0.019149 0.000000 0.000000 0.000000 0.019149 0.000000 0.000000 0.000000 0.004226 0.000000 0.000000 0.000000 Baker, H.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 52.223 52.223 236.657 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 Cl -1 35.453 CHLORIDE ION non-polymer C6 H12 O5 164.156 alpha-L-fucopyranose alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose L-saccharide, alpha linking C6 H12 O6 180.156 beta-D-galactopyranose beta-D-galactose; D-galactose; galactose D-saccharide, beta 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 C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer 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 C8 H15 N O6 221.208 2-acetamido-2-deoxy-beta-D-glucopyranose N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE D-saccharide, beta 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 C11 H19 N O9 309.270 N-acetyl-alpha-neuraminic acid N-acetylneuraminic acid; sialic acid; alpha-sialic acid; O-SIALIC ACID D-saccharide, alpha linking C4 H6 O6 150.087 S,R MESO-TARTARIC ACID non-polymer 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 CL N 75 R C N 76 S C N 77 R C N 78 S C N 79 S C N 80 N C N 81 N O N 82 N O N 83 N O N 84 N O N 85 N O 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 H N 95 N H N 96 N H N 97 N H N 98 R C N 99 R C N 100 S C N 101 R C N 102 R C N 103 N C N 104 N O N 105 N O N 106 N O N 107 N O N 108 N O N 109 N O N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N N N 123 S C N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N O N 130 N N 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 H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N N N 143 S C N 144 N C N 145 N O N 146 N C N 147 N C N 148 N C N 149 N O N 150 N O N 151 N O 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 H N 159 N H N 160 N H N 161 N N N 162 N C N 163 N C N 164 N O N 165 N O N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N C N 172 N O N 173 N C N 174 N O N 175 N C N 176 N O N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N N N 186 S C N 187 N C N 188 N O N 189 N C Y 190 N C Y 191 N N Y 192 N C Y 193 N C Y 194 N N N 195 N O 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 H N 204 N H N 205 N H N 206 N O N 207 N H N 208 N H N 209 N N N 210 S C N 211 N C N 212 N O N 213 S C N 214 N C N 215 N C N 216 N C N 217 N O 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 H N 228 N H N 229 N H N 230 N H N 231 N N N 232 S C N 233 N C N 234 N O N 235 N C N 236 N C N 237 N C N 238 N C N 239 N O 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 H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N N N 254 S C N 255 N C N 256 N O N 257 N C N 258 N C N 259 N C N 260 N C N 261 N N N 262 N O 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 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 H N 278 N N N 279 S C N 280 N C N 281 N O N 282 N C N 283 N C N 284 N S N 285 N C N 286 N O N 287 N H N 288 N H N 289 N H 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 R C N 299 R C N 300 R C N 301 S C N 302 R C N 303 N C N 304 N C N 305 N C N 306 N N N 307 N O N 308 N O N 309 N O N 310 N O N 311 N O N 312 N O 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 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N N N 329 S C N 330 N C N 331 N O N 332 N C Y 333 N C Y 334 N C Y 335 N C Y 336 N C Y 337 N C Y 338 N C N 339 N O N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N N N 352 S C N 353 N C N 354 N O N 355 N C N 356 N C N 357 N C N 358 N O 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 N N 369 S C N 370 N C N 371 N O N 372 N C N 373 N O N 374 N O N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N C N 383 R C N 384 N C N 385 S C N 386 R C N 387 R C N 388 R C N 389 R C N 390 N C N 391 N C N 392 N C N 393 N N N 394 N O N 395 N O N 396 N O N 397 N O N 398 N O N 399 N O N 400 N O N 401 N O N 402 N O N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 N O N 423 N O N 424 N C N 425 S C N 426 N O N 427 R C N 428 N O N 429 N C N 430 N O N 431 N O N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N N N 439 S C N 440 N C N 441 N O N 442 R C N 443 N O N 444 N C N 445 N O N 446 N H N 447 N H N 448 N H N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N N N 456 S C N 457 N C N 458 N O N 459 N C Y 460 N C Y 461 N C Y 462 N C Y 463 N C Y 464 N C Y 465 N C N 466 N O N 467 N O N 468 N H N 469 N H N 470 N H N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N N N 480 S C N 481 N C N 482 N O N 483 N C N 484 N C N 485 N C N 486 N O N 487 N H N 488 N H N 489 N H N 490 N H N 491 N H N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 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 sing 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 sing 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 sing 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 sing 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 sing 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 doub N 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 doub N 132 N sing N 133 N sing N 134 N sing 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 doub 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 doub N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N doub 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 sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N doub N 183 N sing N 184 N sing N 185 N sing N 186 N sing Y 187 N sing Y 188 N doub Y 189 N doub N 190 N sing Y 191 N sing N 192 N sing Y 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 sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub 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 sing N 223 N sing N 224 N sing N 225 N sing N 226 N doub 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 sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N doub 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 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 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 N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing 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 sing 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 doub N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N doub N 321 N sing N 322 N sing N 323 N sing N 324 N sing Y 325 N doub Y 326 N sing Y 327 N sing N 328 N sing Y 329 N doub N 330 N sing Y 331 N doub N 332 N sing Y 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N doub N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 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 doub N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N doub N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N doub N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N doub N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N doub N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N doub N 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N doub N 445 N sing N 446 N sing N 447 N sing N 448 N sing Y 449 N doub Y 450 N sing Y 451 N sing N 452 N sing Y 453 N doub N 454 N sing Y 455 N doub N 456 N sing Y 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N doub N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 374 1298 1308 10.1016/j.jmb.2007.09.091 17996251 Crystal structures of the staphylococcal toxin SSL5 in complex with sialyl Lewis X reveal a conserved binding site that shares common features with viral and bacterial sialic acid binding proteins 2007 10.2210/pdb2r61/pdb pdb_00002r61 110 1 mirrors IMAGE PLATE 2006-11-23 MAR scanner 345 mm plate VariMax-HF Mirror SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU MICROMAX-007 HF 24366.910 Exotoxin 3 UNP residues 31-234 1 man polymer 820.744 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose 1 man branched 35.453 CHLORIDE ION 1 syn non-polymer 150.087 S,R MESO-TARTARIC ACID 1 syn non-polymer 92.094 GLYCEROL 1 syn non-polymer 18.015 water 59 nat water superantigen-like protein SSL5 Sialyl-Lewis X antigen, beta anomer no no GPGSSEHKAKYENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDAHQAFTRIQIFGKDIERLKARKNPGLDIF VVKEAENRNGTVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYK KFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR GPGSSEHKAKYENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDAHQAFTRIQIFGKDIERLKARKNPGLDIF VVKEAENRNGTVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYK KFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR 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 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 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 n n n n n n n n n n n n n n n n n n n n n n Staphylococcus Gl10 Escherichia sample ssl5 1280 Staphylococcus aureus 562 Escherichia coli plasmid pET32a.3C 1 3.31 62.85 VAPOR DIFFUSION, SITTING DROP 7.4 20% PEG 3340, 0.2M disodium tartrate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K 291 atom_site pdbx_unobs_or_zero_occ_atoms pdbx_validate_chiral software struct_conn atom_site chem_comp entity entity_name_com pdbx_branch_scheme pdbx_chem_comp_identifier pdbx_entity_branch pdbx_entity_branch_descriptor pdbx_entity_branch_link pdbx_entity_branch_list pdbx_entity_nonpoly pdbx_molecule_features pdbx_nonpoly_scheme pdbx_struct_assembly_gen struct_asym struct_conn struct_ref_seq_dif struct_site struct_site_gen chem_comp chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_unobs_or_zero_occ_atoms repository Initial release Carbohydrate remediation repository Remediation Advisory Version format compliance Advisory Atomic model Data collection Derived calculations Refinement description Atomic model Data collection Database references Derived calculations Structure summary Advisory Data collection Database references Refinement description Structure summary 1 0 2007-11-27 1 1 2011-07-13 2 0 2019-07-10 3 0 2020-07-29 3 1 2023-10-25 _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _software.version _struct_conn.pdbx_leaving_atom_flag _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.type_symbol _chem_comp.name _chem_comp.type _pdbx_struct_assembly_gen.asym_id_list _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_ref_seq_dif.details _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession X NAG 603 n B NAG 1 X GAL 602 n B GAL 2 X SIA 601 n B SIA 3 X FUC 604 n B FUC 4 LFucpa a-L-fucopyranose a-L-Fucp Fuc DGalpb b-D-galactopyranose b-D-Galp Gal DGlcpNAcb N-acetyl-b-D-glucopyranosamine b-D-GlcpNAc GlcNAc DNeup5Aca N-acetyl-a-D-neuraminic acid a-D-Neup5Ac Neu5Ac SSL5 SSL5 complexed with sialyl Lewis X at pH 4.6 RCSB Y PDBJ 2007-09-05 REL REL oligosaccharide DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROH 2 GMML 1.0 Glycam Condensed Sequence WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2 2 PDB2Glycan 1.1.0 WURCS [][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}} 2 PDB-CARE LINUCS C1 O4 GAL NAG 2 1 2 O1 HO4 sing C2 O3 SIA GAL 3 2 2 O2 HO3 sing C1 O3 FUC NAG 4 1 2 O1 HO3 sing n n n n CL CHLORIDE ION SRT S,R MESO-TARTARIC ACID GOL GLYCEROL HOH water THE TETRASACCHARIDE SIALYL-LEWIS X IS PRESENT AS A LIGAND IN THIS STRUCTURE AND IS NOT COVALENTLY BOUND TO THE PROTEIN MOLECULE. THE CONFLICTS BETWEEN THE SEQUENCE FOR THIS STRUCTURE AND THE DATABASE SEQUENCE ARISE FROM THE ALLELIC VARIATION BETWEEN STAPHYLOCOCCUS AUREUS STRAINS SEEN FOR SOME OF THESE SUPERANTIGEN-LIKE PROTEINS. 1M4V PDB ENTRY 1M4V PDB experimental model Antigen oligosaccharide with branches Sialyl-Lewis X antigen, beta anomer Oligosaccharide CL 205 3 CL CL 205 A SRT 206 4 SRT SRT 206 A GOL 207 5 GOL GOL 207 A HOH 208 6 HOH HOH 605 A HOH 209 6 HOH HOH 606 A HOH 210 6 HOH HOH 607 A HOH 211 6 HOH HOH 608 A HOH 212 6 HOH HOH 609 A HOH 213 6 HOH HOH 610 A HOH 214 6 HOH HOH 611 A HOH 215 6 HOH HOH 612 A HOH 216 6 HOH HOH 613 A HOH 217 6 HOH HOH 614 A HOH 218 6 HOH HOH 615 A HOH 219 6 HOH HOH 616 A HOH 220 6 HOH HOH 617 A HOH 221 6 HOH HOH 618 A HOH 222 6 HOH HOH 619 A HOH 223 6 HOH HOH 620 A HOH 224 6 HOH HOH 621 A HOH 225 6 HOH HOH 622 A HOH 226 6 HOH HOH 623 A HOH 227 6 HOH HOH 624 A HOH 228 6 HOH HOH 625 A HOH 229 6 HOH HOH 626 A HOH 230 6 HOH HOH 627 A HOH 231 6 HOH HOH 628 A HOH 232 6 HOH HOH 629 A HOH 233 6 HOH HOH 630 A HOH 234 6 HOH HOH 631 A HOH 235 6 HOH HOH 632 A HOH 236 6 HOH HOH 633 A HOH 237 6 HOH HOH 634 A HOH 238 6 HOH HOH 635 A HOH 239 6 HOH HOH 636 A HOH 240 6 HOH HOH 637 A HOH 241 6 HOH HOH 638 A HOH 242 6 HOH HOH 639 A HOH 243 6 HOH HOH 640 A HOH 244 6 HOH HOH 641 A HOH 245 6 HOH HOH 642 A HOH 246 6 HOH HOH 643 A HOH 247 6 HOH HOH 644 A HOH 248 6 HOH HOH 645 A HOH 249 6 HOH HOH 646 A HOH 250 6 HOH HOH 647 A HOH 251 6 HOH HOH 648 A HOH 252 6 HOH HOH 649 A HOH 253 6 HOH HOH 650 A HOH 254 6 HOH HOH 651 A HOH 255 6 HOH HOH 652 A HOH 256 6 HOH HOH 653 A HOH 257 6 HOH HOH 654 A HOH 258 6 HOH HOH 655 A HOH 259 6 HOH HOH 656 A HOH 260 6 HOH HOH 657 A HOH 261 6 HOH HOH 658 A HOH 262 6 HOH HOH 659 A HOH 263 6 HOH HOH 660 A HOH 13 6 HOH HOH 661 A HOH 115 6 HOH HOH 662 A HOH 116 6 HOH HOH 663 A 2.750 2.750 35.070 35.070 Phaser MODE: MR_AUTO n 1 -3 A n 2 -2 A n 3 -1 A n 4 0 A n 5 1 A n 6 2 A n 7 3 A n 8 4 A n 9 5 A n 10 6 A n 11 7 A GLU 8 n 12 GLU 8 A ASN 9 n 13 ASN 9 A VAL 10 n 14 VAL 10 A THR 11 n 15 THR 11 A LYS 12 n 16 LYS 12 A ASP 13 n 17 ASP 13 A ILE 14 n 18 ILE 14 A PHE 15 n 19 PHE 15 A ASP 16 n 20 ASP 16 A LEU 17 n 21 LEU 17 A ARG 18 n 22 ARG 18 A ASP 19 n 23 ASP 19 A TYR 20 n 24 TYR 20 A TYR 21 n 25 TYR 21 A SER 22 n 26 SER 22 A GLY 23 n 27 GLY 23 A ALA 24 n 28 ALA 24 A SER 25 n 29 SER 25 A LYS 26 n 30 LYS 26 A GLU 27 n 31 GLU 27 A LEU 28 n 32 LEU 28 A LYS 29 n 33 LYS 29 A ASN 30 n 34 ASN 30 A VAL 31 n 35 VAL 31 A THR 32 n 36 THR 32 A GLY 33 n 37 GLY 33 A TYR 34 n 38 TYR 34 A ARG 35 n 39 ARG 35 A TYR 36 n 40 TYR 36 A SER 37 n 41 SER 37 A LYS 38 n 42 LYS 38 A GLY 39 n 43 GLY 39 A GLY 40 n 44 GLY 40 A LYS 41 n 45 LYS 41 A HIS 42 n 46 HIS 42 A TYR 43 n 47 TYR 43 A LEU 44 n 48 LEU 44 A ILE 45 n 49 ILE 45 A PHE 46 n 50 PHE 46 A ASP 47 n 51 ASP 47 A ALA 48 n 52 ALA 48 A HIS 49 n 53 HIS 49 A GLN 50 n 54 GLN 50 A ALA 51 n 55 ALA 51 A PHE 52 n 56 PHE 52 A THR 53 n 57 THR 53 A ARG 54 n 58 ARG 54 A ILE 55 n 59 ILE 55 A GLN 56 n 60 GLN 56 A ILE 57 n 61 ILE 57 A PHE 58 n 62 PHE 58 A GLY 59 n 63 GLY 59 A LYS 60 n 64 LYS 60 A ASP 61 n 65 ASP 61 A ILE 62 n 66 ILE 62 A GLU 63 n 67 GLU 63 A ARG 64 n 68 ARG 64 A LEU 65 n 69 LEU 65 A LYS 66 n 70 LYS 66 A ALA 67 n 71 ALA 67 A ARG 68 n 72 ARG 68 A LYS 69 n 73 LYS 69 A ASN 70 n 74 ASN 70 A PRO 71 n 75 PRO 71 A GLY 72 n 76 GLY 72 A LEU 73 n 77 LEU 73 A ASP 74 n 78 ASP 74 A ILE 75 n 79 ILE 75 A PHE 76 n 80 PHE 76 A VAL 77 n 81 VAL 77 A VAL 78 n 82 VAL 78 A LYS 79 n 83 LYS 79 A GLU 80 n 84 GLU 80 A ALA 81 n 85 ALA 81 A GLU 82 n 86 GLU 82 A ASN 83 n 87 ASN 83 A ARG 84 n 88 ARG 84 A n 89 85 A n 90 86 A THR 87 n 91 THR 87 A VAL 88 n 92 VAL 88 A PHE 89 n 93 PHE 89 A SER 90 n 94 SER 90 A TYR 91 n 95 TYR 91 A GLY 92 n 96 GLY 92 A GLY 93 n 97 GLY 93 A VAL 94 n 98 VAL 94 A THR 95 n 99 THR 95 A LYS 96 n 100 LYS 96 A LYS 97 n 101 LYS 97 A ASN 98 n 102 ASN 98 A GLN 99 n 103 GLN 99 A GLY 100 n 104 GLY 100 A ALA 101 n 105 ALA 101 A TYR 102 n 106 TYR 102 A TYR 103 n 107 TYR 103 A ASP 104 n 108 ASP 104 A TYR 105 n 109 TYR 105 A LEU 106 n 110 LEU 106 A ASN 107 n 111 ASN 107 A ALA 108 n 112 ALA 108 A PRO 109 n 113 PRO 109 A LYS 110 n 114 LYS 110 A PHE 111 n 115 PHE 111 A VAL 112 n 116 VAL 112 A ILE 113 n 117 ILE 113 A LYS 114 n 118 LYS 114 A LYS 115 n 119 LYS 115 A GLU 116 n 120 GLU 116 A VAL 117 n 121 VAL 117 A ASP 118 n 122 ASP 118 A ALA 119 n 123 ALA 119 A GLY 120 n 124 GLY 120 A VAL 121 n 125 VAL 121 A TYR 122 n 126 TYR 122 A THR 123 n 127 THR 123 A HIS 124 n 128 HIS 124 A VAL 125 n 129 VAL 125 A LYS 126 n 130 LYS 126 A ARG 127 n 131 ARG 127 A HIS 128 n 132 HIS 128 A TYR 129 n 133 TYR 129 A ILE 130 n 134 ILE 130 A TYR 131 n 135 TYR 131 A LYS 132 n 136 LYS 132 A GLU 133 n 137 GLU 133 A GLU 134 n 138 GLU 134 A VAL 135 n 139 VAL 135 A SER 136 n 140 SER 136 A LEU 137 n 141 LEU 137 A LYS 138 n 142 LYS 138 A GLU 139 n 143 GLU 139 A LEU 140 n 144 LEU 140 A ASP 141 n 145 ASP 141 A PHE 142 n 146 PHE 142 A LYS 143 n 147 LYS 143 A LEU 144 n 148 LEU 144 A ARG 145 n 149 ARG 145 A GLN 146 n 150 GLN 146 A TYR 147 n 151 TYR 147 A LEU 148 n 152 LEU 148 A ILE 149 n 153 ILE 149 A GLN 150 n 154 GLN 150 A ASN 151 n 155 ASN 151 A PHE 152 n 156 PHE 152 A ASP 153 n 157 ASP 153 A LEU 154 n 158 LEU 154 A TYR 155 n 159 TYR 155 A LYS 156 n 160 LYS 156 A LYS 157 n 161 LYS 157 A PHE 158 n 162 PHE 158 A PRO 159 n 163 PRO 159 A LYS 160 n 164 LYS 160 A ASP 161 n 165 ASP 161 A SER 162 n 166 SER 162 A LYS 163 n 167 LYS 163 A ILE 164 n 168 ILE 164 A LYS 165 n 169 LYS 165 A VAL 166 n 170 VAL 166 A ILE 167 n 171 ILE 167 A MET 168 n 172 MET 168 A LYS 169 n 173 LYS 169 A ASP 170 n 174 ASP 170 A GLY 171 n 175 GLY 171 A GLY 172 n 176 GLY 172 A TYR 173 n 177 TYR 173 A TYR 174 n 178 TYR 174 A THR 175 n 179 THR 175 A PHE 176 n 180 PHE 176 A GLU 177 n 181 GLU 177 A LEU 178 n 182 LEU 178 A ASN 179 n 183 ASN 179 A LYS 180 n 184 LYS 180 A LYS 181 n 185 LYS 181 A LEU 182 n 186 LEU 182 A GLN 183 n 187 GLN 183 A PRO 184 n 188 PRO 184 A HIS 185 n 189 HIS 185 A ARG 186 n 190 ARG 186 A MET 187 n 191 MET 187 A SER 188 n 192 SER 188 A ASP 189 n 193 ASP 189 A VAL 190 n 194 VAL 190 A ILE 191 n 195 ILE 191 A ASP 192 n 196 ASP 192 A GLY 193 n 197 GLY 193 A ARG 194 n 198 ARG 194 A ASN 195 n 199 ASN 195 A ILE 196 n 200 ILE 196 A GLU 197 n 201 GLU 197 A LYS 198 n 202 LYS 198 A MET 199 n 203 MET 199 A GLU 200 n 204 GLU 200 A ALA 201 n 205 ALA 201 A ASN 202 n 206 ASN 202 A ILE 203 n 207 ILE 203 A ARG 204 n 208 ARG 204 A 2.1932 2.1944 1.9455 7.3972 6.5135 9.1837 0.0439 0.0545 0.4121 0.1487 -0.4436 0.4456 -0.6143 -0.4818 0.3997 0.3730 0.1331 0.0292 0.4032 0.1559 0.1191 refined 5.3300 1.3970 30.7560 X-RAY DIFFRACTION 7.0195 -3.7469 -2.0353 15.7255 0.0385 2.1128 -0.4269 1.1273 0.4364 -0.6081 0.4184 -0.8834 -0.5446 -0.0872 0.0085 0.4143 -0.0091 0.0133 0.6577 0.0325 0.1085 refined 7.3070 -5.0090 12.5790 X-RAY DIFFRACTION 5.7776 2.2649 -2.1521 4.3649 0.5575 5.7002 0.0888 0.8523 0.5128 -0.8875 0.0387 -0.0519 -0.3797 0.3168 -0.1275 0.3227 0.0158 -0.0374 0.6012 0.0631 0.0222 refined 11.1330 -7.3620 18.7320 X-RAY DIFFRACTION 2.2706 0.1375 -0.1987 3.3822 0.5418 1.8701 0.1185 -0.0816 0.1485 0.1397 0.0603 -0.0833 -0.1378 -0.0376 -0.1788 0.2589 0.0203 -0.0097 0.3652 0.0476 -0.0342 refined 8.6120 -8.3280 39.6300 X-RAY DIFFRACTION A 8 A 12 A 36 A 40 X-RAY DIFFRACTION 1 A 37 A 41 A 53 A 57 X-RAY DIFFRACTION 2 A 54 A 58 A 84 A 88 X-RAY DIFFRACTION 3 A 87 A 91 A 204 A 208 X-RAY DIFFRACTION 4 author_and_software_defined_assembly PISA 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O SER 90 A O SER 94 A N GLN 56 A N GLN 60 A O ILE 57 A O ILE 61 A N HIS 42 A N HIS 46 A O ILE 45 A O ILE 49 A N TYR 34 A N TYR 38 A N LEU 28 A N LEU 32 A O ILE 75 A O ILE 79 A N ASP 74 A N ASP 78 A O THR 95 A O THR 99 A O LYS 126 A O LYS 130 A N PHE 111 A N PHE 115 A N LYS 114 A N LYS 118 A O ALA 201 A O ALA 205 A O GLU 200 A O GLU 204 A N LYS 165 A N LYS 169 A N VAL 166 A N VAL 170 A O TYR 174 A O TYR 178 A N VAL 135 A N VAL 139 A O ILE 191 A O ILE 195 1 A CD LYS 38 A CD LYS 42 0 Y 1 A CE LYS 38 A CE LYS 42 0 Y 1 A NZ LYS 38 A NZ LYS 42 0 Y 1 A GLY -3 A GLY 1 1 Y 1 A PRO -2 A PRO 2 1 Y 1 A GLY -1 A GLY 3 1 Y 1 A SER 0 A SER 4 1 Y 1 A SER 1 A SER 5 1 Y 1 A GLU 2 A GLU 6 1 Y 1 A HIS 3 A HIS 7 1 Y 1 A LYS 4 A LYS 8 1 Y 1 A ALA 5 A ALA 9 1 Y 1 A LYS 6 A LYS 10 1 Y 1 A TYR 7 A TYR 11 1 Y 1 A ASN 85 A ASN 89 1 Y 1 A GLY 86 A GLY 90 1 Y 1 A A CG CD LYS LYS 38 38 -0.215 0.034 1.520 1.305 N 1 A ASN 9 -105.89 64.42 1 A ASN 30 38.23 42.19 1 A PHE 46 -112.75 -87.53 1 A ALA 67 -23.64 -47.82 1 A ARG 68 -149.97 -68.97 1 A ALA 81 103.46 160.31 1 A ASN 83 -94.66 -99.64 1 A ASP 104 -133.61 -100.38 1 A VAL 117 -141.12 -151.54 1 A ASP 118 -53.40 72.26 1 A LYS 160 44.98 -127.34 1 A ASP 161 -77.41 23.08 16.542 -0.010 0.000 0.000 -0.010 0.000 0.02 0.926 0.868 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.26859 0.20949 0.21216 2.750 35.070 439 8789 4.800 99.970 22.525 0.250 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.586 0.336 0.800 0.800 1.200 PDB ENTRY 1M4V MAXIMUM LIKELIHOOD MASK 2.750 35.070 59 1761 73 0 1629 0.017 0.022 1733 1.744 2.002 2317 7.650 5.000 193 36.676 23.647 85 19.933 15.000 320 25.588 15.000 11 0.115 0.200 250 0.005 0.020 1271 0.226 0.200 631 0.329 0.200 1122 0.137 0.200 84 0.195 0.200 26 0.107 0.200 8 0.628 1.500 990 1.064 2.000 1554 1.852 3.000 831 2.881 4.500 763 0.359 0.281 2.821 28 604 632 20 100.000 2.750 59.164 2R61 9300 0.129 0.129 1 5.000 7.400 99.900 0.484 2.75 2.90 1.5 10136 1301 0.484 1 7.80 100.00 data reduction A.G.W. Leslie andrew@mrc-lmb.cam.ac.uk http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ MOSFLM package data scaling Phil Evans pre@mrc-lmb.cam.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/INDEX.html SCALA other phasing R. J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER other refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program 5.3.0037 data extraction PDB sw-help@rcsb.rutgers.edu July 2, 2007 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 3.000 N Crystal structure of the Staphylococcal superantigen-like protein SSL5 in complex with sialyl-Lewis X at pH 7.4 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N A THR 11 A THR 15 HELX_P A SER 22 A SER 26 1 1 12 A PHE 58 A PHE 62 HELX_P A GLU 63 A GLU 67 1 2 6 A LEU 137 A LEU 141 HELX_P A ASP 153 A ASP 157 1 3 17 A GLN 183 A GLN 187 HELX_P A MET 187 A MET 191 5 4 5 covale 1.340 both B NAG 1 B O4 NAG 1_555 B GAL 2 B C1 GAL 1_555 covale 1.325 both B NAG 1 B O3 NAG 1_555 B FUC 4 B C1 FUC 1_555 covale 1.383 both B GAL 2 B O3 GAL 1_555 B SIA 3 B C2 SIA 1_555 SUGAR BINDING PROTEIN SSL5, superantigen-like, sialyl Lewis X, sialic acid binding, CHIPS, SUGAR BINDING PROTEIN Q9ZFS6_STAAU UNP 1 31 Q9ZFS6 SEHESKYENVTKDIFDLRDYYSRASKELKNVTGYRYSKGGKHYLIFDKNRKFTRIQIFGKDIERIKKRKNPGLDIFVVKE AENRNGTVYSYGGVTKKNQGAYYDYLSAPRFVIKKEVGAGVSVHVKRYYIYKEEISLKELDFKLRQYLIQDFDLYKKFPK ASKIKVTMKDGGYYTFELNKKLQTNRMSDVIDGRNIEKIEANIR 31 234 2R61 1 204 Q9ZFS6 A 1 5 208 1 expression tag GLY -3 2R61 A Q9ZFS6 UNP 1 1 expression tag PRO -2 2R61 A Q9ZFS6 UNP 2 1 expression tag GLY -1 2R61 A Q9ZFS6 UNP 3 1 expression tag SER 0 2R61 A Q9ZFS6 UNP 4 1 GLU SEE REMARK 999 LYS 4 2R61 A Q9ZFS6 UNP 34 8 1 SER SEE REMARK 999 ALA 5 2R61 A Q9ZFS6 UNP 35 9 1 ARG SEE REMARK 999 GLY 23 2R61 A Q9ZFS6 UNP 53 27 1 LYS SEE REMARK 999 ALA 48 2R61 A Q9ZFS6 UNP 78 52 1 ASN SEE REMARK 999 HIS 49 2R61 A Q9ZFS6 UNP 79 53 1 ARG SEE REMARK 999 GLN 50 2R61 A Q9ZFS6 UNP 80 54 1 LYS SEE REMARK 999 ALA 51 2R61 A Q9ZFS6 UNP 81 55 1 ILE SEE REMARK 999 LEU 65 2R61 A Q9ZFS6 UNP 95 69 1 LYS SEE REMARK 999 ALA 67 2R61 A Q9ZFS6 UNP 97 71 1 TYR SEE REMARK 999 PHE 89 2R61 A Q9ZFS6 UNP 119 93 1 SER SEE REMARK 999 ASN 107 2R61 A Q9ZFS6 UNP 137 111 1 ARG SEE REMARK 999 LYS 110 2R61 A Q9ZFS6 UNP 140 114 1 GLY SEE REMARK 999 ASP 118 2R61 A Q9ZFS6 UNP 148 122 1 SER SEE REMARK 999 TYR 122 2R61 A Q9ZFS6 UNP 152 126 1 VAL SEE REMARK 999 THR 123 2R61 A Q9ZFS6 UNP 153 127 1 TYR SEE REMARK 999 HIS 128 2R61 A Q9ZFS6 UNP 158 132 1 ILE SEE REMARK 999 VAL 135 2R61 A Q9ZFS6 UNP 165 139 1 ASP SEE REMARK 999 ASN 151 2R61 A Q9ZFS6 UNP 181 155 1 ALA SEE REMARK 999 ASP 161 2R61 A Q9ZFS6 UNP 191 165 1 THR SEE REMARK 999 ILE 167 2R61 A Q9ZFS6 UNP 197 171 1 THR SEE REMARK 999 PRO 184 2R61 A Q9ZFS6 UNP 214 188 1 ASN SEE REMARK 999 HIS 185 2R61 A Q9ZFS6 UNP 215 189 1 ILE SEE REMARK 999 MET 199 2R61 A Q9ZFS6 UNP 229 203 6 5 2 parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel A PHE 89 A PHE 93 A TYR 91 A TYR 95 A ARG 54 A ARG 58 A ILE 57 A ILE 61 A HIS 42 A HIS 46 A ILE 45 A ILE 49 A LYS 26 A LYS 30 A SER 37 A SER 41 A LYS 69 A LYS 73 A VAL 77 A VAL 81 A VAL 94 A VAL 98 A LYS 96 A LYS 100 A GLY 120 A GLY 124 A ARG 127 A ARG 131 A LYS 110 A LYS 114 A VAL 117 A VAL 121 A ILE 196 A ILE 200 A ILE 203 A ILE 207 A LYS 163 A LYS 167 A MET 168 A MET 172 A TYR 173 A TYR 177 A GLU 177 A GLU 181 A GLU 134 A GLU 138 A SER 136 A SER 140 A VAL 190 A VAL 194 A ASP 192 A ASP 196 96 P 43 21 2