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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF PUTATIVE PEPTIDE:N-GLYCOSIDASE F (PNGAS (YP_210507.1) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 2.30 A RESOLUTION
Keywords PUTATIVE PEPTIDE:N-GLYCOSIDASE F (PNGASE F), STRUCTURAL GENO JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTU INITIATIVE, PSI-2, HYDROLASE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3KS7     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   PUTATIVE PUTATIVE PNGASE F  A 391 2997 48
2  Protein   PUTATIVE PUTATIVE PNGASE F  B 390 2995 48
3  Protein   PUTATIVE PUTATIVE PNGASE F  C 390 3002 48
4  Protein   PUTATIVE PUTATIVE PNGASE F  D 392 3015 48
5  Ligand   PUTATIVE PUTATIVE PNGASE F  A 11 0 29
6  Ligand   PUTATIVE PUTATIVE PNGASE F  B 11 0 29
7  Ligand   PUTATIVE PUTATIVE PNGASE F  C 9 0 24
8  Ligand   PUTATIVE PUTATIVE PNGASE F  D 8 0 23
9 Water     456 0 456
total       2058 12009 753
Proteins
Unit 1 ASN25 LEU26 PRO27 ALA28 LYS29 GLY30 ASP31 LEU32 HIS33 ILE34 PRO35 VAL36 PHE37 GLU38 ASN39 VAL40 ASN41 VAL42 ARG43 PHE44 SER45 PRO46 ASP47 THR48 TYR49 PRO50 ASP51 ASN52 TYR53 ASN54 GLU55 ALA56 ASP57 GLY58 THR59 GLY60 VAL61 TYR62 HIS63 LEU64 VAL65 ASN66 GLY67 ARG68 ILE69 ILE70 LEU71 LYS72 LYS73 ILE74 THR75 LEU76 PRO77 GLU78 TYR79 LYS80 ARG81 ASN82 VAL83 SER84 VAL85 SER86 LEU87 LYS88 VAL89 THR90 LEU91 ALA92 SER93 ASN94 GLY95 ASP96 ARG97 TRP98 ASP99 LYS100 SER101 GLY102 SER103 CYS104 PHE105 VAL106 LEU107 PRO108 LYS109 SER110 SER111 ALA112 ILE113 ASN114 LEU115 LEU116 THR117 ILE118 ALA119 ARG120 ASP121 GLY122 MSE123 LYS124 PHE125 PRO126 SER127 VAL128 ASP129 SER130 LEU131 LYS132 LEU133 GLU134 LYS135 MSE136 VAL137 GLY138 ILE139 VAL140 PRO141 GLY142 LYS143 ASP144 TYR145 LEU146 PRO147 THR148 VAL149 GLU150 LEU151 MSE152 ARG153 PHE154 MSE155 THR156 PRO157 PHE158 GLY159 ILE160 GLY161 HIS162 TYR163 SER164 ASN165 ASN166 ASN167 ASP168 SER169 LEU170 SER171 SER172 LYS173 ARG174 ARG175 PRO176 VAL177 TYR178 ILE179 PRO180 LYS181 TRP182 GLU183 SER184 ASN185 VAL186 THR187 TRP188 GLN189 GLN190 ASP191 ILE192 THR193 ASP194 LEU195 TYR196 PRO197 LEU198 LEU199 GLU200 GLY201 GLU202 ALA203 TYR204 VAL205 GLY206 ILE207 TYR208 ILE209 ASP210 THR211 TRP212 THR213 SER214 GLU215 GLY216 TYR217 LEU218 VAL219 ASN220 ALA221 ASP222 ILE223 ASP224 VAL225 LYS226 GLU227 SER228 ARG229 LEU230 ALA231 CYS232 ASP233 VAL234 LEU235 PRO236 LYS237 ARG238 HIS239 VAL240 GLU241 PRO242 LEU243 MSE244 ASN245 THR246 VAL247 TYR248 TYR249 MSE250 GLY251 GLN252 SER253 TYR254 PRO255 ASP256 ILE257 PHE258 ALA259 ARG260 ARG261 ASP262 VAL263 SER264 THR265 ASP266 PHE267 THR268 VAL269 PRO270 LYS271 GLY272 ALA273 LYS274 ASN275 ILE276 ARG277 LEU278 LYS279 TYR280 ILE281 VAL282 THR283 GLY284 HIS285 GLY286 GLY287 HIS288 SER289 GLY290 GLY291 ASP292 GLU293 PHE294 VAL295 GLN296 LYS297 ARG298 ASN299 ILE300 ILE301 SER302 VAL303 ASP304 GLY305 LYS306 GLU307 VAL308 LEU309 ASN310 PHE311 ILE312 PRO313 TRP314 ARG315 ASP316 ASP317 CYS318 ALA319 SER320 PHE321 ARG322 ARG323 PHE324 ASN325 PRO326 ALA327 THR328 GLY329 VAL330 TRP331 LEU332 ILE333 LYS334 ARG335 LEU336 ALA337 SER338 TYR339 ILE340 GLY341 GLU342 LYS343 GLY344 TYR345 THR346 GLU347 LYS348 GLU349 VAL350 GLU351 GLU352 PRO353 LEU354 ALA355 SER356 SER357 ASP358 LEU359 SER360 ARG361 SER362 ASN363 TRP364 CYS365 PRO366 GLY367 SER368 ASP369 VAL370 VAL371 PRO372 GLU373 GLU374 ALA375 VAL376 ILE377 GLY378 THR379 LEU380 ALA381 PRO382 GLY383 LYS384 HIS385 THR386 PHE387 THR388 VAL389 SER390 ILE391 PRO392 GLU393 ALA394 GLN395 ALA396 VAL397 ASP398 GLY399 ASN400 LYS401 LEU402 ASN403 HIS404 TRP405 LEU406 VAL407 SER408 ALA409 TYR410 LEU411 VAL412 TRP413 GLU414 GLU415
Unit 2 LEU26 PRO27 ALA28 LYS29 GLY30 ASP31 LEU32 HIS33 ILE34 PRO35 VAL36 PHE37 GLU38 ASN39 VAL40 ASN41 VAL42 ARG43 PHE44 SER45 PRO46 ASP47 THR48 TYR49 PRO50 ASP51 ASN52 TYR53 ASN54 GLU55 ALA56 ASP57 GLY58 THR59 GLY60 VAL61 TYR62 HIS63 LEU64 VAL65 ASN66 GLY67 ARG68 ILE69 ILE70 LEU71 LYS72 LYS73 ILE74 THR75 LEU76 PRO77 GLU78 TYR79 LYS80 ARG81 ASN82 VAL83 SER84 VAL85 SER86 LEU87 LYS88 VAL89 THR90 LEU91 ALA92 SER93 ASN94 GLY95 ASP96 ARG97 TRP98 ASP99 LYS100 SER101 GLY102 SER103 CYS104 PHE105 VAL106 LEU107 PRO108 LYS109 SER110 SER111 ALA112 ILE113 ASN114 LEU115 LEU116 THR117 ILE118 ALA119 ARG120 ASP121 GLY122 MSE123 LYS124 PHE125 PRO126 SER127 VAL128 ASP129 SER130 LEU131 LYS132 LEU133 GLU134 LYS135 MSE136 VAL137 GLY138 ILE139 VAL140 PRO141 GLY142 LYS143 ASP144 TYR145 LEU146 PRO147 THR148 VAL149 GLU150 LEU151 MSE152 ARG153 PHE154 MSE155 THR156 PRO157 PHE158 GLY159 ILE160 GLY161 HIS162 TYR163 SER164 ASN165 ASN166 ASN167 ASP168 SER169 LEU170 SER171 SER172 LYS173 ARG174 ARG175 PRO176 VAL177 TYR178 ILE179 PRO180 LYS181 TRP182 GLU183 SER184 ASN185 VAL186 THR187 TRP188 GLN189 GLN190 ASP191 ILE192 THR193 ASP194 LEU195 TYR196 PRO197 LEU198 LEU199 GLU200 GLY201 GLU202 ALA203 TYR204 VAL205 GLY206 ILE207 TYR208 ILE209 ASP210 THR211 TRP212 THR213 SER214 GLU215 GLY216 TYR217 LEU218 VAL219 ASN220 ALA221 ASP222 ILE223 ASP224 VAL225 LYS226 GLU227 SER228 ARG229 LEU230 ALA231 CYS232 ASP233 VAL234 LEU235 PRO236 LYS237 ARG238 HIS239 VAL240 GLU241 PRO242 LEU243 MSE244 ASN245 THR246 VAL247 TYR248 TYR249 MSE250 GLY251 GLN252 SER253 TYR254 PRO255 ASP256 ILE257 PHE258 ALA259 ARG260 ARG261 ASP262 VAL263 SER264 THR265 ASP266 PHE267 THR268 VAL269 PRO270 LYS271 GLY272 ALA273 LYS274 ASN275 ILE276 ARG277 LEU278 LYS279 TYR280 ILE281 VAL282 THR283 GLY284 HIS285 GLY286 GLY287 HIS288 SER289 GLY290 GLY291 ASP292 GLU293 PHE294 VAL295 GLN296 LYS297 ARG298 ASN299 ILE300 ILE301 SER302 VAL303 ASP304 GLY305 LYS306 GLU307 VAL308 LEU309 ASN310 PHE311 ILE312 PRO313 TRP314 ARG315 ASP316 ASP317 CYS318 ALA319 SER320 PHE321 ARG322 ARG323 PHE324 ASN325 PRO326 ALA327 THR328 GLY329 VAL330 TRP331 LEU332 ILE333 LYS334 ARG335 LEU336 ALA337 SER338 TYR339 ILE340 GLY341 GLU342 LYS343 GLY344 TYR345 THR346 GLU347 LYS348 GLU349 VAL350 GLU351 GLU352 PRO353 LEU354 ALA355 SER356 SER357 ASP358 LEU359 SER360 ARG361 SER362 ASN363 TRP364 CYS365 PRO366 GLY367 SER368 ASP369 VAL370 VAL371 PRO372 GLU373 GLU374 ALA375 VAL376 ILE377 GLY378 THR379 LEU380 ALA381 PRO382 GLY383 LYS384 HIS385 THR386 PHE387 THR388 VAL389 SER390 ILE391 PRO392 GLU393 ALA394 GLN395 ALA396 VAL397 ASP398 GLY399 ASN400 LYS401 LEU402 ASN403 HIS404 TRP405 LEU406 VAL407 SER408 ALA409 TYR410 LEU411 VAL412 TRP413 GLU414 GLU415
Unit 3 LEU26 PRO27 ALA28 LYS29 GLY30 ASP31 LEU32 HIS33 ILE34 PRO35 VAL36 PHE37 GLU38 ASN39 VAL40 ASN41 VAL42 ARG43 PHE44 SER45 PRO46 ASP47 THR48 TYR49 PRO50 ASP51 ASN52 TYR53 ASN54 GLU55 ALA56 ASP57 GLY58 THR59 GLY60 VAL61 TYR62 HIS63 LEU64 VAL65 ASN66 GLY67 ARG68 ILE69 ILE70 LEU71 LYS72 LYS73 ILE74 THR75 LEU76 PRO77 GLU78 TYR79 LYS80 ARG81 ASN82 VAL83 SER84 VAL85 SER86 LEU87 LYS88 VAL89 THR90 LEU91 ALA92 SER93 ASN94 GLY95 ASP96 ARG97 TRP98 ASP99 LYS100 SER101 GLY102 SER103 CYS104 PHE105 VAL106 LEU107 PRO108 LYS109 SER110 SER111 ALA112 ILE113 ASN114 LEU115 LEU116 THR117 ILE118 ALA119 ARG120 ASP121 GLY122 MSE123 LYS124 PHE125 PRO126 SER127 VAL128 ASP129 SER130 LEU131 LYS132 LEU133 GLU134 LYS135 MSE136 VAL137 GLY138 ILE139 VAL140 PRO141 GLY142 LYS143 ASP144 TYR145 LEU146 PRO147 THR148 VAL149 GLU150 LEU151 MSE152 ARG153 PHE154 MSE155 THR156 PRO157 PHE158 GLY159 ILE160 GLY161 HIS162 TYR163 SER164 ASN165 ASN166 ASN167 ASP168 SER169 LEU170 SER171 SER172 LYS173 ARG174 ARG175 PRO176 VAL177 TYR178 ILE179 PRO180 LYS181 TRP182 GLU183 SER184 ASN185 VAL186 THR187 TRP188 GLN189 GLN190 ASP191 ILE192 THR193 ASP194 LEU195 TYR196 PRO197 LEU198 LEU199 GLU200 GLY201 GLU202 ALA203 TYR204 VAL205 GLY206 ILE207 TYR208 ILE209 ASP210 THR211 TRP212 THR213 SER214 GLU215 GLY216 TYR217 LEU218 VAL219 ASN220 ALA221 ASP222 ILE223 ASP224 VAL225 LYS226 GLU227 SER228 ARG229 LEU230 ALA231 CYS232 ASP233 VAL234 LEU235 PRO236 LYS237 ARG238 HIS239 VAL240 GLU241 PRO242 LEU243 MSE244 ASN245 THR246 VAL247 TYR248 TYR249 MSE250 GLY251 GLN252 SER253 TYR254 PRO255 ASP256 ILE257 PHE258 ALA259 ARG260 ARG261 ASP262 VAL263 SER264 THR265 ASP266 PHE267 THR268 VAL269 PRO270 LYS271 GLY272 ALA273 LYS274 ASN275 ILE276 ARG277 LEU278 LYS279 TYR280 ILE281 VAL282 THR283 GLY284 HIS285 GLY286 GLY287 HIS288 SER289 GLY290 GLY291 ASP292 GLU293 PHE294 VAL295 GLN296 LYS297 ARG298 ASN299 ILE300 ILE301 SER302 VAL303 ASP304 GLY305 LYS306 GLU307 VAL308 LEU309 ASN310 PHE311 ILE312 PRO313 TRP314 ARG315 ASP316 ASP317 CYS318 ALA319 SER320 PHE321 ARG322 ARG323 PHE324 ASN325 PRO326 ALA327 THR328 GLY329 VAL330 TRP331 LEU332 ILE333 LYS334 ARG335 LEU336 ALA337 SER338 TYR339 ILE340 GLY341 GLU342 LYS343 GLY344 TYR345 THR346 GLU347 LYS348 GLU349 VAL350 GLU351 GLU352 PRO353 LEU354 ALA355 SER356 SER357 ASP358 LEU359 SER360 ARG361 SER362 ASN363 TRP364 CYS365 PRO366 GLY367 SER368 ASP369 VAL370 VAL371 PRO372 GLU373 GLU374 ALA375 VAL376 ILE377 GLY378 THR379 LEU380 ALA381 PRO382 GLY383 LYS384 HIS385 THR386 PHE387 THR388 VAL389 SER390 ILE391 PRO392 GLU393 ALA394 GLN395 ALA396 VAL397 ASP398 GLY399 ASN400 LYS401 LEU402 ASN403 HIS404 TRP405 LEU406 VAL407 SER408 ALA409 TYR410 LEU411 VAL412 TRP413 GLU414 GLU415
Unit 4 LYS24 ASN25 LEU26 PRO27 ALA28 LYS29 GLY30 ASP31 LEU32 HIS33 ILE34 PRO35 VAL36 PHE37 GLU38 ASN39 VAL40 ASN41 VAL42 ARG43 PHE44 SER45 PRO46 ASP47 THR48 TYR49 PRO50 ASP51 ASN52 TYR53 ASN54 GLU55 ALA56 ASP57 GLY58 THR59 GLY60 VAL61 TYR62 HIS63 LEU64 VAL65 ASN66 GLY67 ARG68 ILE69 ILE70 LEU71 LYS72 LYS73 ILE74 THR75 LEU76 PRO77 GLU78 TYR79 LYS80 ARG81 ASN82 VAL83 SER84 VAL85 SER86 LEU87 LYS88 VAL89 THR90 LEU91 ALA92 SER93 ASN94 GLY95 ASP96 ARG97 TRP98 ASP99 LYS100 SER101 GLY102 SER103 CYS104 PHE105 VAL106 LEU107 PRO108 LYS109 SER110 SER111 ALA112 ILE113 ASN114 LEU115 LEU116 THR117 ILE118 ALA119 ARG120 ASP121 GLY122 MSE123 LYS124 PHE125 PRO126 SER127 VAL128 ASP129 SER130 LEU131 LYS132 LEU133 GLU134 LYS135 MSE136 VAL137 GLY138 ILE139 VAL140 PRO141 GLY142 LYS143 ASP144 TYR145 LEU146 PRO147 THR148 VAL149 GLU150 LEU151 MSE152 ARG153 PHE154 MSE155 THR156 PRO157 PHE158 GLY159 ILE160 GLY161 HIS162 TYR163 SER164 ASN165 ASN166 ASN167 ASP168 SER169 LEU170 SER171 SER172 LYS173 ARG174 ARG175 PRO176 VAL177 TYR178 ILE179 PRO180 LYS181 TRP182 GLU183 SER184 ASN185 VAL186 THR187 TRP188 GLN189 GLN190 ASP191 ILE192 THR193 ASP194 LEU195 TYR196 PRO197 LEU198 LEU199 GLU200 GLY201 GLU202 ALA203 TYR204 VAL205 GLY206 ILE207 TYR208 ILE209 ASP210 THR211 TRP212 THR213 SER214 GLU215 GLY216 TYR217 LEU218 VAL219 ASN220 ALA221 ASP222 ILE223 ASP224 VAL225 LYS226 GLU227 SER228 ARG229 LEU230 ALA231 CYS232 ASP233 VAL234 LEU235 PRO236 LYS237 ARG238 HIS239 VAL240 GLU241 PRO242 LEU243 MSE244 ASN245 THR246 VAL247 TYR248 TYR249 MSE250 GLY251 GLN252 SER253 TYR254 PRO255 ASP256 ILE257 PHE258 ALA259 ARG260 ARG261 ASP262 VAL263 SER264 THR265 ASP266 PHE267 THR268 VAL269 PRO270 LYS271 GLY272 ALA273 LYS274 ASN275 ILE276 ARG277 LEU278 LYS279 TYR280 ILE281 VAL282 THR283 GLY284 HIS285 GLY286 GLY287 HIS288 SER289 GLY290 GLY291 ASP292 GLU293 PHE294 VAL295 GLN296 LYS297 ARG298 ASN299 ILE300 ILE301 SER302 VAL303 ASP304 GLY305 LYS306 GLU307 VAL308 LEU309 ASN310 PHE311 ILE312 PRO313 TRP314 ARG315 ASP316 ASP317 CYS318 ALA319 SER320 PHE321 ARG322 ARG323 PHE324 ASN325 PRO326 ALA327 THR328 GLY329 VAL330 TRP331 LEU332 ILE333 LYS334 ARG335 LEU336 ALA337 SER338 TYR339 ILE340 GLY341 GLU342 LYS343 GLY344 TYR345 THR346 GLU347 LYS348 GLU349 VAL350 GLU351 GLU352 PRO353 LEU354 ALA355 SER356 SER357 ASP358 LEU359 SER360 ARG361 SER362 ASN363 TRP364 CYS365 PRO366 GLY367 SER368 ASP369 VAL370 VAL371 PRO372 GLU373 GLU374 ALA375 VAL376 ILE377 GLY378 THR379 LEU380 ALA381 PRO382 GLY383 LYS384 HIS385 THR386 PHE387 THR388 VAL389 SER390 ILE391 PRO392 GLU393 ALA394 GLN395 ALA396 VAL397 ASP398 GLY399 ASN400 LYS401 LEU402 ASN403 HIS404 TRP405 LEU406 VAL407 SER408 ALA409 TYR410 LEU411 VAL412 TRP413 GLU414 GLU415
Ligands
Unit 5 IOD4 IOD6 CL9 CL11 CL12 EDO416 EDO417 EDO418 EDO419 EDO420 EDO421
Unit 6 IOD1 IOD5 CL8 CL14 CL16 EDO416 EDO417 EDO418 EDO419 EDO420 EDO421
Unit 7 IOD2 CL10 CL13 CL15 EDO416 EDO417 EDO418 EDO419 EDO420
Unit 8 IOD3 IOD7 CL17 EDO18 EDO416 EDO417 EDO418 EDO419
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany