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Sequence, Chains, Asymmetric and Biological Units

Title DBR1 IN COMPLEX WITH SYNTHETIC LINEAR RNA
Keywords NUCLEASE, PHOSPHODIESTERASE, METALLOHYDROLASE, METALLOPHOSPHOESTERASE, LARIAT RNA, HYDROLASE, METALLOENZYM HYDROLASE-RNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   4PEH     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  A 349 2857 0
2  DNA/RNA    V 4 43 26
3  Protein   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  B 349 2857 0
4  DNA/RNA    W 5 47 26
5  Protein   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  C 349 2857 0
6  DNA/RNA    X 6 69 26
7  Protein   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  D 349 2857 0
8  DNA/RNA    Y 5 65 26
9  Protein   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  E 349 2857 0
10  DNA/RNA    Z 4 43 26
11  Ligand   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  A 3 0 12
12  Ligand   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  B 3 0 11
13  Ligand   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  C 4 0 16
14  Ligand   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  D 2 0 6
15  Ligand   RNA LARIAT DEBRANCHING ENZYME, PUTATIVE  E 2 0 6
16 Water     1007 0 1007
total       2790 14552 1188
Proteins
Unit 1 GLN5 ILE6 GLN7 HIS8 ILE9 ALA10 ILE11 VAL12 GLY13 SER14 VAL15 HIS16 GLY17 LYS18 TYR19 ARG20 GLU21 MET22 TYR23 ARG24 GLN25 LEU26 SER27 GLU28 TYR29 GLU30 LYS31 SER32 THR33 GLY34 LYS35 GLU36 ILE37 SER38 PHE39 VAL40 ILE41 CYS42 THR43 GLY44 ASP45 MET46 GLN47 THR48 LEU49 ARG50 TYR51 GLU52 ALA53 ASP54 LEU55 VAL56 TYR57 LEU58 LYS59 VAL60 PRO61 PRO62 LYS63 TYR64 LYS65 GLN66 MET67 GLY68 ASP69 PHE70 HIS71 LEU72 TYR73 TYR74 GLU75 GLY76 LYS77 GLU78 LYS79 ALA80 PRO81 TYR82 LEU83 THR84 LEU85 PHE86 ILE87 GLY88 GLY89 ASN90 HIS91 GLU92 SER93 SER94 ASN95 VAL96 LEU97 LEU98 HIS99 LEU100 TYR101 ASN102 GLY103 GLY104 PHE105 VAL106 CYS107 PHE108 ASN109 MET110 TYR111 TYR112 LEU113 GLY114 VAL115 CYS116 SER117 CYS118 ILE119 ASN120 ILE121 ASN122 GLY123 LEU124 ARG125 ILE126 VAL127 GLY128 VAL129 SER130 GLY131 ILE132 TYR133 LYS134 SER135 PHE136 ASP137 GLU138 LYS139 LYS140 PRO141 TYR142 THR143 TYR144 PRO145 PRO146 SER147 PRO148 ASN149 ASP150 VAL151 VAL152 SER153 LEU154 PHE155 HIS156 THR157 ARG158 ASN159 TYR160 VAL161 ILE162 GLN163 MET164 LEU165 SER166 ASN167 LEU168 SER169 GLN170 SER171 SER172 GLN173 ILE174 ASP175 ILE176 SER177 LEU178 SER179 HIS180 ASP181 TRP182 PRO183 GLN184 GLY185 ILE186 VAL187 MET188 LYS189 GLY190 ASN191 TYR192 LYS193 GLN194 LEU195 TYR196 ARG197 PHE198 GLN199 PRO200 GLY201 PHE202 LYS203 LYS204 ASP205 GLY206 ALA207 SER208 LEU209 GLY210 SER211 PRO212 ILE213 ASN214 LYS215 VAL216 ILE217 LEU218 ASN219 THR220 LEU221 LYS222 PRO223 LYS224 TYR225 TRP226 ILE227 SER228 GLY229 HIS230 MET231 HIS232 CYS233 GLU234 TYR235 HIS236 ALA237 GLU238 GLU239 GLY240 PRO241 THR242 HIS243 PHE244 ILE245 ALA246 LEU247 GLY248 LYS249 ILE250 GLY251 TYR252 LYS253 ASN254 ALA255 ILE256 SER257 TYR258 LEU259 ASP260 LEU261 PRO262 LEU263 LYS264 GLN265 LYS266 THR267 ASP268 LEU269 GLU270 TYR271 ASP272 LYS273 ASP274 TRP275 VAL276 CYS277 ASN278 LEU279 ILE280 MET281 THR282 TRP283 PRO284 ALA285 PHE286 SER287 ASN288 LYS289 ALA290 GLN291 PHE292 PRO293 ASP294 LEU295 SER296 TYR297 SER298 ILE299 SER300 GLU301 LEU302 LEU303 SER304 LYS305 ARG306 THR307 LYS308 GLU309 LEU310 ASP311 LYS312 LYS313 ILE314 ILE315 GLU316 LEU317 TRP318 GLU319 LYS320 TYR321 ILE322 GLY323 LEU324 LYS325 ILE326 ILE327 TYR328 ASP329 SER330 ASP331 THR332 PHE333 ASP334 ILE335 GLN336 PHE337 THR338 SER339 ARG340 ARG341 PHE342 TYR343 ILE344 GLU345 LYS346 ILE347 TYR348 ASN349 GLU350 LEU351 ASN352 ILE353
Unit 3 GLN5 ILE6 GLN7 HIS8 ILE9 ALA10 ILE11 VAL12 GLY13 SER14 VAL15 HIS16 GLY17 LYS18 TYR19 ARG20 GLU21 MET22 TYR23 ARG24 GLN25 LEU26 SER27 GLU28 TYR29 GLU30 LYS31 SER32 THR33 GLY34 LYS35 GLU36 ILE37 SER38 PHE39 VAL40 ILE41 CYS42 THR43 GLY44 ASP45 MET46 GLN47 THR48 LEU49 ARG50 TYR51 GLU52 ALA53 ASP54 LEU55 VAL56 TYR57 LEU58 LYS59 VAL60 PRO61 PRO62 LYS63 TYR64 LYS65 GLN66 MET67 GLY68 ASP69 PHE70 HIS71 LEU72 TYR73 TYR74 GLU75 GLY76 LYS77 GLU78 LYS79 ALA80 PRO81 TYR82 LEU83 THR84 LEU85 PHE86 ILE87 GLY88 GLY89 ASN90 HIS91 GLU92 SER93 SER94 ASN95 VAL96 LEU97 LEU98 HIS99 LEU100 TYR101 ASN102 GLY103 GLY104 PHE105 VAL106 CYS107 PHE108 ASN109 MET110 TYR111 TYR112 LEU113 GLY114 VAL115 CYS116 SER117 CYS118 ILE119 ASN120 ILE121 ASN122 GLY123 LEU124 ARG125 ILE126 VAL127 GLY128 VAL129 SER130 GLY131 ILE132 TYR133 LYS134 SER135 PHE136 ASP137 GLU138 LYS139 LYS140 PRO141 TYR142 THR143 TYR144 PRO145 PRO146 SER147 PRO148 ASN149 ASP150 VAL151 VAL152 SER153 LEU154 PHE155 HIS156 THR157 ARG158 ASN159 TYR160 VAL161 ILE162 GLN163 MET164 LEU165 SER166 ASN167 LEU168 SER169 GLN170 SER171 SER172 GLN173 ILE174 ASP175 ILE176 SER177 LEU178 SER179 HIS180 ASP181 TRP182 PRO183 GLN184 GLY185 ILE186 VAL187 MET188 LYS189 GLY190 ASN191 TYR192 LYS193 GLN194 LEU195 TYR196 ARG197 PHE198 GLN199 PRO200 GLY201 PHE202 LYS203 LYS204 ASP205 GLY206 ALA207 SER208 LEU209 GLY210 SER211 PRO212 ILE213 ASN214 LYS215 VAL216 ILE217 LEU218 ASN219 THR220 LEU221 LYS222 PRO223 LYS224 TYR225 TRP226 ILE227 SER228 GLY229 HIS230 MET231 HIS232 CYS233 GLU234 TYR235 HIS236 ALA237 GLU238 GLU239 GLY240 PRO241 THR242 HIS243 PHE244 ILE245 ALA246 LEU247 GLY248 LYS249 ILE250 GLY251 TYR252 LYS253 ASN254 ALA255 ILE256 SER257 TYR258 LEU259 ASP260 LEU261 PRO262 LEU263 LYS264 GLN265 LYS266 THR267 ASP268 LEU269 GLU270 TYR271 ASP272 LYS273 ASP274 TRP275 VAL276 CYS277 ASN278 LEU279 ILE280 MET281 THR282 TRP283 PRO284 ALA285 PHE286 SER287 ASN288 LYS289 ALA290 GLN291 PHE292 PRO293 ASP294 LEU295 SER296 TYR297 SER298 ILE299 SER300 GLU301 LEU302 LEU303 SER304 LYS305 ARG306 THR307 LYS308 GLU309 LEU310 ASP311 LYS312 LYS313 ILE314 ILE315 GLU316 LEU317 TRP318 GLU319 LYS320 TYR321 ILE322 GLY323 LEU324 LYS325 ILE326 ILE327 TYR328 ASP329 SER330 ASP331 THR332 PHE333 ASP334 ILE335 GLN336 PHE337 THR338 SER339 ARG340 ARG341 PHE342 TYR343 ILE344 GLU345 LYS346 ILE347 TYR348 ASN349 GLU350 LEU351 ASN352 ILE353
Unit 5 GLN5 ILE6 GLN7 HIS8 ILE9 ALA10 ILE11 VAL12 GLY13 SER14 VAL15 HIS16 GLY17 LYS18 TYR19 ARG20 GLU21 MET22 TYR23 ARG24 GLN25 LEU26 SER27 GLU28 TYR29 GLU30 LYS31 SER32 THR33 GLY34 LYS35 GLU36 ILE37 SER38 PHE39 VAL40 ILE41 CYS42 THR43 GLY44 ASP45 MET46 GLN47 THR48 LEU49 ARG50 TYR51 GLU52 ALA53 ASP54 LEU55 VAL56 TYR57 LEU58 LYS59 VAL60 PRO61 PRO62 LYS63 TYR64 LYS65 GLN66 MET67 GLY68 ASP69 PHE70 HIS71 LEU72 TYR73 TYR74 GLU75 GLY76 LYS77 GLU78 LYS79 ALA80 PRO81 TYR82 LEU83 THR84 LEU85 PHE86 ILE87 GLY88 GLY89 ASN90 HIS91 GLU92 SER93 SER94 ASN95 VAL96 LEU97 LEU98 HIS99 LEU100 TYR101 ASN102 GLY103 GLY104 PHE105 VAL106 CYS107 PHE108 ASN109 MET110 TYR111 TYR112 LEU113 GLY114 VAL115 CYS116 SER117 CYS118 ILE119 ASN120 ILE121 ASN122 GLY123 LEU124 ARG125 ILE126 VAL127 GLY128 VAL129 SER130 GLY131 ILE132 TYR133 LYS134 SER135 PHE136 ASP137 GLU138 LYS139 LYS140 PRO141 TYR142 THR143 TYR144 PRO145 PRO146 SER147 PRO148 ASN149 ASP150 VAL151 VAL152 SER153 LEU154 PHE155 HIS156 THR157 ARG158 ASN159 TYR160 VAL161 ILE162 GLN163 MET164 LEU165 SER166 ASN167 LEU168 SER169 GLN170 SER171 SER172 GLN173 ILE174 ASP175 ILE176 SER177 LEU178 SER179 HIS180 ASP181 TRP182 PRO183 GLN184 GLY185 ILE186 VAL187 MET188 LYS189 GLY190 ASN191 TYR192 LYS193 GLN194 LEU195 TYR196 ARG197 PHE198 GLN199 PRO200 GLY201 PHE202 LYS203 LYS204 ASP205 GLY206 ALA207 SER208 LEU209 GLY210 SER211 PRO212 ILE213 ASN214 LYS215 VAL216 ILE217 LEU218 ASN219 THR220 LEU221 LYS222 PRO223 LYS224 TYR225 TRP226 ILE227 SER228 GLY229 HIS230 MET231 HIS232 CYS233 GLU234 TYR235 HIS236 ALA237 GLU238 GLU239 GLY240 PRO241 THR242 HIS243 PHE244 ILE245 ALA246 LEU247 GLY248 LYS249 ILE250 GLY251 TYR252 LYS253 ASN254 ALA255 ILE256 SER257 TYR258 LEU259 ASP260 LEU261 PRO262 LEU263 LYS264 GLN265 LYS266 THR267 ASP268 LEU269 GLU270 TYR271 ASP272 LYS273 ASP274 TRP275 VAL276 CYS277 ASN278 LEU279 ILE280 MET281 THR282 TRP283 PRO284 ALA285 PHE286 SER287 ASN288 LYS289 ALA290 GLN291 PHE292 PRO293 ASP294 LEU295 SER296 TYR297 SER298 ILE299 SER300 GLU301 LEU302 LEU303 SER304 LYS305 ARG306 THR307 LYS308 GLU309 LEU310 ASP311 LYS312 LYS313 ILE314 ILE315 GLU316 LEU317 TRP318 GLU319 LYS320 TYR321 ILE322 GLY323 LEU324 LYS325 ILE326 ILE327 TYR328 ASP329 SER330 ASP331 THR332 PHE333 ASP334 ILE335 GLN336 PHE337 THR338 SER339 ARG340 ARG341 PHE342 TYR343 ILE344 GLU345 LYS346 ILE347 TYR348 ASN349 GLU350 LEU351 ASN352 ILE353
Unit 7 GLN5 ILE6 GLN7 HIS8 ILE9 ALA10 ILE11 VAL12 GLY13 SER14 VAL15 HIS16 GLY17 LYS18 TYR19 ARG20 GLU21 MET22 TYR23 ARG24 GLN25 LEU26 SER27 GLU28 TYR29 GLU30 LYS31 SER32 THR33 GLY34 LYS35 GLU36 ILE37 SER38 PHE39 VAL40 ILE41 CYS42 THR43 GLY44 ASP45 MET46 GLN47 THR48 LEU49 ARG50 TYR51 GLU52 ALA53 ASP54 LEU55 VAL56 TYR57 LEU58 LYS59 VAL60 PRO61 PRO62 LYS63 TYR64 LYS65 GLN66 MET67 GLY68 ASP69 PHE70 HIS71 LEU72 TYR73 TYR74 GLU75 GLY76 LYS77 GLU78 LYS79 ALA80 PRO81 TYR82 LEU83 THR84 LEU85 PHE86 ILE87 GLY88 GLY89 ASN90 HIS91 GLU92 SER93 SER94 ASN95 VAL96 LEU97 LEU98 HIS99 LEU100 TYR101 ASN102 GLY103 GLY104 PHE105 VAL106 CYS107 PHE108 ASN109 MET110 TYR111 TYR112 LEU113 GLY114 VAL115 CYS116 SER117 CYS118 ILE119 ASN120 ILE121 ASN122 GLY123 LEU124 ARG125 ILE126 VAL127 GLY128 VAL129 SER130 GLY131 ILE132 TYR133 LYS134 SER135 PHE136 ASP137 GLU138 LYS139 LYS140 PRO141 TYR142 THR143 TYR144 PRO145 PRO146 SER147 PRO148 ASN149 ASP150 VAL151 VAL152 SER153 LEU154 PHE155 HIS156 THR157 ARG158 ASN159 TYR160 VAL161 ILE162 GLN163 MET164 LEU165 SER166 ASN167 LEU168 SER169 GLN170 SER171 SER172 GLN173 ILE174 ASP175 ILE176 SER177 LEU178 SER179 HIS180 ASP181 TRP182 PRO183 GLN184 GLY185 ILE186 VAL187 MET188 LYS189 GLY190 ASN191 TYR192 LYS193 GLN194 LEU195 TYR196 ARG197 PHE198 GLN199 PRO200 GLY201 PHE202 LYS203 LYS204 ASP205 GLY206 ALA207 SER208 LEU209 GLY210 SER211 PRO212 ILE213 ASN214 LYS215 VAL216 ILE217 LEU218 ASN219 THR220 LEU221 LYS222 PRO223 LYS224 TYR225 TRP226 ILE227 SER228 GLY229 HIS230 MET231 HIS232 CYS233 GLU234 TYR235 HIS236 ALA237 GLU238 GLU239 GLY240 PRO241 THR242 HIS243 PHE244 ILE245 ALA246 LEU247 GLY248 LYS249 ILE250 GLY251 TYR252 LYS253 ASN254 ALA255 ILE256 SER257 TYR258 LEU259 ASP260 LEU261 PRO262 LEU263 LYS264 GLN265 LYS266 THR267 ASP268 LEU269 GLU270 TYR271 ASP272 LYS273 ASP274 TRP275 VAL276 CYS277 ASN278 LEU279 ILE280 MET281 THR282 TRP283 PRO284 ALA285 PHE286 SER287 ASN288 LYS289 ALA290 GLN291 PHE292 PRO293 ASP294 LEU295 SER296 TYR297 SER298 ILE299 SER300 GLU301 LEU302 LEU303 SER304 LYS305 ARG306 THR307 LYS308 GLU309 LEU310 ASP311 LYS312 LYS313 ILE314 ILE315 GLU316 LEU317 TRP318 GLU319 LYS320 TYR321 ILE322 GLY323 LEU324 LYS325 ILE326 ILE327 TYR328 ASP329 SER330 ASP331 THR332 PHE333 ASP334 ILE335 GLN336 PHE337 THR338 SER339 ARG340 ARG341 PHE342 TYR343 ILE344 GLU345 LYS346 ILE347 TYR348 ASN349 GLU350 LEU351 ASN352 ILE353
Unit 9 GLN5 ILE6 GLN7 HIS8 ILE9 ALA10 ILE11 VAL12 GLY13 SER14 VAL15 HIS16 GLY17 LYS18 TYR19 ARG20 GLU21 MET22 TYR23 ARG24 GLN25 LEU26 SER27 GLU28 TYR29 GLU30 LYS31 SER32 THR33 GLY34 LYS35 GLU36 ILE37 SER38 PHE39 VAL40 ILE41 CYS42 THR43 GLY44 ASP45 MET46 GLN47 THR48 LEU49 ARG50 TYR51 GLU52 ALA53 ASP54 LEU55 VAL56 TYR57 LEU58 LYS59 VAL60 PRO61 PRO62 LYS63 TYR64 LYS65 GLN66 MET67 GLY68 ASP69 PHE70 HIS71 LEU72 TYR73 TYR74 GLU75 GLY76 LYS77 GLU78 LYS79 ALA80 PRO81 TYR82 LEU83 THR84 LEU85 PHE86 ILE87 GLY88 GLY89 ASN90 HIS91 GLU92 SER93 SER94 ASN95 VAL96 LEU97 LEU98 HIS99 LEU100 TYR101 ASN102 GLY103 GLY104 PHE105 VAL106 CYS107 PHE108 ASN109 MET110 TYR111 TYR112 LEU113 GLY114 VAL115 CYS116 SER117 CYS118 ILE119 ASN120 ILE121 ASN122 GLY123 LEU124 ARG125 ILE126 VAL127 GLY128 VAL129 SER130 GLY131 ILE132 TYR133 LYS134 SER135 PHE136 ASP137 GLU138 LYS139 LYS140 PRO141 TYR142 THR143 TYR144 PRO145 PRO146 SER147 PRO148 ASN149 ASP150 VAL151 VAL152 SER153 LEU154 PHE155 HIS156 THR157 ARG158 ASN159 TYR160 VAL161 ILE162 GLN163 MET164 LEU165 SER166 ASN167 LEU168 SER169 GLN170 SER171 SER172 GLN173 ILE174 ASP175 ILE176 SER177 LEU178 SER179 HIS180 ASP181 TRP182 PRO183 GLN184 GLY185 ILE186 VAL187 MET188 LYS189 GLY190 ASN191 TYR192 LYS193 GLN194 LEU195 TYR196 ARG197 PHE198 GLN199 PRO200 GLY201 PHE202 LYS203 LYS204 ASP205 GLY206 ALA207 SER208 LEU209 GLY210 SER211 PRO212 ILE213 ASN214 LYS215 VAL216 ILE217 LEU218 ASN219 THR220 LEU221 LYS222 PRO223 LYS224 TYR225 TRP226 ILE227 SER228 GLY229 HIS230 MET231 HIS232 CYS233 GLU234 TYR235 HIS236 ALA237 GLU238 GLU239 GLY240 PRO241 THR242 HIS243 PHE244 ILE245 ALA246 LEU247 GLY248 LYS249 ILE250 GLY251 TYR252 LYS253 ASN254 ALA255 ILE256 SER257 TYR258 LEU259 ASP260 LEU261 PRO262 LEU263 LYS264 GLN265 LYS266 THR267 ASP268 LEU269 GLU270 TYR271 ASP272 LYS273 ASP274 TRP275 VAL276 CYS277 ASN278 LEU279 ILE280 MET281 THR282 TRP283 PRO284 ALA285 PHE286 SER287 ASN288 LYS289 ALA290 GLN291 PHE292 PRO293 ASP294 LEU295 SER296 TYR297 SER298 ILE299 SER300 GLU301 LEU302 LEU303 SER304 LYS305 ARG306 THR307 LYS308 GLU309 LEU310 ASP311 LYS312 LYS313 ILE314 ILE315 GLU316 LEU317 TRP318 GLU319 LYS320 TYR321 ILE322 GLY323 LEU324 LYS325 ILE326 ILE327 TYR328 ASP329 SER330 ASP331 THR332 PHE333 ASP334 ILE335 GLN336 PHE337 THR338 SER339 ARG340 ARG341 PHE342 TYR343 ILE344 GLU345 LYS346 ILE347 TYR348 ASN349 GLU350 LEU351 ASN352 ILE353
Nucleic acids
Unit 2 A500 A2P501 C502 A503
Unit 4 A500 A2P501 C502 A503 A504
Unit 6 U499 A500 A2P501 C502 A503 A504
Unit 8 A500 A2P501 C502 A503 A504
Unit 10 A500 A2P501 C502 A503
Ligands
Unit 11 MN401 SO4402 GOL403
Unit 12 MN401 SO4402 SO4403
Unit 13 MN401 SO4402 SO4403 SO4404
Unit 14 MN401 SO4402
Unit 15 MN401 SO4402
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany