27 HOH HOH . F 3 HOH B 13 247 31 HOH HOH . F 3 HOH B 14 248 32 HOH HOH . F 3 HOH B 15 249 33 HOH HOH . F 3 HOH B 16 250 34 HOH HOH . F 3 HOH B 17 251 36 HOH HOH . F 3 HOH B 18 252 38 HOH HOH . F 3 HOH B 19 253 39 HOH HOH . F 3 HOH B 20 254 40 HOH HOH . F 3 HOH B 21 255 41 HOH HOH . F 3 HOH B 22 256 47 HOH HOH . F 3 HOH B 23 257 48 HOH HOH . F 3 HOH B 24 258 51 HOH HOH . F 3 HOH B 25 259 52 HOH HOH . F 3 HOH B 26 260 56 HOH HOH . F 3 HOH B 27 261 57 HOH HOH . F 3 HOH B 28 262 59 HOH HOH . F 3 HOH B 29 263 65 HOH HOH . F 3 HOH B 30 264 67 HOH HOH . F 3 HOH B 31 265 68 HOH HOH . F 3 HOH B 32 266 69 HOH HOH . F 3 HOH B 33 267 71 HOH HOH . F 3 HOH B 34 268 74 HOH HOH . F 3 HOH B 35 269 75 HOH HOH . F 3 HOH B 36 270 84 HOH HOH . F 3 HOH B 37 271 85 HOH HOH . F 3 HOH B 38 272 87 HOH HOH . F 3 HOH B 39 273 88 HOH HOH . F 3 HOH B 40 274 90 HOH HOH . F 3 HOH B 41 275 101 HOH HOH . F 3 HOH B 42 276 102 HOH HOH . F 3 HOH B 43 277 103 HOH HOH . F 3 HOH B 44 278 104 HOH HOH . F 3 HOH B 45 279 105 HOH HOH . F 3 HOH B 46 280 107 HOH HOH . F 3 HOH B 47 281 112 HOH HOH . F 3 HOH B 48 282 114 HOH HOH . F 3 HOH B 49 283 115 HOH HOH . F 3 HOH B 50 284 117 HOH HOH . F 3 HOH B 51 285 128 HOH HOH . F 3 HOH B 52 286 129 HOH HOH . F 3 HOH B 53 287 130 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 CS MTM . . . D 2 -43.402 -19.024 -10.342 1 29.03 ? CS MTM 234 B 1 HETATM 2 S S5' MTM . . . D 2 -43.508 -17.254 -10.368 1 31.51 ? S5' MTM 234 B 1 HETATM 3 C C5' MTM . . . D 2 -45.28 -17.039 -10.274 1 26.67 ? C5' MTM 234 B 1 HETATM 4 C C4' MTM . . . D 2 -45.943 -17.213 -11.656 1 27.9 ? C4' MTM 234 B 1 HETATM 5 N N4' MTM . . . D 2 -47.378 -17.315 -11.423 1 27.42 ? N4' MTM 234 B 1 HETATM 6 C C2' MTM . . . D 2 -46.933 -15.026 -11.951 1 27.58 ? C2' MTM 234 B 1 HETATM 7 O O2' MTM . . . D 2 -47.536 -14.228 -12.991 1 27.01 ? O2' MTM 234 B 1 HETATM 8 C C3' MTM . . . D 2 -45.835 -15.921 -12.49 1 28.74 ? C3' MTM 234 B 1 HETATM 9 O O3' MTM . . . D 2 -45.946 -16.191 -13.931 1 27.16 ? O3' MTM 234 B 1 HETATM 10 C C1' MTM . . . D 2 -47.923 -15.985 -11.276 1 26.64 ? C1' MTM 234 B 1 HETATM 11 C C9 MTM . . . D 2 -48.339 -15.573 -9.853 1 27.43 ? C9 MTM 234 B 1 HETATM 12 C C8 MTM . . . D 2 -49.025 -16.559 -8.941 1 27.29 ? C8 MTM 234 B 1 HETATM 13 N N7 MTM . . . D 2 -48.955 -16.044 -7.678 1 26.57 ? N7 MTM 234 B 1 HETATM 14 C C5 MTM . . . D 2 -48.214 -14.892 -7.612 1 25.72 ? C5 MTM 234 B 1 HETATM 15 C C6 MTM . . . D 2 -47.758 -13.994 -6.542 1 26.73 ? C6 MTM 234 B 1 HETATM 16 N N6 MTM . . . D 2 -48.168 -14.181 -5.252 1 24.04 ? N6 MTM 234 B 1 HETATM 17 N N1 MTM . . . D 2 -46.987 -12.925 -6.897 1 24.2 ? N1 MTM 234 B 1 HETATM 18 C C2 MTM . . . D 2 -46.606 -12.715 -8.197 1 28.89 ? C2 MTM 234 B 1 HETATM 19 N N3 MTM . . . D 2 -46.954 -13.53 -9.227 1 25.94 ? N3 MTM 234 B 1 HETATM 20 C C4 MTM . . . D 2 -47.722 -14.628 -8.965 1 26.56 ? C4 MTM 234 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #