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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURE OF PURPLE ACID PHOSPHATASE PPD1 ISOLATED FROM YELL (LUPINUS LUTEUS) SEEDS
Keywords THREE-DOMAIN HEME-CU NITRITE REDUCTASE, ELECTRON TRANSFER, OXIDOREDUCTASE, PROTON CHANNEL, DENITRIFICATION
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3ZK4     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  A 569 4544 0
2  Protein   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  B 571 4558 0
3  Protein   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  C 568 4534 0
4  Ligand    D 2 0 28
5  Ligand    E 2 0 28
6  Ligand    F 2 0 28
7  Ligand    G 2 0 28
8  Ligand    H 2 0 28
9  Ligand    I 3 0 38
10  Ligand    J 2 0 28
11  Ligand    K 3 0 38
12  Ligand   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  A 8 0 53
13  Ligand   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  B 5 0 35
14  Ligand   DIPHOSPHONUCLEOTIDE PHOSPHATASE 1  C 7 0 55
15 Water     2543 0 2543
total       4289 13636 2930
Proteins
Unit 1 HIS22 ALA23 TYR24 ILE25 LYS26 ALA27 THR28 PRO29 ASN30 VAL31 LEU32 GLY33 PHE34 GLU35 GLY36 HIS37 TYR38 THR39 GLU40 TRP41 VAL42 THR43 LEU44 GLN45 TYR46 SER47 ASN48 ASN49 LYS50 PRO51 SER52 ILE53 ASP54 ASP55 TRP56 ILE57 GLY58 VAL59 PHE60 SER61 PRO62 ALA63 ASN64 PHE65 SER66 ALA67 SER68 THR69 CYS70 PRO71 GLY72 GLU73 ASN74 LYS75 MET76 THR77 ASN78 PRO79 PRO80 PHE81 LEU82 CYS83 SER84 ALA85 PRO86 ILE87 LYS88 PHE89 GLN90 TYR91 ALA92 ASN93 PHE94 SER95 SER96 HIS97 SER98 TYR99 LYS100 ASP101 THR102 GLY103 LYS104 GLY105 SER106 LEU107 LYS108 LEU109 GLN110 LEU111 ILE112 ASN113 GLN114 ARG115 SER116 ASP117 PHE118 SER119 PHE120 ALA121 LEU122 PHE123 THR124 GLY125 GLY126 LEU127 THR128 ASN129 PRO130 LYS131 LEU132 ILE133 ALA134 VAL135 SER136 ASN137 LYS138 VAL139 SER140 PHE141 VAL142 ASN143 PRO144 ASN145 ALA146 PRO147 VAL148 TYR149 PRO150 ARG151 LEU152 ALA153 GLN154 GLY155 LYS156 THR157 TRP158 ASP159 GLU160 ILE161 THR162 VAL163 THR164 TRP165 THR166 SER167 GLY168 TYR169 ASP170 ILE171 ASN172 ASP173 ALA174 GLU175 PRO176 PHE177 VAL178 GLU179 TRP180 GLY181 PRO182 LYS183 GLU184 GLY185 ASN186 LEU187 VAL188 LYS189 THR190 PRO191 ALA192 GLY193 THR194 LEU195 THR196 PHE197 ASP198 ARG199 ASN200 THR201 MET202 CYS203 GLY204 ALA205 PRO206 ALA207 ARG208 THR209 VAL210 GLY211 TRP212 ARG213 ASP214 PRO215 GLY216 TYR217 ILE218 HIS219 THR220 SER221 PHE222 LEU223 LYS224 GLU225 LEU226 TRP227 PRO228 ASN229 ARG230 GLU231 TYR232 THR233 TYR234 LYS235 LEU236 GLY237 HIS238 ARG239 LEU240 PHE241 ASN242 GLY243 THR244 THR245 ILE246 TRP247 SER248 LYS249 GLU250 TYR251 HIS252 PHE253 LYS254 ALA255 SER256 PRO257 TYR258 PRO259 GLY260 GLN261 SER262 SER263 VAL264 GLN265 ARG266 VAL267 VAL268 ILE269 PHE270 GLY271 ASP272 MET273 GLY274 LYS275 ALA276 GLU277 ALA278 ASP279 GLY280 SER281 ASN282 GLU283 TYR284 ASN285 ASN286 PHE287 GLN288 PRO289 GLY290 SER291 LEU292 ASN293 THR294 THR295 LYS296 GLN297 ILE298 ILE299 GLN300 ASP301 LEU302 GLU303 ASP304 ILE305 ASP306 ILE307 VAL308 PHE309 HIS310 ILE311 GLY312 ASP313 LEU314 CYS315 TYR316 ALA317 ASN318 GLY319 TYR320 ILE321 SER322 GLN323 TRP324 ASP325 GLN326 PHE327 THR328 ALA329 GLN330 ILE331 GLU332 PRO333 ILE334 ALA335 SER336 THR337 VAL338 PRO339 TYR340 MET341 THR342 ALA343 SER344 GLY345 ASN346 HIS347 GLU348 ARG349 ASP350 TRP351 PRO352 GLY353 THR354 GLY355 SER356 PHE357 TYR358 GLY359 ASN360 LEU361 ASP362 SER363 GLY364 GLY365 GLU366 CYS367 GLY368 VAL369 PRO370 ALA371 GLN372 THR373 MET374 PHE375 PHE376 VAL377 PRO378 ALA379 GLU380 ASN381 ARG382 GLU383 LYS384 PHE385 TRP386 TYR387 SER388 THR389 ASP390 TYR391 GLY392 MET393 PHE394 ARG395 PHE396 CYS397 ILE398 ALA399 HIS400 THR401 GLU402 LEU403 ASP404 TRP405 ARG406 LYS407 GLY408 THR409 GLU410 GLN411 TYR412 GLU413 PHE414 ILE415 GLU416 LYS417 CYS418 LEU419 ALA420 SER421 VAL422 ASP423 ARG424 GLN425 LYS426 GLN427 PRO428 TRP429 LEU430 ILE431 PHE432 LEU433 ALA434 HIS435 ARG436 VAL437 LEU438 GLY439 TYR440 SER441 SER442 ALA443 GLY444 PHE445 TYR446 VAL447 GLN448 GLU449 GLY450 SER451 PHE452 GLU453 GLU454 PRO455 MET456 GLY457 ARG458 GLU459 ASP460 LEU461 GLN462 HIS463 LEU464 TRP465 GLN466 LYS467 TYR468 LYS469 VAL470 ASP471 ILE472 ALA473 MET474 TYR475 GLY476 HIS477 VAL478 HIS479 ASN480 TYR481 GLU482 ARG483 THR484 CYS485 PRO486 ILE487 TYR488 GLN489 ASN490 VAL491 CYS492 THR493 ASN494 LYS495 GLU496 LYS497 HIS498 ASN499 TYR500 LYS501 GLY502 ASN503 LEU504 ASN505 GLY506 THR507 ILE508 HIS509 VAL510 VAL511 VAL512 GLY513 GLY514 GLY515 GLY516 ALA517 SER518 LEU519 ALA520 GLU521 PHE522 ALA523 PRO524 ILE525 ASN526 THR527 THR528 TRP529 SER530 ILE531 PHE532 LYS533 ASP534 HIS535 ASP536 PHE537 GLY538 PHE539 VAL540 LYS541 LEU542 THR543 ALA544 PHE545 ASP546 HIS547 SER548 ASN549 LEU550 LEU551 LEU552 GLU553 TYR554 ARG555 LYS556 SER557 SER558 ASP559 GLY560 GLN561 VAL562 TYR563 ASP564 SER565 PHE566 THR567 ILE568 SER569 ARG570 ASP571 TYR572 ARG573 ASP574 ILE575 LEU576 ALA577 CYS578 SER579 VAL580 ASP581 SER582 CYS583 PRO584 THR585 THR586 THR587 LEU588 ALA589 SER590
Unit 2 ASP20 GLU21 HIS22 ALA23 TYR24 ILE25 LYS26 ALA27 THR28 PRO29 ASN30 VAL31 LEU32 GLY33 PHE34 GLU35 GLY36 HIS37 TYR38 THR39 GLU40 TRP41 VAL42 THR43 LEU44 GLN45 TYR46 SER47 ASN48 ASN49 LYS50 PRO51 SER52 ILE53 ASP54 ASP55 TRP56 ILE57 GLY58 VAL59 PHE60 SER61 PRO62 ALA63 ASN64 PHE65 SER66 ALA67 SER68 THR69 CYS70 PRO71 GLY72 GLU73 ASN74 LYS75 MET76 THR77 ASN78 PRO79 PRO80 PHE81 LEU82 CYS83 SER84 ALA85 PRO86 ILE87 LYS88 PHE89 GLN90 TYR91 ALA92 ASN93 PHE94 SER95 SER96 HIS97 SER98 TYR99 LYS100 ASP101 THR102 GLY103 LYS104 GLY105 SER106 LEU107 LYS108 LEU109 GLN110 LEU111 ILE112 ASN113 GLN114 ARG115 SER116 ASP117 PHE118 SER119 PHE120 ALA121 LEU122 PHE123 THR124 GLY125 GLY126 LEU127 THR128 ASN129 PRO130 LYS131 LEU132 ILE133 ALA134 VAL135 SER136 ASN137 LYS138 VAL139 SER140 PHE141 VAL142 ASN143 PRO144 ASN145 ALA146 PRO147 VAL148 TYR149 PRO150 ARG151 LEU152 ALA153 GLN154 GLY155 LYS156 THR157 TRP158 ASP159 GLU160 ILE161 THR162 VAL163 THR164 TRP165 THR166 SER167 GLY168 TYR169 ASP170 ILE171 ASN172 ASP173 ALA174 GLU175 PRO176 PHE177 VAL178 GLU179 TRP180 GLY181 PRO182 LYS183 GLU184 GLY185 ASN186 LEU187 VAL188 LYS189 THR190 PRO191 ALA192 GLY193 THR194 LEU195 THR196 PHE197 ASP198 ARG199 ASN200 THR201 MET202 CYS203 GLY204 ALA205 PRO206 ALA207 ARG208 THR209 VAL210 GLY211 TRP212 ARG213 ASP214 PRO215 GLY216 TYR217 ILE218 HIS219 THR220 SER221 PHE222 LEU223 LYS224 GLU225 LEU226 TRP227 PRO228 ASN229 ARG230 GLU231 TYR232 THR233 TYR234 LYS235 LEU236 GLY237 HIS238 ARG239 LEU240 PHE241 ASN242 GLY243 THR244 THR245 ILE246 TRP247 SER248 LYS249 GLU250 TYR251 HIS252 PHE253 LYS254 ALA255 SER256 PRO257 TYR258 PRO259 GLY260 GLN261 SER262 SER263 VAL264 GLN265 ARG266 VAL267 VAL268 ILE269 PHE270 GLY271 ASP272 MET273 GLY274 LYS275 ALA276 GLU277 ALA278 ASP279 GLY280 SER281 ASN282 GLU283 TYR284 ASN285 ASN286 PHE287 GLN288 PRO289 GLY290 SER291 LEU292 ASN293 THR294 THR295 LYS296 GLN297 ILE298 ILE299 GLN300 ASP301 LEU302 GLU303 ASP304 ILE305 ASP306 ILE307 VAL308 PHE309 HIS310 ILE311 GLY312 ASP313 LEU314 CYS315 TYR316 ALA317 ASN318 GLY319 TYR320 ILE321 SER322 GLN323 TRP324 ASP325 GLN326 PHE327 THR328 ALA329 GLN330 ILE331 GLU332 PRO333 ILE334 ALA335 SER336 THR337 VAL338 PRO339 TYR340 MET341 THR342 ALA343 SER344 GLY345 ASN346 HIS347 GLU348 ARG349 ASP350 TRP351 PRO352 GLY353 THR354 GLY355 SER356 PHE357 TYR358 GLY359 ASN360 LEU361 ASP362 SER363 GLY364 GLY365 GLU366 CYS367 GLY368 VAL369 PRO370 ALA371 GLN372 THR373 MET374 PHE375 PHE376 VAL377 PRO378 ALA379 GLU380 ASN381 ARG382 GLU383 LYS384 PHE385 TRP386 TYR387 SER388 THR389 ASP390 TYR391 GLY392 MET393 PHE394 ARG395 PHE396 CYS397 ILE398 ALA399 HIS400 THR401 GLU402 LEU403 ASP404 TRP405 ARG406 LYS407 GLY408 THR409 GLU410 GLN411 TYR412 GLU413 PHE414 ILE415 GLU416 LYS417 CYS418 LEU419 ALA420 SER421 VAL422 ASP423 ARG424 GLN425 LYS426 GLN427 PRO428 TRP429 LEU430 ILE431 PHE432 LEU433 ALA434 HIS435 ARG436 VAL437 LEU438 GLY439 TYR440 SER441 SER442 ALA443 GLY444 PHE445 TYR446 VAL447 GLN448 GLU449 GLY450 SER451 PHE452 GLU453 GLU454 PRO455 MET456 GLY457 ARG458 GLU459 ASP460 LEU461 GLN462 HIS463 LEU464 TRP465 GLN466 LYS467 TYR468 LYS469 VAL470 ASP471 ILE472 ALA473 MET474 TYR475 GLY476 HIS477 VAL478 HIS479 ASN480 TYR481 GLU482 ARG483 THR484 CYS485 PRO486 ILE487 TYR488 GLN489 ASN490 VAL491 CYS492 THR493 ASN494 LYS495 GLU496 LYS497 HIS498 ASN499 TYR500 LYS501 GLY502 ASN503 LEU504 ASN505 GLY506 THR507 ILE508 HIS509 VAL510 VAL511 VAL512 GLY513 GLY514 GLY515 GLY516 ALA517 SER518 LEU519 ALA520 GLU521 PHE522 ALA523 PRO524 ILE525 ASN526 THR527 THR528 TRP529 SER530 ILE531 PHE532 LYS533 ASP534 HIS535 ASP536 PHE537 GLY538 PHE539 VAL540 LYS541 LEU542 THR543 ALA544 PHE545 ASP546 HIS547 SER548 ASN549 LEU550 LEU551 LEU552 GLU553 TYR554 ARG555 LYS556 SER557 SER558 ASP559 GLY560 GLN561 VAL562 TYR563 ASP564 SER565 PHE566 THR567 ILE568 SER569 ARG570 ASP571 TYR572 ARG573 ASP574 ILE575 LEU576 ALA577 CYS578 SER579 VAL580 ASP581 SER582 CYS583 PRO584 THR585 THR586 THR587 LEU588 ALA589 SER590
Unit 3 ALA23 TYR24 ILE25 LYS26 ALA27 THR28 PRO29 ASN30 VAL31 LEU32 GLY33 PHE34 GLU35 GLY36 HIS37 TYR38 THR39 GLU40 TRP41 VAL42 THR43 LEU44 GLN45 TYR46 SER47 ASN48 ASN49 LYS50 PRO51 SER52 ILE53 ASP54 ASP55 TRP56 ILE57 GLY58 VAL59 PHE60 SER61 PRO62 ALA63 ASN64 PHE65 SER66 ALA67 SER68 THR69 CYS70 PRO71 GLY72 GLU73 ASN74 LYS75 MET76 THR77 ASN78 PRO79 PRO80 PHE81 LEU82 CYS83 SER84 ALA85 PRO86 ILE87 LYS88 PHE89 GLN90 TYR91 ALA92 ASN93 PHE94 SER95 SER96 HIS97 SER98 TYR99 LYS100 ASP101 THR102 GLY103 LYS104 GLY105 SER106 LEU107 LYS108 LEU109 GLN110 LEU111 ILE112 ASN113 GLN114 ARG115 SER116 ASP117 PHE118 SER119 PHE120 ALA121 LEU122 PHE123 THR124 GLY125 GLY126 LEU127 THR128 ASN129 PRO130 LYS131 LEU132 ILE133 ALA134 VAL135 SER136 ASN137 LYS138 VAL139 SER140 PHE141 VAL142 ASN143 PRO144 ASN145 ALA146 PRO147 VAL148 TYR149 PRO150 ARG151 LEU152 ALA153 GLN154 GLY155 LYS156 THR157 TRP158 ASP159 GLU160 ILE161 THR162 VAL163 THR164 TRP165 THR166 SER167 GLY168 TYR169 ASP170 ILE171 ASN172 ASP173 ALA174 GLU175 PRO176 PHE177 VAL178 GLU179 TRP180 GLY181 PRO182 LYS183 GLU184 GLY185 ASN186 LEU187 VAL188 LYS189 THR190 PRO191 ALA192 GLY193 THR194 LEU195 THR196 PHE197 ASP198 ARG199 ASN200 THR201 MET202 CYS203 GLY204 ALA205 PRO206 ALA207 ARG208 THR209 VAL210 GLY211 TRP212 ARG213 ASP214 PRO215 GLY216 TYR217 ILE218 HIS219 THR220 SER221 PHE222 LEU223 LYS224 GLU225 LEU226 TRP227 PRO228 ASN229 ARG230 GLU231 TYR232 THR233 TYR234 LYS235 LEU236 GLY237 HIS238 ARG239 LEU240 PHE241 ASN242 GLY243 THR244 THR245 ILE246 TRP247 SER248 LYS249 GLU250 TYR251 HIS252 PHE253 LYS254 ALA255 SER256 PRO257 TYR258 PRO259 GLY260 GLN261 SER262 SER263 VAL264 GLN265 ARG266 VAL267 VAL268 ILE269 PHE270 GLY271 ASP272 MET273 GLY274 LYS275 ALA276 GLU277 ALA278 ASP279 GLY280 SER281 ASN282 GLU283 TYR284 ASN285 ASN286 PHE287 GLN288 PRO289 GLY290 SER291 LEU292 ASN293 THR294 THR295 LYS296 GLN297 ILE298 ILE299 GLN300 ASP301 LEU302 GLU303 ASP304 ILE305 ASP306 ILE307 VAL308 PHE309 HIS310 ILE311 GLY312 ASP313 LEU314 CYS315 TYR316 ALA317 ASN318 GLY319 TYR320 ILE321 SER322 GLN323 TRP324 ASP325 GLN326 PHE327 THR328 ALA329 GLN330 ILE331 GLU332 PRO333 ILE334 ALA335 SER336 THR337 VAL338 PRO339 TYR340 MET341 THR342 ALA343 SER344 GLY345 ASN346 HIS347 GLU348 ARG349 ASP350 TRP351 PRO352 GLY353 THR354 GLY355 SER356 PHE357 TYR358 GLY359 ASN360 LEU361 ASP362 SER363 GLY364 GLY365 GLU366 CYS367 GLY368 VAL369 PRO370 ALA371 GLN372 THR373 MET374 PHE375 PHE376 VAL377 PRO378 ALA379 GLU380 ASN381 ARG382 GLU383 LYS384 PHE385 TRP386 TYR387 SER388 THR389 ASP390 TYR391 GLY392 MET393 PHE394 ARG395 PHE396 CYS397 ILE398 ALA399 HIS400 THR401 GLU402 LEU403 ASP404 TRP405 ARG406 LYS407 GLY408 THR409 GLU410 GLN411 TYR412 GLU413 PHE414 ILE415 GLU416 LYS417 CYS418 LEU419 ALA420 SER421 VAL422 ASP423 ARG424 GLN425 LYS426 GLN427 PRO428 TRP429 LEU430 ILE431 PHE432 LEU433 ALA434 HIS435 ARG436 VAL437 LEU438 GLY439 TYR440 SER441 SER442 ALA443 GLY444 PHE445 TYR446 VAL447 GLN448 GLU449 GLY450 SER451 PHE452 GLU453 GLU454 PRO455 MET456 GLY457 ARG458 GLU459 ASP460 LEU461 GLN462 HIS463 LEU464 TRP465 GLN466 LYS467 TYR468 LYS469 VAL470 ASP471 ILE472 ALA473 MET474 TYR475 GLY476 HIS477 VAL478 HIS479 ASN480 TYR481 GLU482 ARG483 THR484 CYS485 PRO486 ILE487 TYR488 GLN489 ASN490 VAL491 CYS492 THR493 ASN494 LYS495 GLU496 LYS497 HIS498 ASN499 TYR500 LYS501 GLY502 ASN503 LEU504 ASN505 GLY506 THR507 ILE508 HIS509 VAL510 VAL511 VAL512 GLY513 GLY514 GLY515 GLY516 ALA517 SER518 LEU519 ALA520 GLU521 PHE522 ALA523 PRO524 ILE525 ASN526 THR527 THR528 TRP529 SER530 ILE531 PHE532 LYS533 ASP534 HIS535 ASP536 PHE537 GLY538 PHE539 VAL540 LYS541 LEU542 THR543 ALA544 PHE545 ASP546 HIS547 SER548 ASN549 LEU550 LEU551 LEU552 GLU553 TYR554 ARG555 LYS556 SER557 SER558 ASP559 GLY560 GLN561 VAL562 TYR563 ASP564 SER565 PHE566 THR567 ILE568 SER569 ARG570 ASP571 TYR572 ARG573 ASP574 ILE575 LEU576 ALA577 CYS578 SER579 VAL580 ASP581 SER582 CYS583 PRO584 THR585 THR586 THR587 LEU588 ALA589 SER590
Ligands
Unit 4 NAG1 NAG2
Unit 5 NAG1 NAG2
Unit 6 NAG1 NAG2
Unit 7 NAG1 NAG2
Unit 8 NAG1 NAG2
Unit 9 NAG1 FUC2 NAG3
Unit 10 NAG1 NAG2
Unit 11 NAG1 FUC2 NAG3
Unit 12 FE800 MN801 GOL901 NAG903 NAG905 PO4999 GOL1000 GOL1001
Unit 13 FE800 MN801 NAG903 NAG925 PO4999
Unit 14 FE800 MN801 NAG802 NAG814 NAG903 PO4999 GOL1000
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany