1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Tengel, T. Sethson, I. Francis, M.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-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 C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE 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 S C N 76 N C N 77 N O N 78 N C N 79 N C N 80 N C N 81 N O N 82 N N N 83 N O N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N N N 95 S C N 96 N C N 97 N O N 98 N C N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N N N 114 S C N 115 N C N 116 N O N 117 N C Y 118 N C Y 119 N N Y 120 N C Y 121 N C Y 122 N N N 123 N O N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N N N 135 S C N 136 N C N 137 N O N 138 S C N 139 N C N 140 N C N 141 N C N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H 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 N N 157 S C N 158 N C N 159 N O N 160 N C N 161 N C N 162 N C N 163 N C N 164 N O N 165 N H N 166 N H 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 N N 179 S C N 180 N C N 181 N O N 182 N C N 183 N C N 184 N C N 185 N C N 186 N N N 187 N O N 188 N H 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 H N 203 N N N 204 S C N 205 N C N 206 N O N 207 N C N 208 N C N 209 N S N 210 N C 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 N N 224 S C N 225 N C N 226 N O N 227 N C Y 228 N C Y 229 N C Y 230 N C Y 231 N C Y 232 N C Y 233 N C N 234 N O N 235 N H 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 N N 247 S C N 248 N C N 249 N O N 250 N C N 251 N O N 252 N O N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N N N 261 S C N 262 N C N 263 N O N 264 R C N 265 N O N 266 N C N 267 N O N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N N N 278 S C N 279 N C N 280 N O N 281 N C Y 282 N C Y 283 N C Y 284 N C Y 285 N C Y 286 N C Y 287 N C N 288 N O N 289 N O N 290 N H N 291 N H N 292 N H N 293 N H 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 N C N 306 N C 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 H N 319 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 doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N doub N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N sing Y 118 N sing Y 119 N doub Y 120 N doub N 121 N sing Y 122 N sing N 123 N sing Y 124 N sing N 125 N sing N 126 N sing 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 doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 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 doub N 156 N sing 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 doub N 177 N sing 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 sing N 199 N sing N 200 N doub 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 doub N 220 N sing N 221 N sing N 222 N sing N 223 N sing Y 224 N doub Y 225 N sing Y 226 N sing N 227 N sing Y 228 N doub N 229 N sing Y 230 N doub N 231 N sing Y 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 sing N 242 N doub N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N doub 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 sing 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 doub N 272 N sing N 273 N sing N 274 N sing N 275 N sing Y 276 N doub Y 277 N sing Y 278 N sing N 279 N sing Y 280 N doub N 281 N sing Y 282 N doub N 283 N sing Y 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 sing N 295 N doub 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 IX Eur.J.Biochem. EJBCAI 0262 0014-2956 269 3659 3668 10.1046/j.1432-1033.2002.03051.x 12153562 Conformational analysis by CD and NMR spectroscopy of a peptide encompassing the amphipathic domain of YopD from Yersinia. 2002 10.2210/pdb1kdl/pdb pdb_00001kdl 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 2768.195 YOPD protein 278-300 1 syn polymer no no DNFMKDVLRLIEQYVSSHTHAMK DNFMKDVLRLIEQYVSSHTHAMK 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 pdbx_struct_assembly pdbx_struct_oper_list struct_conf struct_conf_type chem_comp_atom chem_comp_bond database_2 pdbx_nmr_software repository Initial release Version format compliance Version format compliance Derived calculations Data collection Database references 1 0 2002-08-21 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-11-29 1 4 2024-05-01 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2001-11-13 REL REL The peptide was chemically synthesized and is found in the cytosol and membrane locations. The sequence of the peptide is naturally found in YERSINIA PESTIS (bacteria). sample structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy 150 1 2D NOESY 2D TOCSY DQF-COSY 15N HSQC 13C HSQC 20 mM SODIUM PHOSPHATE BUFFER 4.5 1 atm 313 K STANDARD SIMULATED ANNEALING PROTOCOL USING XPLOR 3.851. DIHEDRAL RESTRAINTS WERE OBTAINED WITH TALOS simulated annealing 1 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE 50% H2O; 10 D2O; 40% TFE Brunger refinement X-PLOR 3.851 Bruker data analysis XwinNMR 2.6 Borgias iterative matrix relaxation MARDIGRAS 3.0 Cornilescu data analysis TALOS 98.040.21.02 600 Bruker DRX 500 Bruker AMX ASP 278 n 1 ASP 278 A ASN 279 n 2 ASN 279 A PHE 280 n 3 PHE 280 A MET 281 n 4 MET 281 A LYS 282 n 5 LYS 282 A ASP 283 n 6 ASP 283 A VAL 284 n 7 VAL 284 A LEU 285 n 8 LEU 285 A ARG 286 n 9 ARG 286 A LEU 287 n 10 LEU 287 A ILE 288 n 11 ILE 288 A GLU 289 n 12 GLU 289 A GLN 290 n 13 GLN 290 A TYR 291 n 14 TYR 291 A VAL 292 n 15 VAL 292 A SER 293 n 16 SER 293 A SER 294 n 17 SER 294 A HIS 295 n 18 HIS 295 A THR 296 n 19 THR 296 A HIS 297 n 20 HIS 297 A ALA 298 n 21 ALA 298 A MET 299 n 22 MET 299 A LYS 300 n 23 LYS 300 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 1 A A O H VAL ILE 284 288 1.42 1 A A O H MET LEU 281 285 1.55 1 A ARG 286 0.311 SIDE CHAIN 1 A ASN 279 -93.03 30.08 1 A HIS 295 -93.02 49.20 Solution structure of the amphipathic domain of YopD from Yersinia 1 N N A PHE 280 A PHE 3 HELX_P A VAL 292 A VAL 15 1 H1 13 STRUCTURAL PROTEIN YERSINIA, YOPD, AMPHIPATHIC ALPHA HELIX, BETA TURN, STRUCTURAL PROTEIN YOPD_YERPS UNP 1 278 Q06131 DNFMKDVLRLIEQYVSSHTHAMK 278 300 1KDL 278 300 Q06131 A 1 1 23 1 P 1