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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF BIPHENYL 2,3-DIOXYGENASE FROM SPHINGOMO YANOIKUYAE B1 BOUND TO BIPHENYL
Keywords RIESKE OXYGENASE, OXIDOREDUCTASE, NON HEME IRON, DIOXYGENASE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2GBX     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  A 449 3566 0
2  Protein   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  B 170 1436 0
3  Protein   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  C 446 3547 0
4  Protein   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  D 170 1436 0
5  Protein   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  E 449 3566 0
6  Protein   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  F 170 1436 0
7  Ligand   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  A 3 0 17
8  Ligand   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  B 3 0 3
9  Ligand   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  C 3 0 17
10  Ligand   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  D 3 0 3
11  Ligand   BIPHENYL 2,3-DIOXYGENASE ALPHA SUBUNIT  E 3 0 17
12  Ligand   BIPHENYL 2,3-DIOXYGENASE BETA SUBUNIT  F 3 0 3
13 Water     187 0 187
total       2059 14987 247
Proteins
Unit 1 THR6 LEU7 VAL8 ASP9 THR10 VAL11 ASN12 ALA13 SER14 GLN15 SER16 ARG17 GLN18 VAL19 PHE20 TRP21 ASP22 GLU23 ASP24 VAL25 TYR26 ALA27 LEU28 GLU29 ILE30 GLU31 ARG32 ILE33 PHE34 SER35 ARG36 ALA37 TRP38 LEU39 MET40 LEU41 GLY42 HIS43 GLU44 SER45 LEU46 VAL47 PRO48 LYS49 PRO50 GLY51 ASP52 PHE53 ILE54 THR55 THR56 TYR57 MET58 ALA59 GLU60 ASP61 LYS62 VAL63 ILE64 LEU65 SER66 HIS67 GLN68 SER69 ASP70 GLY71 THR72 PHE73 ARG74 ALA75 PHE76 ILE77 ASN78 SER79 CYS80 SER81 HIS82 ARG83 GLY84 ASN85 GLN86 ILE87 CYS88 HIS89 ALA90 ASP91 SER92 GLY93 ASN94 ALA95 LYS96 ALA97 PHE98 VAL99 CYS100 ASN101 TYR102 HIS103 GLY104 TRP105 VAL106 PHE107 GLY108 GLN109 ASP110 GLY111 SER112 LEU113 VAL114 ASP115 VAL116 PRO117 LEU118 GLU119 SER120 ARG121 CYS122 TYR123 HIS124 ASN125 SER126 LEU127 ASP128 LYS129 GLN130 LYS131 LEU132 ALA133 ALA134 LYS135 SER136 VAL137 ARG138 VAL139 GLU140 THR141 TYR142 LYS143 GLY144 PHE145 ILE146 PHE147 GLY148 CYS149 HIS150 ASP151 PRO152 GLU153 ALA154 PRO155 SER156 LEU157 GLU158 ASP159 TYR160 LEU161 GLY162 GLU163 PHE164 ARG165 TYR166 TYR167 LEU168 ASP169 THR170 ILE171 TRP172 GLU173 GLY174 ALA175 GLY176 GLY177 GLY178 MET179 GLU180 LEU181 LEU182 GLY183 PRO184 PRO185 MET186 LYS187 SER188 LEU189 LEU190 GLN191 CYS192 ASN193 TRP194 LYS195 VAL196 PRO197 ALA198 GLU199 ASN200 PHE201 ILE202 GLY203 ASP204 GLY205 TYR206 HIS207 VAL208 GLY209 TRP210 THR211 HIS212 ALA213 ALA214 ALA215 LEU216 SER217 GLN218 ILE219 GLY220 GLY221 GLU222 LEU223 ALA224 GLY225 LEU226 ALA227 GLY228 ASN229 ARG230 ALA231 ASP232 ILE233 PRO234 PHE235 ASP236 ASP237 LEU238 GLY239 LEU240 GLN241 PHE242 THR243 THR244 ARG245 HIS246 GLY247 HIS248 GLY249 PHE250 GLY251 VAL252 ILE253 ASP254 ASN255 ALA256 ALA257 ALA258 GLY259 LEU260 HIS261 ILE262 LYS263 ARG264 GLU265 GLY266 TRP267 THR268 LYS269 PHE270 LEU271 GLU272 ASP273 THR274 ARG275 GLY276 GLU277 VAL278 ARG279 ARG280 LYS281 PHE282 GLY283 PRO284 GLU285 ARG286 GLU287 ARG288 LEU289 TYR290 LEU291 GLY292 HIS293 TRP294 ASN295 CYS296 SER297 ILE298 PHE299 PRO300 ASN301 CYS302 SER303 PHE304 LEU305 TYR306 GLY307 THR308 ASN309 THR310 PHE311 LYS312 ILE313 TRP314 HIS315 PRO316 ARG317 GLY318 PRO319 HIS320 GLU321 ILE322 GLU323 VAL324 TRP325 THR326 TYR327 THR328 ILE329 VAL330 PRO331 ARG332 ASP333 ALA334 ASP335 PRO336 ALA337 THR338 LYS339 SER340 MET341 ILE342 GLN343 ARG344 GLU345 ALA346 ILE347 ARG348 THR349 PHE350 GLY351 THR352 ALA353 GLY354 THR355 LEU356 GLU357 SER358 ASP359 ASP360 GLY361 GLU362 ASN363 MET364 SER365 SER366 ALA367 THR368 TYR369 ILE370 ASN371 ARG372 GLY373 VAL374 ILE375 THR376 ARG377 ASN378 GLY379 ARG380 MET381 ASN382 SER383 THR384 MET385 GLY386 VAL387 GLY388 TYR389 GLU390 GLY391 PRO392 HIS393 PRO394 VAL395 TYR396 PRO397 GLY398 ILE399 VAL400 GLY401 ILE402 SER403 PHE404 ILE405 GLY406 GLU407 THR408 SER409 TYR410 ARG411 GLY412 PHE413 TYR414 ARG415 PHE416 TRP417 LYS418 GLU419 MET420 ILE421 ASP422 ALA423 PRO424 ASP425 TRP426 ALA427 SER428 VAL429 LYS430 ALA431 ASN432 ASP433 ASP434 THR435 TRP436 ASP437 SER438 VAL439 PHE440 PRO441 ASN442 ARG443 ASN444 PHE445 TRP446 ASN447 GLU448 LYS449 LEU450 ASN451 ALA452 ALA453 GLU454
Unit 2 GLN5 ILE6 PRO7 VAL8 THR9 PRO10 ASP11 VAL12 HIS13 TYR14 ASP15 ILE16 GLU17 ALA18 HIS19 TYR20 ARG21 ALA22 GLU23 VAL24 ARG25 MET26 PHE27 GLN28 THR29 GLY30 GLN31 TYR32 ARG33 GLU34 TRP35 LEU36 GLN37 GLY38 MET39 VAL40 ALA41 GLU42 ASP43 ILE44 HIS45 TYR46 TRP47 MET48 PRO49 ILE50 TYR51 GLU52 GLN53 ARG54 LEU55 THR56 ARG57 ASP58 ARG59 ARG60 PRO61 ASP62 PRO63 THR64 PRO65 ASP66 ASP67 ALA68 ALA69 ILE70 TYR71 ASN72 ASP73 ASP74 PHE75 GLY76 GLU77 LEU78 LYS79 GLN80 ARG81 VAL82 GLU83 ARG84 LEU85 TYR86 SER87 GLY88 GLN89 VAL90 TRP91 MET92 GLU93 ASP94 PRO95 PRO96 SER97 LYS98 ILE99 ARG100 TYR101 PHE102 VAL103 SER104 ASN105 VAL106 GLU107 ALA108 PHE109 GLU110 ALA111 GLY112 ASN113 GLY114 GLU115 LEU116 ASP117 VAL118 LEU119 SER120 ASN121 ILE122 LEU123 VAL124 TYR125 ARG126 ASN127 ARG128 ARG129 GLN130 THR131 GLU132 VAL133 THR134 VAL135 HIS136 THR137 LEU138 GLY139 ARG140 GLU141 ASP142 LYS143 LEU144 ARG145 ARG146 ASP147 GLY148 ASN149 GLY150 PHE151 LYS152 VAL153 PHE154 ARG155 ARG156 LYS157 LEU158 ILE159 LEU160 ASP161 ALA162 ARG163 VAL164 THR165 GLN166 ASP167 LYS168 ASN169 LEU170 TYR171 PHE172 PHE173 CYS174
Unit 3 THR6 LEU7 VAL8 ASP9 THR10 VAL11 ASN12 ALA13 SER14 GLN15 SER16 ARG17 GLN18 VAL19 PHE20 TRP21 ASP22 GLU23 ASP24 VAL25 TYR26 ALA27 LEU28 GLU29 ILE30 GLU31 ARG32 ILE33 PHE34 SER35 ARG36 ALA37 TRP38 LEU39 MET40 LEU41 GLY42 HIS43 GLU44 SER45 LEU46 VAL47 PRO48 LYS49 PRO50 GLY51 ASP52 PHE53 ILE54 THR55 THR56 TYR57 MET58 ALA59 GLU60 ASP61 LYS62 VAL63 ILE64 LEU65 SER66 HIS67 GLN68 SER69 ASP70 GLY71 THR72 PHE73 ARG74 ALA75 PHE76 ILE77 ASN78 SER79 CYS80 SER81 HIS82 ARG83 GLY84 ASN85 GLN86 ILE87 CYS88 HIS89 ALA90 ASP91 SER92 GLY93 ASN94 ALA95 LYS96 ALA97 PHE98 VAL99 CYS100 ASN101 TYR102 HIS103 GLY104 TRP105 VAL106 PHE107 GLY108 GLN109 ASP110 GLY111 SER112 LEU113 VAL114 ASP115 VAL116 PRO117 LEU118 GLU119 SER120 ARG121 CYS122 TYR123 HIS124 ASN125 SER126 LEU127 ASP128 LYS129 GLN130 LYS131 LEU132 ALA133 ALA134 LYS135 SER136 VAL137 ARG138 VAL139 GLU140 THR141 TYR142 LYS143 GLY144 PHE145 ILE146 PHE147 GLY148 CYS149 HIS150 ASP151 PRO152 GLU153 ALA154 PRO155 SER156 LEU157 GLU158 ASP159 TYR160 LEU161 GLY162 GLU163 PHE164 ARG165 TYR166 TYR167 LEU168 ASP169 THR170 ILE171 TRP172 GLU173 GLY174 ALA175 GLY176 GLY177 GLY178 MET179 GLU180 LEU181 LEU182 GLY183 PRO184 PRO185 MET186 LYS187 SER188 LEU189 LEU190 GLN191 CYS192 ASN193 TRP194 LYS195 VAL196 PRO197 ALA198 GLU199 ASN200 PHE201 ILE202 GLY203 ASP204 GLY205 TYR206 HIS207 VAL208 GLY209 TRP210 THR211 HIS212 ALA213 ALA214 ALA215 LEU216 SER217 GLN218 ILE219 GLY220 GLY221 GLU222 LEU223 ALA224 GLY225 LEU226 ALA227 GLY228 ASN229 ARG230 ALA231 ASP232 ILE233 PRO234 PHE235 ASP236 ASP237 LEU238 GLY239 LEU240 GLN241 PHE242 THR243 THR244 ARG245 HIS246 GLY247 HIS248 GLY249 PHE250 GLY251 VAL252 ILE253 ASP254 ASN255 ALA256 ALA257 ALA258 GLY259 LEU260 HIS261 ILE262 LYS263 ARG264 GLU265 GLY266 TRP267 THR268 LYS269 PHE270 LEU271 GLU272 ASP273 THR274 ARG275 GLY276 GLU277 VAL278 ARG279 ARG280 LYS281 PHE282 GLY283 PRO284 GLU285 ARG286 GLU287 ARG288 LEU289 TYR290 LEU291 GLY292 HIS293 TRP294 ASN295 CYS296 SER297 ILE298 PHE299 PRO300 ASN301 CYS302 SER303 PHE304 LEU305 TYR306 GLY307 THR308 ASN309 THR310 PHE311 LYS312 ILE313 TRP314 HIS315 PRO316 ARG317 GLY318 PRO319 HIS320 GLU321 ILE322 GLU323 VAL324 TRP325 THR326 TYR327 THR328 ILE329 VAL330 PRO331 ARG332 ASP333 ALA334 ASP335 PRO336 ALA337 THR338 LYS339 SER340 MET341 ILE342 GLN343 ARG344 GLU345 ALA346 ILE347 ARG348 THR349 PHE350 GLY351 THR352 ALA353 GLY354 THR355 LEU356 GLU357 SER358 ASP359 ASP360 GLY361 GLU362 ASN363 MET364 SER365 SER366 ALA367 THR368 TYR369 ILE370 ASN371 ARG372 GLY373 VAL374 ILE375 THR376 ARG377 ASN378 GLY379 ARG380 MET381 ASN382 SER383 THR384 MET385 GLY386 VAL387 GLY388 TYR389 GLU390 GLY391 PRO392 HIS393 PRO394 VAL395 TYR396 PRO397 GLY398 ILE399 VAL400 GLY401 ILE402 SER403 PHE404 ILE405 GLY406 GLU407 THR408 SER409 TYR410 ARG411 GLY412 PHE413 TYR414 ARG415 PHE416 TRP417 LYS418 GLU419 MET420 ILE421 ASP422 ALA423 PRO424 ASP425 TRP426 ALA427 SER428 VAL429 LYS430 ALA431 ASN432 ASP433 ASP434 THR435 TRP436 ASP437 SER438 VAL439 PHE440 PRO441 ASN442 ARG443 ASN444 PHE445 TRP446 ASN447 GLU448 LYS449 LEU450 ASN451
Unit 4 GLN5 ILE6 PRO7 VAL8 THR9 PRO10 ASP11 VAL12 HIS13 TYR14 ASP15 ILE16 GLU17 ALA18 HIS19 TYR20 ARG21 ALA22 GLU23 VAL24 ARG25 MET26 PHE27 GLN28 THR29 GLY30 GLN31 TYR32 ARG33 GLU34 TRP35 LEU36 GLN37 GLY38 MET39 VAL40 ALA41 GLU42 ASP43 ILE44 HIS45 TYR46 TRP47 MET48 PRO49 ILE50 TYR51 GLU52 GLN53 ARG54 LEU55 THR56 ARG57 ASP58 ARG59 ARG60 PRO61 ASP62 PRO63 THR64 PRO65 ASP66 ASP67 ALA68 ALA69 ILE70 TYR71 ASN72 ASP73 ASP74 PHE75 GLY76 GLU77 LEU78 LYS79 GLN80 ARG81 VAL82 GLU83 ARG84 LEU85 TYR86 SER87 GLY88 GLN89 VAL90 TRP91 MET92 GLU93 ASP94 PRO95 PRO96 SER97 LYS98 ILE99 ARG100 TYR101 PHE102 VAL103 SER104 ASN105 VAL106 GLU107 ALA108 PHE109 GLU110 ALA111 GLY112 ASN113 GLY114 GLU115 LEU116 ASP117 VAL118 LEU119 SER120 ASN121 ILE122 LEU123 VAL124 TYR125 ARG126 ASN127 ARG128 ARG129 GLN130 THR131 GLU132 VAL133 THR134 VAL135 HIS136 THR137 LEU138 GLY139 ARG140 GLU141 ASP142 LYS143 LEU144 ARG145 ARG146 ASP147 GLY148 ASN149 GLY150 PHE151 LYS152 VAL153 PHE154 ARG155 ARG156 LYS157 LEU158 ILE159 LEU160 ASP161 ALA162 ARG163 VAL164 THR165 GLN166 ASP167 LYS168 ASN169 LEU170 TYR171 PHE172 PHE173 CYS174
Unit 5 THR6 LEU7 VAL8 ASP9 THR10 VAL11 ASN12 ALA13 SER14 GLN15 SER16 ARG17 GLN18 VAL19 PHE20 TRP21 ASP22 GLU23 ASP24 VAL25 TYR26 ALA27 LEU28 GLU29 ILE30 GLU31 ARG32 ILE33 PHE34 SER35 ARG36 ALA37 TRP38 LEU39 MET40 LEU41 GLY42 HIS43 GLU44 SER45 LEU46 VAL47 PRO48 LYS49 PRO50 GLY51 ASP52 PHE53 ILE54 THR55 THR56 TYR57 MET58 ALA59 GLU60 ASP61 LYS62 VAL63 ILE64 LEU65 SER66 HIS67 GLN68 SER69 ASP70 GLY71 THR72 PHE73 ARG74 ALA75 PHE76 ILE77 ASN78 SER79 CYS80 SER81 HIS82 ARG83 GLY84 ASN85 GLN86 ILE87 CYS88 HIS89 ALA90 ASP91 SER92 GLY93 ASN94 ALA95 LYS96 ALA97 PHE98 VAL99 CYS100 ASN101 TYR102 HIS103 GLY104 TRP105 VAL106 PHE107 GLY108 GLN109 ASP110 GLY111 SER112 LEU113 VAL114 ASP115 VAL116 PRO117 LEU118 GLU119 SER120 ARG121 CYS122 TYR123 HIS124 ASN125 SER126 LEU127 ASP128 LYS129 GLN130 LYS131 LEU132 ALA133 ALA134 LYS135 SER136 VAL137 ARG138 VAL139 GLU140 THR141 TYR142 LYS143 GLY144 PHE145 ILE146 PHE147 GLY148 CYS149 HIS150 ASP151 PRO152 GLU153 ALA154 PRO155 SER156 LEU157 GLU158 ASP159 TYR160 LEU161 GLY162 GLU163 PHE164 ARG165 TYR166 TYR167 LEU168 ASP169 THR170 ILE171 TRP172 GLU173 GLY174 ALA175 GLY176 GLY177 GLY178 MET179 GLU180 LEU181 LEU182 GLY183 PRO184 PRO185 MET186 LYS187 SER188 LEU189 LEU190 GLN191 CYS192 ASN193 TRP194 LYS195 VAL196 PRO197 ALA198 GLU199 ASN200 PHE201 ILE202 GLY203 ASP204 GLY205 TYR206 HIS207 VAL208 GLY209 TRP210 THR211 HIS212 ALA213 ALA214 ALA215 LEU216 SER217 GLN218 ILE219 GLY220 GLY221 GLU222 LEU223 ALA224 GLY225 LEU226 ALA227 GLY228 ASN229 ARG230 ALA231 ASP232 ILE233 PRO234 PHE235 ASP236 ASP237 LEU238 GLY239 LEU240 GLN241 PHE242 THR243 THR244 ARG245 HIS246 GLY247 HIS248 GLY249 PHE250 GLY251 VAL252 ILE253 ASP254 ASN255 ALA256 ALA257 ALA258 GLY259 LEU260 HIS261 ILE262 LYS263 ARG264 GLU265 GLY266 TRP267 THR268 LYS269 PHE270 LEU271 GLU272 ASP273 THR274 ARG275 GLY276 GLU277 VAL278 ARG279 ARG280 LYS281 PHE282 GLY283 PRO284 GLU285 ARG286 GLU287 ARG288 LEU289 TYR290 LEU291 GLY292 HIS293 TRP294 ASN295 CYS296 SER297 ILE298 PHE299 PRO300 ASN301 CYS302 SER303 PHE304 LEU305 TYR306 GLY307 THR308 ASN309 THR310 PHE311 LYS312 ILE313 TRP314 HIS315 PRO316 ARG317 GLY318 PRO319 HIS320 GLU321 ILE322 GLU323 VAL324 TRP325 THR326 TYR327 THR328 ILE329 VAL330 PRO331 ARG332 ASP333 ALA334 ASP335 PRO336 ALA337 THR338 LYS339 SER340 MET341 ILE342 GLN343 ARG344 GLU345 ALA346 ILE347 ARG348 THR349 PHE350 GLY351 THR352 ALA353 GLY354 THR355 LEU356 GLU357 SER358 ASP359 ASP360 GLY361 GLU362 ASN363 MET364 SER365 SER366 ALA367 THR368 TYR369 ILE370 ASN371 ARG372 GLY373 VAL374 ILE375 THR376 ARG377 ASN378 GLY379 ARG380 MET381 ASN382 SER383 THR384 MET385 GLY386 VAL387 GLY388 TYR389 GLU390 GLY391 PRO392 HIS393 PRO394 VAL395 TYR396 PRO397 GLY398 ILE399 VAL400 GLY401 ILE402 SER403 PHE404 ILE405 GLY406 GLU407 THR408 SER409 TYR410 ARG411 GLY412 PHE413 TYR414 ARG415 PHE416 TRP417 LYS418 GLU419 MET420 ILE421 ASP422 ALA423 PRO424 ASP425 TRP426 ALA427 SER428 VAL429 LYS430 ALA431 ASN432 ASP433 ASP434 THR435 TRP436 ASP437 SER438 VAL439 PHE440 PRO441 ASN442 ARG443 ASN444 PHE445 TRP446 ASN447 GLU448 LYS449 LEU450 ASN451 ALA452 ALA453 GLU454
Unit 6 GLN5 ILE6 PRO7 VAL8 THR9 PRO10 ASP11 VAL12 HIS13 TYR14 ASP15 ILE16 GLU17 ALA18 HIS19 TYR20 ARG21 ALA22 GLU23 VAL24 ARG25 MET26 PHE27 GLN28 THR29 GLY30 GLN31 TYR32 ARG33 GLU34 TRP35 LEU36 GLN37 GLY38 MET39 VAL40 ALA41 GLU42 ASP43 ILE44 HIS45 TYR46 TRP47 MET48 PRO49 ILE50 TYR51 GLU52 GLN53 ARG54 LEU55 THR56 ARG57 ASP58 ARG59 ARG60 PRO61 ASP62 PRO63 THR64 PRO65 ASP66 ASP67 ALA68 ALA69 ILE70 TYR71 ASN72 ASP73 ASP74 PHE75 GLY76 GLU77 LEU78 LYS79 GLN80 ARG81 VAL82 GLU83 ARG84 LEU85 TYR86 SER87 GLY88 GLN89 VAL90 TRP91 MET92 GLU93 ASP94 PRO95 PRO96 SER97 LYS98 ILE99 ARG100 TYR101 PHE102 VAL103 SER104 ASN105 VAL106 GLU107 ALA108 PHE109 GLU110 ALA111 GLY112 ASN113 GLY114 GLU115 LEU116 ASP117 VAL118 LEU119 SER120 ASN121 ILE122 LEU123 VAL124 TYR125 ARG126 ASN127 ARG128 ARG129 GLN130 THR131 GLU132 VAL133 THR134 VAL135 HIS136 THR137 LEU138 GLY139 ARG140 GLU141 ASP142 LYS143 LEU144 ARG145 ARG146 ASP147 GLY148 ASN149 GLY150 PHE151 LYS152 VAL153 PHE154 ARG155 ARG156 LYS157 LEU158 ILE159 LEU160 ASP161 ALA162 ARG163 VAL164 THR165 GLN166 ASP167 LYS168 ASN169 LEU170 TYR171 PHE172 PHE173 CYS174
Ligands
Unit 7 FES455 FE456 BNL457
Unit 8 ZN460 ZN464 ZN468
Unit 9 FES455 FE456 BNL458
Unit 10 ZN462 ZN465 ZN469
Unit 11 FES455 FE456 BNL459
Unit 12 ZN463 ZN466 ZN467
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany