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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF NAPHTHALENE 1,2-DIOXYGENASE FROM RHODOC
Keywords RIESKE NON-HEME IRON OXYGENASE, OXIDOREDUCTASE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   2B1X     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  A 441 3514 0
2  Protein   NAPHTHALENE DIOXYGENASE SMALL SUBUNIT  B 167 1340 0
3  Protein   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  C 441 3514 0
4  Protein   NAPHTHALENE DIOXYGENASE SMALL SUBUNIT  D 167 1340 0
5  Protein   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  E 441 3514 0
6  Protein   NAPHTHALENE DIOXYGENASE SMALL SUBUNIT  F 167 1340 0
7  Ligand   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  A 6 0 37
8  Ligand   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  C 5 0 29
9  Ligand   NAPHTHALENE DIOXYGENASE LARGE SUBUNIT  E 8 0 53
10 Water     1112 0 1112
total       2955 14562 1231
Proteins
Unit 1 MET1 LEU2 SER3 ASN4 GLU5 LEU6 ARG7 GLN8 THR9 LEU10 GLN11 LYS12 GLY13 LEU14 HIS15 ASP16 VAL17 ASN18 SER19 ASP20 TRP21 THR22 VAL23 PRO24 ALA25 ALA26 ILE27 ILE28 ASN29 ASP30 PRO31 GLU32 VAL33 HIS34 ASP35 VAL36 GLU37 ARG38 GLU39 ARG40 ILE41 PHE42 GLY43 HIS44 ALA45 TRP46 VAL47 PHE48 LEU49 ALA50 HIS51 GLU52 SER53 GLU54 ILE55 PRO56 GLU57 ARG58 GLY59 ASP60 TYR61 VAL62 VAL63 ARG64 TYR65 ILE66 SER67 GLU68 ASP69 GLN70 PHE71 ILE72 VAL73 CYS74 ARG75 ASP76 GLU77 GLY78 GLY79 GLU80 ILE81 ARG82 GLY83 HIS84 LEU85 ASN86 ALA87 CYS88 ARG89 HIS90 ARG91 GLY92 MET93 GLN94 VAL95 CYS96 ARG97 ALA98 GLU99 MET100 GLY101 ASN102 THR103 SER104 HIS105 PHE106 ARG107 CYS108 PRO109 TYR110 HIS111 GLY112 TRP113 THR114 TYR115 SER116 ASN117 THR118 GLY119 SER120 LEU121 VAL122 GLY123 VAL124 PRO125 ALA126 GLY127 LYS128 ASP129 ALA130 TYR131 GLY132 ASN133 GLN134 LEU135 LYS136 LYS137 SER138 ASP139 TRP140 ASN141 LEU142 ARG143 PRO144 MET145 PRO146 ASN147 LEU148 ALA149 SER150 TYR151 LYS152 GLY153 LEU154 ILE155 PHE156 GLY157 SER158 LEU159 ASP160 PRO161 HIS162 ALA163 ASP164 SER165 LEU166 GLU167 ASP168 TYR169 LEU170 GLY171 ASP172 LEU173 LYS174 PHE175 TYR176 LEU177 ASP178 ILE179 VAL180 LEU181 ASP182 ARG183 SER184 ASP185 ALA186 GLY187 LEU188 GLN189 VAL190 VAL191 GLY192 ALA193 PRO194 GLN195 ARG196 TRP197 VAL198 ILE199 ASP200 ALA201 ASN202 TRP203 LYS204 LEU205 GLY206 ALA207 ASP208 ASN209 PHE210 VAL211 GLY212 ASP213 ALA214 TYR215 HIS216 THR217 MET218 MET219 THR220 HIS221 ARG222 SER223 MET224 VAL225 GLU226 LEU227 GLY228 LEU229 ALA230 PRO231 PRO232 ASP233 PRO234 GLN235 PHE236 ALA237 LEU238 TYR239 GLY240 GLU241 HIS242 ILE243 HIS244 THR245 GLY246 HIS247 GLY248 HIS249 GLY250 LEU251 GLY252 ILE253 ILE254 GLY255 PRO256 PRO257 PRO258 GLY259 MET260 PRO261 LEU262 PRO263 GLU264 PHE265 MET266 GLY267 LEU268 PRO269 GLU270 ASN271 ILE272 VAL273 GLU274 GLU275 LEU276 GLU277 ARG278 ARG279 LEU280 THR281 PRO282 GLU283 GLN284 VAL285 GLU286 ILE287 PHE288 ARG289 PRO290 THR291 ALA292 PHE293 ILE294 HIS295 GLY296 THR297 VAL298 PHE299 PRO300 ASN301 LEU302 SER303 ILE304 GLY305 ASN306 PHE307 LEU308 MET309 GLY310 LYS311 ASP312 HIS313 LEU314 SER315 ALA316 PRO317 THR318 ALA319 PHE320 LEU321 THR322 LEU323 ARG324 LEU325 TRP326 HIS327 PRO328 LEU329 GLY330 PRO331 ASP332 LYS333 MET334 GLU335 VAL336 MET337 SER338 PHE339 PHE340 LEU341 VAL342 GLU343 LYS344 ASP345 ALA346 PRO347 ASP348 TRP349 PHE350 LYS351 ASP352 GLU353 SER354 TYR355 LYS356 SER357 TYR358 LEU359 ARG360 THR361 PHE362 GLY363 ILE364 SER365 GLY366 GLY367 PHE368 GLU369 GLN370 ASP371 ASP372 ALA373 GLU374 ASN375 TRP376 ARG377 SER378 ILE379 THR380 ARG381 VAL382 MET383 GLY384 GLY385 GLN386 PHE387 ALA388 LYS389 THR390 GLY391 GLU392 LEU393 ASN394 TYR395 GLN396 MET397 GLY398 ARG399 GLY400 VAL401 LEU402 GLU403 PRO404 ASP405 PRO406 ASN407 TRP408 THR409 GLY410 PRO411 GLY412 GLU413 ALA414 TYR415 PRO416 LEU417 ASP418 TYR419 ALA420 GLU421 ALA422 ASN423 GLN424 ARG425 ASN426 PHE427 LEU428 GLU429 TYR430 TRP431 MET432 GLN433 LEU434 MET435 LEU436 ALA437 GLU438 SER439 PRO440 LEU441
Unit 2 ARG513 VAL514 SER515 ASP516 THR517 THR518 VAL519 ARG520 GLU521 ILE522 THR523 GLU524 TRP525 LEU526 TYR527 MET528 GLU529 ALA530 GLU531 LEU532 LEU533 ASP534 ALA535 GLY536 LYS537 TYR538 ARG539 GLU540 TRP541 LEU542 ALA543 LEU544 VAL545 THR546 GLU547 ASP548 LEU549 SER550 TYR551 VAL552 VAL553 PRO554 ILE555 ARG556 VAL557 THR558 ARG559 GLU560 ARG561 GLU562 ALA563 VAL564 THR565 ASP566 VAL567 VAL568 GLU569 GLY570 MET571 THR572 HIS573 MET574 ASP575 ASP576 ASP577 ALA578 ASP579 SER580 MET581 GLU582 MET583 ARG584 VAL585 LEU586 ARG587 LEU588 GLU589 THR590 GLU591 TYR592 ALA593 TRP594 ALA595 GLU596 ASP597 PRO598 PRO599 SER600 ARG601 SER602 ARG603 HIS604 PHE605 VAL606 THR607 ASN608 VAL609 ARG610 VAL611 ALA612 THR613 GLY614 ASP615 SER616 GLU617 ASP618 GLU619 PHE620 LYS621 VAL622 THR623 SER624 ASN625 LEU626 LEU627 LEU628 TYR629 ARG630 THR631 ARG632 GLY633 ASP634 VAL635 ALA636 THR637 TYR638 ASP639 VAL640 LEU641 SER642 GLY643 GLU644 ARG645 THR646 ASP647 VAL648 LEU649 ARG650 ARG651 ALA652 GLY653 ASP654 SER655 PHE656 LEU657 MET658 ALA659 LYS660 ARG661 VAL662 VAL663 LEU664 LEU665 ASP666 GLN667 THR668 THR669 ILE670 MET671 THR672 HIS673 ASN674 LEU675 ALA676 LEU677 ILE678 MET679
Unit 3 MET1 LEU2 SER3 ASN4 GLU5 LEU6 ARG7 GLN8 THR9 LEU10 GLN11 LYS12 GLY13 LEU14 HIS15 ASP16 VAL17 ASN18 SER19 ASP20 TRP21 THR22 VAL23 PRO24 ALA25 ALA26 ILE27 ILE28 ASN29 ASP30 PRO31 GLU32 VAL33 HIS34 ASP35 VAL36 GLU37 ARG38 GLU39 ARG40 ILE41 PHE42 GLY43 HIS44 ALA45 TRP46 VAL47 PHE48 LEU49 ALA50 HIS51 GLU52 SER53 GLU54 ILE55 PRO56 GLU57 ARG58 GLY59 ASP60 TYR61 VAL62 VAL63 ARG64 TYR65 ILE66 SER67 GLU68 ASP69 GLN70 PHE71 ILE72 VAL73 CYS74 ARG75 ASP76 GLU77 GLY78 GLY79 GLU80 ILE81 ARG82 GLY83 HIS84 LEU85 ASN86 ALA87 CYS88 ARG89 HIS90 ARG91 GLY92 MET93 GLN94 VAL95 CYS96 ARG97 ALA98 GLU99 MET100 GLY101 ASN102 THR103 SER104 HIS105 PHE106 ARG107 CYS108 PRO109 TYR110 HIS111 GLY112 TRP113 THR114 TYR115 SER116 ASN117 THR118 GLY119 SER120 LEU121 VAL122 GLY123 VAL124 PRO125 ALA126 GLY127 LYS128 ASP129 ALA130 TYR131 GLY132 ASN133 GLN134 LEU135 LYS136 LYS137 SER138 ASP139 TRP140 ASN141 LEU142 ARG143 PRO144 MET145 PRO146 ASN147 LEU148 ALA149 SER150 TYR151 LYS152 GLY153 LEU154 ILE155 PHE156 GLY157 SER158 LEU159 ASP160 PRO161 HIS162 ALA163 ASP164 SER165 LEU166 GLU167 ASP168 TYR169 LEU170 GLY171 ASP172 LEU173 LYS174 PHE175 TYR176 LEU177 ASP178 ILE179 VAL180 LEU181 ASP182 ARG183 SER184 ASP185 ALA186 GLY187 LEU188 GLN189 VAL190 VAL191 GLY192 ALA193 PRO194 GLN195 ARG196 TRP197 VAL198 ILE199 ASP200 ALA201 ASN202 TRP203 LYS204 LEU205 GLY206 ALA207 ASP208 ASN209 PHE210 VAL211 GLY212 ASP213 ALA214 TYR215 HIS216 THR217 MET218 MET219 THR220 HIS221 ARG222 SER223 MET224 VAL225 GLU226 LEU227 GLY228 LEU229 ALA230 PRO231 PRO232 ASP233 PRO234 GLN235 PHE236 ALA237 LEU238 TYR239 GLY240 GLU241 HIS242 ILE243 HIS244 THR245 GLY246 HIS247 GLY248 HIS249 GLY250 LEU251 GLY252 ILE253 ILE254 GLY255 PRO256 PRO257 PRO258 GLY259 MET260 PRO261 LEU262 PRO263 GLU264 PHE265 MET266 GLY267 LEU268 PRO269 GLU270 ASN271 ILE272 VAL273 GLU274 GLU275 LEU276 GLU277 ARG278 ARG279 LEU280 THR281 PRO282 GLU283 GLN284 VAL285 GLU286 ILE287 PHE288 ARG289 PRO290 THR291 ALA292 PHE293 ILE294 HIS295 GLY296 THR297 VAL298 PHE299 PRO300 ASN301 LEU302 SER303 ILE304 GLY305 ASN306 PHE307 LEU308 MET309 GLY310 LYS311 ASP312 HIS313 LEU314 SER315 ALA316 PRO317 THR318 ALA319 PHE320 LEU321 THR322 LEU323 ARG324 LEU325 TRP326 HIS327 PRO328 LEU329 GLY330 PRO331 ASP332 LYS333 MET334 GLU335 VAL336 MET337 SER338 PHE339 PHE340 LEU341 VAL342 GLU343 LYS344 ASP345 ALA346 PRO347 ASP348 TRP349 PHE350 LYS351 ASP352 GLU353 SER354 TYR355 LYS356 SER357 TYR358 LEU359 ARG360 THR361 PHE362 GLY363 ILE364 SER365 GLY366 GLY367 PHE368 GLU369 GLN370 ASP371 ASP372 ALA373 GLU374 ASN375 TRP376 ARG377 SER378 ILE379 THR380 ARG381 VAL382 MET383 GLY384 GLY385 GLN386 PHE387 ALA388 LYS389 THR390 GLY391 GLU392 LEU393 ASN394 TYR395 GLN396 MET397 GLY398 ARG399 GLY400 VAL401 LEU402 GLU403 PRO404 ASP405 PRO406 ASN407 TRP408 THR409 GLY410 PRO411 GLY412 GLU413 ALA414 TYR415 PRO416 LEU417 ASP418 TYR419 ALA420 GLU421 ALA422 ASN423 GLN424 ARG425 ASN426 PHE427 LEU428 GLU429 TYR430 TRP431 MET432 GLN433 LEU434 MET435 LEU436 ALA437 GLU438 SER439 PRO440 LEU441
Unit 4 ARG513 VAL514 SER515 ASP516 THR517 THR518 VAL519 ARG520 GLU521 ILE522 THR523 GLU524 TRP525 LEU526 TYR527 MET528 GLU529 ALA530 GLU531 LEU532 LEU533 ASP534 ALA535 GLY536 LYS537 TYR538 ARG539 GLU540 TRP541 LEU542 ALA543 LEU544 VAL545 THR546 GLU547 ASP548 LEU549 SER550 TYR551 VAL552 VAL553 PRO554 ILE555 ARG556 VAL557 THR558 ARG559 GLU560 ARG561 GLU562 ALA563 VAL564 THR565 ASP566 VAL567 VAL568 GLU569 GLY570 MET571 THR572 HIS573 MET574 ASP575 ASP576 ASP577 ALA578 ASP579 SER580 MET581 GLU582 MET583 ARG584 VAL585 LEU586 ARG587 LEU588 GLU589 THR590 GLU591 TYR592 ALA593 TRP594 ALA595 GLU596 ASP597 PRO598 PRO599 SER600 ARG601 SER602 ARG603 HIS604 PHE605 VAL606 THR607 ASN608 VAL609 ARG610 VAL611 ALA612 THR613 GLY614 ASP615 SER616 GLU617 ASP618 GLU619 PHE620 LYS621 VAL622 THR623 SER624 ASN625 LEU626 LEU627 LEU628 TYR629 ARG630 THR631 ARG632 GLY633 ASP634 VAL635 ALA636 THR637 TYR638 ASP639 VAL640 LEU641 SER642 GLY643 GLU644 ARG645 THR646 ASP647 VAL648 LEU649 ARG650 ARG651 ALA652 GLY653 ASP654 SER655 PHE656 LEU657 MET658 ALA659 LYS660 ARG661 VAL662 VAL663 LEU664 LEU665 ASP666 GLN667 THR668 THR669 ILE670 MET671 THR672 HIS673 ASN674 LEU675 ALA676 LEU677 ILE678 MET679
Unit 5 MET1 LEU2 SER3 ASN4 GLU5 LEU6 ARG7 GLN8 THR9 LEU10 GLN11 LYS12 GLY13 LEU14 HIS15 ASP16 VAL17 ASN18 SER19 ASP20 TRP21 THR22 VAL23 PRO24 ALA25 ALA26 ILE27 ILE28 ASN29 ASP30 PRO31 GLU32 VAL33 HIS34 ASP35 VAL36 GLU37 ARG38 GLU39 ARG40 ILE41 PHE42 GLY43 HIS44 ALA45 TRP46 VAL47 PHE48 LEU49 ALA50 HIS51 GLU52 SER53 GLU54 ILE55 PRO56 GLU57 ARG58 GLY59 ASP60 TYR61 VAL62 VAL63 ARG64 TYR65 ILE66 SER67 GLU68 ASP69 GLN70 PHE71 ILE72 VAL73 CYS74 ARG75 ASP76 GLU77 GLY78 GLY79 GLU80 ILE81 ARG82 GLY83 HIS84 LEU85 ASN86 ALA87 CYS88 ARG89 HIS90 ARG91 GLY92 MET93 GLN94 VAL95 CYS96 ARG97 ALA98 GLU99 MET100 GLY101 ASN102 THR103 SER104 HIS105 PHE106 ARG107 CYS108 PRO109 TYR110 HIS111 GLY112 TRP113 THR114 TYR115 SER116 ASN117 THR118 GLY119 SER120 LEU121 VAL122 GLY123 VAL124 PRO125 ALA126 GLY127 LYS128 ASP129 ALA130 TYR131 GLY132 ASN133 GLN134 LEU135 LYS136 LYS137 SER138 ASP139 TRP140 ASN141 LEU142 ARG143 PRO144 MET145 PRO146 ASN147 LEU148 ALA149 SER150 TYR151 LYS152 GLY153 LEU154 ILE155 PHE156 GLY157 SER158 LEU159 ASP160 PRO161 HIS162 ALA163 ASP164 SER165 LEU166 GLU167 ASP168 TYR169 LEU170 GLY171 ASP172 LEU173 LYS174 PHE175 TYR176 LEU177 ASP178 ILE179 VAL180 LEU181 ASP182 ARG183 SER184 ASP185 ALA186 GLY187 LEU188 GLN189 VAL190 VAL191 GLY192 ALA193 PRO194 GLN195 ARG196 TRP197 VAL198 ILE199 ASP200 ALA201 ASN202 TRP203 LYS204 LEU205 GLY206 ALA207 ASP208 ASN209 PHE210 VAL211 GLY212 ASP213 ALA214 TYR215 HIS216 THR217 MET218 MET219 THR220 HIS221 ARG222 SER223 MET224 VAL225 GLU226 LEU227 GLY228 LEU229 ALA230 PRO231 PRO232 ASP233 PRO234 GLN235 PHE236 ALA237 LEU238 TYR239 GLY240 GLU241 HIS242 ILE243 HIS244 THR245 GLY246 HIS247 GLY248 HIS249 GLY250 LEU251 GLY252 ILE253 ILE254 GLY255 PRO256 PRO257 PRO258 GLY259 MET260 PRO261 LEU262 PRO263 GLU264 PHE265 MET266 GLY267 LEU268 PRO269 GLU270 ASN271 ILE272 VAL273 GLU274 GLU275 LEU276 GLU277 ARG278 ARG279 LEU280 THR281 PRO282 GLU283 GLN284 VAL285 GLU286 ILE287 PHE288 ARG289 PRO290 THR291 ALA292 PHE293 ILE294 HIS295 GLY296 THR297 VAL298 PHE299 PRO300 ASN301 LEU302 SER303 ILE304 GLY305 ASN306 PHE307 LEU308 MET309 GLY310 LYS311 ASP312 HIS313 LEU314 SER315 ALA316 PRO317 THR318 ALA319 PHE320 LEU321 THR322 LEU323 ARG324 LEU325 TRP326 HIS327 PRO328 LEU329 GLY330 PRO331 ASP332 LYS333 MET334 GLU335 VAL336 MET337 SER338 PHE339 PHE340 LEU341 VAL342 GLU343 LYS344 ASP345 ALA346 PRO347 ASP348 TRP349 PHE350 LYS351 ASP352 GLU353 SER354 TYR355 LYS356 SER357 TYR358 LEU359 ARG360 THR361 PHE362 GLY363 ILE364 SER365 GLY366 GLY367 PHE368 GLU369 GLN370 ASP371 ASP372 ALA373 GLU374 ASN375 TRP376 ARG377 SER378 ILE379 THR380 ARG381 VAL382 MET383 GLY384 GLY385 GLN386 PHE387 ALA388 LYS389 THR390 GLY391 GLU392 LEU393 ASN394 TYR395 GLN396 MET397 GLY398 ARG399 GLY400 VAL401 LEU402 GLU403 PRO404 ASP405 PRO406 ASN407 TRP408 THR409 GLY410 PRO411 GLY412 GLU413 ALA414 TYR415 PRO416 LEU417 ASP418 TYR419 ALA420 GLU421 ALA422 ASN423 GLN424 ARG425 ASN426 PHE427 LEU428 GLU429 TYR430 TRP431 MET432 GLN433 LEU434 MET435 LEU436 ALA437 GLU438 SER439 PRO440 LEU441
Unit 6 ARG513 VAL514 SER515 ASP516 THR517 THR518 VAL519 ARG520 GLU521 ILE522 THR523 GLU524 TRP525 LEU526 TYR527 MET528 GLU529 ALA530 GLU531 LEU532 LEU533 ASP534 ALA535 GLY536 LYS537 TYR538 ARG539 GLU540 TRP541 LEU542 ALA543 LEU544 VAL545 THR546 GLU547 ASP548 LEU549 SER550 TYR551 VAL552 VAL553 PRO554 ILE555 ARG556 VAL557 THR558 ARG559 GLU560 ARG561 GLU562 ALA563 VAL564 THR565 ASP566 VAL567 VAL568 GLU569 GLY570 MET571 THR572 HIS573 MET574 ASP575 ASP576 ASP577 ALA578 ASP579 SER580 MET581 GLU582 MET583 ARG584 VAL585 LEU586 ARG587 LEU588 GLU589 THR590 GLU591 TYR592 ALA593 TRP594 ALA595 GLU596 ASP597 PRO598 PRO599 SER600 ARG601 SER602 ARG603 HIS604 PHE605 VAL606 THR607 ASN608 VAL609 ARG610 VAL611 ALA612 THR613 GLY614 ASP615 SER616 GLU617 ASP618 GLU619 PHE620 LYS621 VAL622 THR623 SER624 ASN625 LEU626 LEU627 LEU628 TYR629 ARG630 THR631 ARG632 GLY633 ASP634 VAL635 ALA636 THR637 TYR638 ASP639 VAL640 LEU641 SER642 GLY643 GLU644 ARG645 THR646 ASP647 VAL648 LEU649 ARG650 ARG651 ALA652 GLY653 ASP654 SER655 PHE656 LEU657 MET658 ALA659 LYS660 ARG661 VAL662 VAL663 LEU664 LEU665 ASP666 GLN667 THR668 THR669 ILE670 MET671 THR672 HIS673 ASN674 LEU675 ALA676 LEU677 ILE678 MET679
Ligands
Unit 7 FES501 FE502 MPD1700 MPD1702 MPD1703 MPD1709
Unit 8 FES501 FE502 MPD1701 MPD1704 MPD1707
Unit 9 FES501 FE502 MPD1705 MPD1708 MPD1710 MPD1711 MPD1712 MPD1713
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany