1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Ferreon, J. Volk, D. Luxon, B. Gorenstein, D. Hilser, V. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N N N 89 S C N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C N 95 N O N 96 N N N 97 N O N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N N N 109 S C N 110 N C N 111 N O N 112 N C N 113 N C N 114 N C N 115 N O N 116 N O N 117 N O N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N N N 128 N C N 129 N C N 130 N O N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N N N 138 S C N 139 N C N 140 N O N 141 N C Y 142 N C Y 143 N N Y 144 N C Y 145 N C Y 146 N N N 147 N O N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N N N 159 S C N 160 N C N 161 N O N 162 S C N 163 N C N 164 N C N 165 N C N 166 N O N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N N N 181 S C N 182 N C N 183 N O N 184 N C N 185 N C N 186 N C N 187 N C N 188 N O N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N H N 202 N N N 203 S C N 204 N C N 205 N O N 206 N C N 207 N C N 208 N C N 209 N C N 210 N N N 211 N O N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N N N 228 S C N 229 N C N 230 N O N 231 N C N 232 N C N 233 N S N 234 N C N 235 N O N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N N N 248 S C N 249 N C N 250 N O N 251 N C Y 252 N C Y 253 N C Y 254 N C Y 255 N C Y 256 N C Y 257 N C N 258 N O N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N N N 271 S C N 272 N C N 273 N O N 274 N C N 275 N C N 276 N C N 277 N O N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N N N 288 S C N 289 N C N 290 N O N 291 N C N 292 N O N 293 N O N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N N N 302 S C N 303 N C N 304 N O N 305 R C N 306 N O N 307 N C N 308 N O N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N N N 319 S C N 320 N C N 321 N O N 322 N C Y 323 N C Y 324 N C Y 325 N C Y 326 N N Y 327 N C Y 328 N C Y 329 N C Y 330 N C Y 331 N C N 332 N O N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N N N 346 S C N 347 N C N 348 N O N 349 N C Y 350 N C Y 351 N C Y 352 N C Y 353 N C Y 354 N C Y 355 N C N 356 N O N 357 N O N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H N 366 N H N 367 N H N 368 N H N 369 N N N 370 S C N 371 N C N 372 N O N 373 N C N 374 N C N 375 N C N 376 N O N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N doub N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N doub N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N doub N 136 N sing N 137 N sing N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub Y 142 N doub N 143 N sing Y 144 N sing N 145 N sing Y 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N doub N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N doub N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N doub N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N doub N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N doub N 242 N sing N 243 N sing N 244 N sing N 245 N sing Y 246 N doub Y 247 N sing Y 248 N sing N 249 N sing Y 250 N doub N 251 N sing Y 252 N doub N 253 N sing Y 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N doub N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N doub N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N doub N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N doub N 311 N sing N 312 N sing N 313 N sing N 314 N sing Y 315 N doub Y 316 N sing Y 317 N sing N 318 N sing Y 319 N doub Y 320 N sing Y 321 N sing N 322 N sing Y 323 N sing Y 324 N doub N 325 N sing Y 326 N doub N 327 N sing Y 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N doub N 339 N sing N 340 N sing N 341 N sing N 342 N sing Y 343 N doub Y 344 N sing Y 345 N sing N 346 N sing Y 347 N doub N 348 N sing Y 349 N doub N 350 N sing Y 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N doub N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing US Biochemistry BICHAW 0033 0006-2960 42 5582 5591 10.1021/bi030005j 12741814 Solution Structure, Dynamics and Thermodynamics of the Native State Ensemble of Sem-5 C-Terminal SH3 Domain 2003 10.2210/pdb1k76/pdb pdb_00001k76 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 7237.967 SEX MUSCLE ABNORMAL PROTEIN 5 SH3 domain (Residues 155-214) C57A 1 man polymer no no HMETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVAPYNSN HMETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVAPYNSN A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Caenorhabditis Escherichia sample Sem-5 6239 Caenorhabditis elegans 562 Escherichia coli BL21 pLysS plasmid pET19B database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2003-05-20 1 1 2008-04-27 1 2 2011-07-13 1 3 2021-10-27 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_ref_seq_dif.details RCSB Y RCSB 2001-10-18 REL The structure was determined using triple-resonance NMR spectroscopy structures with the least restraint violations,structures with the lowest energy 50 1 3D 15N-NOESY-HSQC 3D 13C-NOESY-HSQC 100 mM NaCl 4.8 ambient 298 K distance geometry simulated annealing molecular dynamics minimized average structure 13C,15N 1mM Sem-5 SH3 domain 50 mM sodium acetate buffer, 10 mM CaCl2, 100 mM NaCl,pH 4.8, 90%h20, 10%d20 90%h20, 10%d20 Brunger structure solution CNS 1.0 MSI processing Felix Varian collection VNMR Brunger, et al. refinement CNS 400 Varian UNITYPLUS n 1 1 A n 2 2 A GLU 3 n 3 GLU 3 A THR 4 n 4 THR 4 A LYS 5 n 5 LYS 5 A PHE 6 n 6 PHE 6 A VAL 7 n 7 VAL 7 A GLN 8 n 8 GLN 8 A ALA 9 n 9 ALA 9 A LEU 10 n 10 LEU 10 A PHE 11 n 11 PHE 11 A ASP 12 n 12 ASP 12 A PHE 13 n 13 PHE 13 A ASN 14 n 14 ASN 14 A PRO 15 n 15 PRO 15 A GLN 16 n 16 GLN 16 A GLU 17 n 17 GLU 17 A SER 18 n 18 SER 18 A GLY 19 n 19 GLY 19 A GLU 20 n 20 GLU 20 A LEU 21 n 21 LEU 21 A ALA 22 n 22 ALA 22 A PHE 23 n 23 PHE 23 A LYS 24 n 24 LYS 24 A ARG 25 n 25 ARG 25 A GLY 26 n 26 GLY 26 A ASP 27 n 27 ASP 27 A VAL 28 n 28 VAL 28 A ILE 29 n 29 ILE 29 A THR 30 n 30 THR 30 A LEU 31 n 31 LEU 31 A ILE 32 n 32 ILE 32 A ASN 33 n 33 ASN 33 A LYS 34 n 34 LYS 34 A ASP 35 n 35 ASP 35 A ASP 36 n 36 ASP 36 A PRO 37 n 37 PRO 37 A ASN 38 n 38 ASN 38 A TRP 39 n 39 TRP 39 A TRP 40 n 40 TRP 40 A GLU 41 n 41 GLU 41 A GLY 42 n 42 GLY 42 A GLN 43 n 43 GLN 43 A LEU 44 n 44 LEU 44 A ASN 45 n 45 ASN 45 A ASN 46 n 46 ASN 46 A ARG 47 n 47 ARG 47 A ARG 48 n 48 ARG 48 A GLY 49 n 49 GLY 49 A ILE 50 n 50 ILE 50 A PHE 51 n 51 PHE 51 A PRO 52 n 52 PRO 52 A SER 53 n 53 SER 53 A ASN 54 n 54 ASN 54 A TYR 55 n 55 TYR 55 A VAL 56 n 56 VAL 56 A ALA 57 n 57 ALA 57 A PRO 58 n 58 PRO 58 A TYR 59 n 59 TYR 59 A ASN 60 n 60 ASN 60 A SER 61 n 61 SER 61 A ASN 62 n 62 ASN 62 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 A O GLY 49 A O GLY 49 A N GLY 42 A N GLY 42 A O GLN 43 A O GLN 43 A N THR 30 A N THR 30 A O ILE 29 A O ILE 29 A N VAL 7 A N VAL 7 A N GLN 8 A N GLN 8 A O ALA 57 A O ALA 57 1 A HIS 1 A HIS 1 1 Y 1 A MET 2 A MET 2 1 Y 1 A A HE2 HG13 PHE VAL 51 56 1.10 1 A A OD2 HD12 ASP LEU 27 44 1.42 1 A A O HA SER ASN 61 62 1.45 1 A A OD1 HD23 ASP LEU 27 44 1.52 1 A A O N ASN ASN 60 62 1.63 1 A A C CA SER ASN 61 62 1.75 1 A ARG 47 0.156 SIDE CHAIN 1 A A C N GLU THR 3 4 1.15 1 A A C N ASN SER 60 61 1.17 1 A A C N SER ASN 61 62 1.15 1 -13.56 2.20 117.20 103.64 A A A CA C N GLU GLU THR 3 3 4 Y 1 -18.01 3.00 111.90 93.89 A A A CG CD CE LYS LYS LYS 5 5 5 N 1 -4.40 0.70 120.80 116.40 A A A CB CG CD2 PHE PHE PHE 11 11 11 N 1 -29.99 2.60 111.60 81.61 A A A CB CG CD LYS LYS LYS 24 24 24 N 1 -7.62 0.50 120.30 112.68 A A A NE CZ NH1 ARG ARG ARG 25 25 25 N 1 3.34 0.50 120.30 123.64 A A A NE CZ NH2 ARG ARG ARG 25 25 25 N 1 -4.94 0.50 120.30 115.36 A A A NE CZ NH2 ARG ARG ARG 47 47 47 N 1 -7.14 0.50 120.30 113.16 A A A NE CZ NH1 ARG ARG ARG 48 48 48 N 1 -12.62 2.00 110.40 97.78 A A A CB CA C ASN ASN ASN 60 60 60 N 1 15.59 1.80 110.60 126.19 A A A N CA CB ASN ASN ASN 60 60 60 N 1 -15.38 2.20 117.20 101.82 A A A CA C N ASN ASN SER 60 60 61 Y 1 -23.46 2.50 121.70 98.24 A A A C N CA SER ASN ASN 61 62 62 Y 1 -23.94 2.20 113.40 89.46 A A A CA CB CG ASN ASN ASN 62 62 62 N 1 -22.90 2.70 111.00 88.10 A A A N CA C ASN ASN ASN 62 62 62 N 1 A A N CA GLU GLU 3 3 -0.282 0.020 1.459 1.177 N 1 A A CA CB GLU GLU 3 3 -0.138 0.022 1.535 1.397 N 1 A A CA C GLU GLU 3 3 -0.273 0.026 1.525 1.252 N 1 A A C N GLU THR 3 4 -0.184 0.023 1.336 1.152 Y 1 A A N CA THR THR 4 4 -0.218 0.020 1.459 1.241 N 1 A A CB CG LYS LYS 5 5 -0.192 0.027 1.521 1.329 N 1 A A CA CB LYS LYS 24 24 -0.141 0.022 1.535 1.394 N 1 A A CD NE ARG ARG 25 25 -0.136 0.017 1.460 1.324 N 1 A A NE CZ ARG ARG 25 25 -0.105 0.013 1.326 1.221 N 1 A A CZ NH1 ARG ARG 47 47 0.115 0.013 1.326 1.441 N 1 A A CD NE ARG ARG 48 48 -0.115 0.017 1.460 1.345 N 1 A A CA C ASN ASN 60 60 -0.226 0.026 1.525 1.299 N 1 A A C N ASN SER 60 61 -0.166 0.023 1.336 1.170 Y 1 A A N CA SER SER 61 61 -0.254 0.020 1.459 1.205 N 1 A A CA CB SER SER 61 61 -0.100 0.015 1.525 1.425 N 1 A A C N SER ASN 61 62 -0.186 0.023 1.336 1.150 Y 1 A A N CA ASN ASN 62 62 -0.290 0.020 1.459 1.169 N 1 A LYS 24 -123.28 -166.19 1 A ASN 45 79.65 -37.75 1 A ASN 46 -171.78 -23.05 1 A ALA 57 -161.34 114.65 1 A ASN 60 38.54 62.24 1 A SER 61 -25.22 94.93 refinement CNS minimized average Solution Structure of the C-terminal Sem-5 SH3 Domain (Minimized Average Structure) 1 N N SIGNALING PROTEIN all beta protein, SIGNALING PROTEIN SEM5_CAEEL UNP 1 155 P29355 ETKFVQALFDFNPQESGELAFKRGDVITLINKDDPNWWEGQLNNRRGIFPSNYVCPYNSN 155 214 1K76 3 62 P29355 A 1 3 62 1 CYS engineered mutation ALA 57 1K76 A P29355 UNP 209 57 5 anti-parallel anti-parallel anti-parallel anti-parallel A ARG 47 A ARG 47 A PRO 52 A PRO 52 A TRP 39 A TRP 39 A LEU 44 A LEU 44 A VAL 28 A VAL 28 A ASN 33 A ASN 33 A PHE 6 A PHE 6 A ALA 9 A ALA 9 A VAL 56 A VAL 56 A PRO 58 A PRO 58