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Sequence, Chains, Asymmetric and Biological Units

Title MUS MUSCULUS TDP2-DNA SUBSTRATE ANALOG (5'-6-AMINOHEXANOL) C
Keywords PROTEIN-DNA COMPLEX, DNA REPAIR, 5'-DNA END PROCESSING, ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE DOMAIN, EEP DOMAIN, 5' RECOGNITION, EEP, 5'-END RECOGNITION, NUCLEAR, HYDROLASE, H DNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   4GZ0     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  A 250 1984 0
2  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  B 250 1984 0
3  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  C 9 183 0
4  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  D 9 183 0
5  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  E 250 1984 0
6  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  F 9 183 0
7  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  K 249 1978 0
8  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  L 9 183 0
9  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  G 249 1978 0
10  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  H 9 183 0
11  Protein   TYROSYL-DNA PHOSPHODIESTERASE 2  I 250 1984 0
12  Other macromolecule   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  J 9 183 0
13  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  A 27 0 108
14  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  B 25 0 100
15  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  C 1 0 8
16  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  D 4 0 20
17  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  E 24 0 96
18  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  F 2 0 12
19  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  K 17 0 68
20  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  L 1 0 8
21  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  G 14 0 56
22  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  H 4 0 17
23  Ligand   TYROSYL-DNA PHOSPHODIESTERASE 2  I 20 0 80
24  Ligand   DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')  J 2 0 12
25 Water     1040 0 1040
total       2733 12990 1625
Proteins
Unit 1 SER121 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Unit 2 SER121 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Unit 5 SER121 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Unit 7 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Unit 9 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Unit 11 SER121 SER122 THR123 ILE124 SER125 PHE126 ILE127 THR128 TRP129 ASN130 ILE131 ASP132 GLY133 LEU134 ASP135 GLY136 CYS137 ASN138 LEU139 PRO140 GLU141 ARG142 ALA143 ARG144 GLY145 VAL146 CYS147 SER148 CYS149 LEU150 ALA151 LEU152 TYR153 SER154 PRO155 ASP156 VAL157 VAL158 PHE159 LEU160 GLN161 GLU162 VAL163 ILE164 PRO165 PRO166 TYR167 CYS168 ALA169 TYR170 LEU171 LYS172 LYS173 ARG174 ALA175 ALA176 SER177 TYR178 THR179 ILE180 ILE181 THR182 GLY183 ASN184 GLU185 GLU186 GLY187 TYR188 PHE189 THR190 ALA191 ILE192 LEU193 LEU194 LYS195 LYS196 GLY197 ARG198 VAL199 LYS200 PHE201 LYS202 SER203 GLN204 GLU205 ILE206 ILE207 PRO208 PHE209 PRO210 ASN211 THR212 LYS213 MET214 MET215 ARG216 ASN217 LEU218 LEU219 CYS220 VAL221 ASN222 VAL223 SER224 LEU225 GLY226 GLY227 ASN228 GLU229 PHE230 CYS231 LEU232 MET233 THR234 SER235 HIS236 LEU237 GLU238 SER239 THR240 ARG241 GLU242 HIS243 SER244 ALA245 GLU246 ARG247 ILE248 ARG249 GLN250 LEU251 LYS252 THR253 VAL254 LEU255 GLY256 LYS257 MET258 GLN259 GLU260 ALA261 PRO262 ASP263 SER264 THR265 THR266 VAL267 ILE268 PHE269 ALA270 GLY271 ASP272 THR273 ASN274 LEU275 ARG276 ASP277 GLN278 GLU279 VAL280 ILE281 LYS282 CYS283 GLY284 GLY285 LEU286 PRO287 ASP288 ASN289 VAL290 PHE291 ASP292 ALA293 TRP294 GLU295 PHE296 LEU297 GLY298 LYS299 PRO300 LYS301 HIS302 CYS303 GLN304 TYR305 THR306 TRP307 ASP308 THR309 LYS310 ALA311 ASN312 ASN313 ASN314 LEU315 ARG316 ILE317 PRO318 ALA319 ALA320 TYR321 LYS322 HIS323 ARG324 PHE325 ASP326 ARG327 ILE328 PHE329 PHE330 ARG331 ALA332 GLU333 GLU334 GLY335 HIS336 LEU337 ILE338 PRO339 GLN340 SER341 LEU342 ASP343 LEU344 VAL345 GLY346 LEU347 GLU348 LYS349 LEU350 ASP351 CYS352 GLY353 ARG354 PHE355 PRO356 SER357 ASP358 HIS359 TRP360 GLY361 LEU362 LEU363 CYS364 THR365 LEU366 ASN367 VAL368 VAL369 LEU370
Other macromolecules
Unit 3 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Unit 4 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Unit 6 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Unit 8 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Unit 10 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Unit 12 DC2 DC3 DG4 DA5 DA6 DT7 DT8 DC9 DG10
Ligands
Unit 13 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 EDO412 EDO413 EDO414 EDO415 EDO416 EDO417 EDO418 EDO419 EDO420 EDO421 EDO422 ACT423 ACT424 ACT425 ACT426 ACT427
Unit 14 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 EDO412 EDO413 EDO414 EDO415 EDO416 EDO417 EDO418 EDO419 EDO420 EDO421 EDO422 ACT423 ACT424 ACT425
Unit 15 6AH101
Unit 16 6AH101 EDO102 EDO103 EDO104
Unit 17 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 EDO412 EDO413 EDO414 EDO415 EDO416 EDO417 EDO418 EDO419 EDO420 ACT421 ACT422 ACT423 ACT424
Unit 18 6AH101 EDO102
Unit 19 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 EDO412 EDO413 EDO414 ACT415 ACT416 ACT417
Unit 20 6AH101
Unit 21 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 ACT412 ACT413 ACT414
Unit 22 6AH101 EDO102 EDO103 EDO104
Unit 23 EDO401 EDO402 EDO403 EDO404 EDO405 EDO406 EDO407 EDO408 EDO409 EDO410 EDO411 EDO412 EDO413 EDO414 EDO415 EDO416 ACT417 ACT418 ACT419 ACT420
Unit 24 6AH101 EDO102
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany