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Sequence, Chains, Asymmetric and Biological Units

Title STRUCTURAL CHARACTERIZATION OF A PUTATIVE ENDOGENOUS METAL C THE PERIPLASMIC NICKEL TRANSPORTER NIKA (NICKEL BUTANE-1,2, TRICARBOXYLATE FORM)
Keywords NICKEL, NICKELLOPHORE, BUTANE-1, 2, 4-TRICARBOXYLATE, TRANSP METAL TRANSPORT
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3DP8     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   NICKEL-BINDING PERIPLASMIC PROTEIN  A 498 3938 0
2  Protein   NICKEL-BINDING PERIPLASMIC PROTEIN  B 497 3947 0
3  Protein   NICKEL-BINDING PERIPLASMIC PROTEIN  C 496 3939 0
4  Ligand   NICKEL-BINDING PERIPLASMIC PROTEIN  A 13 0 61
5  Ligand   NICKEL-BINDING PERIPLASMIC PROTEIN  B 13 0 57
6  Ligand   NICKEL-BINDING PERIPLASMIC PROTEIN  C 7 0 28
7 Water     265 0 265
total       1789 11824 411
Proteins
Unit 1 ALA2 PRO3 ASP4 GLU5 ILE6 THR7 THR8 ALA9 TRP10 PRO11 VAL12 ASN13 VAL14 GLY15 PRO16 LEU17 ASN18 PRO19 HIS20 LEU21 TYR22 THR23 PRO24 ASN25 GLN26 MET27 PHE28 ALA29 GLN30 SER31 MET32 VAL33 TYR34 GLU35 PRO36 LEU37 VAL38 LYS39 TYR40 GLN41 ALA42 ASP43 GLY44 SER45 VAL46 ILE47 PRO48 TRP49 LEU50 ALA51 LYS52 SER53 TRP54 THR55 HIS56 SER57 GLU58 ASP59 GLY60 LYS61 THR62 TRP63 THR64 PHE65 THR66 LEU67 ARG68 ASP69 ASP70 VAL71 LYS72 PHE73 SER74 ASN75 GLY76 GLU77 PRO78 PHE79 ASP80 ALA81 GLU82 ALA83 ALA84 ALA85 GLU86 ASN87 PHE88 ARG89 ALA90 VAL91 LEU92 ASP93 ASN94 ARG95 GLN96 ARG97 HIS98 ALA99 TRP100 LEU101 GLU102 LEU103 ALA104 ASN105 GLN106 ILE107 VAL108 ASP109 VAL110 LYS111 ALA112 LEU113 SER114 LYS115 THR116 GLU117 LEU118 GLN119 ILE120 THR121 LEU122 LYS123 SER124 ALA125 TYR126 TYR127 PRO128 PHE129 LEU130 GLN131 GLU132 LEU133 ALA134 LEU135 PRO136 ARG137 PRO138 PHE139 ARG140 PHE141 ILE142 ALA143 PRO144 SER145 GLN146 PHE147 LYS148 ASN149 HIS150 GLU151 THR152 MET153 ASN154 GLY155 ILE156 LYS157 ALA158 PRO159 ILE160 GLY161 THR162 GLY163 PRO164 TRP165 ILE166 LEU167 GLN168 GLU169 SER170 LYS171 LEU172 ASN173 GLN174 TYR175 ASP176 VAL177 PHE178 VAL179 ARG180 ASN181 GLU182 ASN183 TYR184 TRP185 GLY186 GLU187 LYS188 PRO189 ALA190 ILE191 LYS192 LYS193 ILE194 THR195 PHE196 ASN197 VAL198 ILE199 PRO200 ASP201 PRO202 THR203 THR204 ARG205 ALA206 VAL207 ALA208 PHE209 GLU210 THR211 GLY212 ASP213 ILE214 ASP215 LEU216 LEU217 TYR218 GLY219 ASN220 GLU221 GLY222 LEU223 LEU224 PRO225 LEU226 ASP227 THR228 PHE229 ALA230 ARG231 PHE232 SER233 GLN234 ASN235 PRO236 ALA237 TYR238 HIS239 THR240 GLN241 LEU242 SER243 GLN244 PRO245 ILE246 GLU247 THR248 VAL249 MET250 LEU251 ALA252 LEU253 ASN254 THR255 ALA256 LYS257 ALA258 PRO259 THR260 ASN261 GLU262 LEU263 ALA264 VAL265 ARG266 GLU267 ALA268 LEU269 ASN270 TYR271 ALA272 VAL273 ASN274 LYS275 LYS276 SER277 LEU278 ILE279 ASP280 ASN281 ALA282 LEU283 TYR284 GLY285 THR286 GLN287 GLN288 VAL289 ALA290 ASP291 THR292 LEU293 PHE294 ALA295 PRO296 SER297 VAL298 PRO299 TYR300 ALA301 ASN302 LEU303 GLY304 LEU305 LYS306 PRO307 SER308 GLN309 TYR310 ASP311 PRO312 GLN313 LYS314 ALA315 LYS316 ALA317 LEU318 LEU319 GLU320 LYS321 ALA322 GLY323 TRP324 THR325 LEU326 PRO327 ALA328 GLY329 LYS330 ASP331 ILE332 ARG333 GLU334 LYS335 ASN336 GLY337 GLN338 PRO339 LEU340 ARG341 ILE342 GLU343 LEU344 SER345 PHE346 ILE347 GLY348 THR349 ASP350 ALA351 LEU352 SER353 LYS354 SER355 MET356 ALA357 GLU358 ILE359 ILE360 GLN361 ALA362 ASP363 MET364 ARG365 GLN366 ILE367 GLY368 ALA369 ASP370 VAL371 SER372 LEU373 ILE374 GLY375 GLU376 GLU377 GLU378 SER379 SER380 ILE381 TYR382 ALA383 ARG384 GLN385 ARG386 ASP387 GLY388 ARG389 PHE390 GLY391 MET392 ILE393 PHE394 HIS395 ARG396 THR397 TRP398 GLY399 ALA400 PRO401 TYR402 ASP403 PRO404 HIS405 ALA406 PHE407 LEU408 SER409 SER410 MET411 ARG412 VAL413 PRO414 SER415 HIS416 ALA417 ASP418 PHE419 GLN420 ALA421 GLN422 GLN423 GLY424 LEU425 ALA426 ASP427 LYS428 PRO429 LEU430 ILE431 ASP432 LYS433 GLU434 ILE435 GLY436 GLU437 VAL438 LEU439 ALA440 THR441 HIS442 ASP443 GLU444 THR445 GLN446 ARG447 GLN448 ALA449 LEU450 TYR451 ARG452 ASP453 ILE454 LEU455 THR456 ARG457 LEU458 HIS459 ASP460 GLU461 ALA462 VAL463 TYR464 LEU465 PRO466 ILE467 SER468 TYR469 ILE470 SER471 MET472 MET473 VAL474 VAL475 SER476 LYS477 PRO478 GLU479 LEU480 GLY481 ASN482 ILE483 PRO484 TYR485 ALA486 PRO487 ILE488 ALA489 THR490 GLU491 ILE492 PRO493 PHE494 GLU495 GLN496 ILE497 LYS498 PRO499
Unit 2 PRO3 ASP4 GLU5 ILE6 THR7 THR8 ALA9 TRP10 PRO11 VAL12 ASN13 VAL14 GLY15 PRO16 LEU17 ASN18 PRO19 HIS20 LEU21 TYR22 THR23 PRO24 ASN25 GLN26 MET27 PHE28 ALA29 GLN30 SER31 MET32 VAL33 TYR34 GLU35 PRO36 LEU37 VAL38 LYS39 TYR40 GLN41 ALA42 ASP43 GLY44 SER45 VAL46 ILE47 PRO48 TRP49 LEU50 ALA51 LYS52 SER53 TRP54 THR55 HIS56 SER57 GLU58 ASP59 GLY60 LYS61 THR62 TRP63 THR64 PHE65 THR66 LEU67 ARG68 ASP69 ASP70 VAL71 LYS72 PHE73 SER74 ASN75 GLY76 GLU77 PRO78 PHE79 ASP80 ALA81 GLU82 ALA83 ALA84 ALA85 GLU86 ASN87 PHE88 ARG89 ALA90 VAL91 LEU92 ASP93 ASN94 ARG95 GLN96 ARG97 HIS98 ALA99 TRP100 LEU101 GLU102 LEU103 ALA104 ASN105 GLN106 ILE107 VAL108 ASP109 VAL110 LYS111 ALA112 LEU113 SER114 LYS115 THR116 GLU117 LEU118 GLN119 ILE120 THR121 LEU122 LYS123 SER124 ALA125 TYR126 TYR127 PRO128 PHE129 LEU130 GLN131 GLU132 LEU133 ALA134 LEU135 PRO136 ARG137 PRO138 PHE139 ARG140 PHE141 ILE142 ALA143 PRO144 SER145 GLN146 PHE147 LYS148 ASN149 HIS150 GLU151 THR152 MET153 ASN154 GLY155 ILE156 LYS157 ALA158 PRO159 ILE160 GLY161 THR162 GLY163 PRO164 TRP165 ILE166 LEU167 GLN168 GLU169 SER170 LYS171 LEU172 ASN173 GLN174 TYR175 ASP176 VAL177 PHE178 VAL179 ARG180 ASN181 GLU182 ASN183 TYR184 TRP185 GLY186 GLU187 LYS188 PRO189 ALA190 ILE191 LYS192 LYS193 ILE194 THR195 PHE196 ASN197 VAL198 ILE199 PRO200 ASP201 PRO202 THR203 THR204 ARG205 ALA206 VAL207 ALA208 PHE209 GLU210 THR211 GLY212 ASP213 ILE214 ASP215 LEU216 LEU217 TYR218 GLY219 ASN220 GLU221 GLY222 LEU223 LEU224 PRO225 LEU226 ASP227 THR228 PHE229 ALA230 ARG231 PHE232 SER233 GLN234 ASN235 PRO236 ALA237 TYR238 HIS239 THR240 GLN241 LEU242 SER243 GLN244 PRO245 ILE246 GLU247 THR248 VAL249 MET250 LEU251 ALA252 LEU253 ASN254 THR255 ALA256 LYS257 ALA258 PRO259 THR260 ASN261 GLU262 LEU263 ALA264 VAL265 ARG266 GLU267 ALA268 LEU269 ASN270 TYR271 ALA272 VAL273 ASN274 LYS275 LYS276 SER277 LEU278 ILE279 ASP280 ASN281 ALA282 LEU283 TYR284 GLY285 THR286 GLN287 GLN288 VAL289 ALA290 ASP291 THR292 LEU293 PHE294 ALA295 PRO296 SER297 VAL298 PRO299 TYR300 ALA301 ASN302 LEU303 GLY304 LEU305 LYS306 PRO307 GLN309 TYR310 ASP311 PRO312 GLN313 LYS314 ALA315 LYS316 ALA317 LEU318 LEU319 GLU320 LYS321 ALA322 GLY323 TRP324 THR325 LEU326 PRO327 ALA328 GLY329 LYS330 ASP331 ILE332 ARG333 GLU334 LYS335 ASN336 GLY337 GLN338 PRO339 LEU340 ARG341 ILE342 GLU343 LEU344 SER345 PHE346 ILE347 GLY348 THR349 ASP350 ALA351 LEU352 SER353 LYS354 SER355 MET356 ALA357 GLU358 ILE359 ILE360 GLN361 ALA362 ASP363 MET364 ARG365 GLN366 ILE367 GLY368 ALA369 ASP370 VAL371 SER372 LEU373 ILE374 GLY375 GLU376 GLU377 GLU378 SER379 SER380 ILE381 TYR382 ALA383 ARG384 GLN385 ARG386 ASP387 GLY388 ARG389 PHE390 GLY391 MET392 ILE393 PHE394 HIS395 ARG396 THR397 TRP398 GLY399 ALA400 PRO401 TYR402 ASP403 PRO404 HIS405 ALA406 PHE407 LEU408 SER409 SER410 MET411 ARG412 VAL413 PRO414 SER415 HIS416 ALA417 ASP418 PHE419 GLN420 ALA421 GLN422 GLN423 GLY424 LEU425 ALA426 ASP427 LYS428 PRO429 LEU430 ILE431 ASP432 LYS433 GLU434 ILE435 GLY436 GLU437 VAL438 LEU439 ALA440 THR441 HIS442 ASP443 GLU444 THR445 GLN446 ARG447 GLN448 ALA449 LEU450 TYR451 ARG452 ASP453 ILE454 LEU455 THR456 ARG457 LEU458 HIS459 ASP460 GLU461 ALA462 VAL463 TYR464 LEU465 PRO466 ILE467 SER468 TYR469 ILE470 SER471 MET472 MET473 VAL474 VAL475 SER476 LYS477 PRO478 GLU479 LEU480 GLY481 ASN482 ILE483 PRO484 TYR485 ALA486 PRO487 ILE488 ALA489 THR490 GLU491 ILE492 PRO493 PHE494 GLU495 GLN496 ILE497 LYS498 PRO499 VAL500
Unit 3 ASP4 GLU5 ILE6 THR7 THR8 ALA9 TRP10 PRO11 VAL12 ASN13 VAL14 GLY15 PRO16 LEU17 ASN18 PRO19 HIS20 LEU21 TYR22 THR23 PRO24 ASN25 GLN26 MET27 PHE28 ALA29 GLN30 SER31 MET32 VAL33 TYR34 GLU35 PRO36 LEU37 VAL38 LYS39 TYR40 GLN41 ALA42 ASP43 GLY44 SER45 VAL46 ILE47 PRO48 TRP49 LEU50 ALA51 LYS52 SER53 TRP54 THR55 HIS56 SER57 GLU58 ASP59 GLY60 LYS61 THR62 TRP63 THR64 PHE65 THR66 LEU67 ARG68 ASP69 ASP70 VAL71 LYS72 PHE73 SER74 ASN75 GLY76 GLU77 PRO78 PHE79 ASP80 ALA81 GLU82 ALA83 ALA84 ALA85 GLU86 ASN87 PHE88 ARG89 ALA90 VAL91 LEU92 ASP93 ASN94 ARG95 GLN96 ARG97 HIS98 ALA99 TRP100 LEU101 GLU102 LEU103 ALA104 ASN105 GLN106 ILE107 VAL108 ASP109 VAL110 LYS111 ALA112 LEU113 SER114 LYS115 THR116 GLU117 LEU118 GLN119 ILE120 THR121 LEU122 LYS123 SER124 ALA125 TYR126 TYR127 PRO128 PHE129 LEU130 GLN131 GLU132 LEU133 ALA134 LEU135 PRO136 ARG137 PRO138 PHE139 ARG140 PHE141 ILE142 ALA143 PRO144 SER145 GLN146 PHE147 LYS148 ASN149 HIS150 GLU151 THR152 MET153 ASN154 GLY155 ILE156 LYS157 ALA158 PRO159 ILE160 GLY161 THR162 GLY163 PRO164 TRP165 ILE166 LEU167 GLN168 GLU169 SER170 LYS171 LEU172 ASN173 GLN174 TYR175 ASP176 VAL177 PHE178 VAL179 ARG180 ASN181 GLU182 ASN183 TYR184 TRP185 GLY186 GLU187 LYS188 PRO189 ALA190 ILE191 LYS192 LYS193 ILE194 THR195 PHE196 ASN197 VAL198 ILE199 PRO200 ASP201 PRO202 THR203 THR204 ARG205 ALA206 VAL207 ALA208 PHE209 GLU210 THR211 GLY212 ASP213 ILE214 ASP215 LEU216 LEU217 TYR218 GLY219 ASN220 GLU221 GLY222 LEU223 LEU224 PRO225 LEU226 ASP227 THR228 PHE229 ALA230 ARG231 PHE232 SER233 GLN234 ASN235 PRO236 ALA237 TYR238 HIS239 THR240 GLN241 LEU242 SER243 GLN244 PRO245 ILE246 GLU247 THR248 VAL249 MET250 LEU251 ALA252 LEU253 ASN254 THR255 ALA256 LYS257 ALA258 PRO259 THR260 ASN261 GLU262 LEU263 ALA264 VAL265 ARG266 GLU267 ALA268 LEU269 ASN270 TYR271 ALA272 VAL273 ASN274 LYS275 LYS276 SER277 LEU278 ILE279 ASP280 ASN281 ALA282 LEU283 TYR284 GLY285 THR286 GLN287 GLN288 VAL289 ALA290 ASP291 THR292 LEU293 PHE294 ALA295 PRO296 SER297 VAL298 PRO299 TYR300 ALA301 ASN302 LEU303 GLY304 LEU305 LYS306 PRO307 SER308 GLN309 TYR310 ASP311 PRO312 GLN313 LYS314 ALA315 LYS316 ALA317 LEU318 LEU319 GLU320 LYS321 ALA322 GLY323 TRP324 THR325 LEU326 PRO327 ALA328 GLY329 LYS330 ASP331 ILE332 ARG333 GLU334 LYS335 ASN336 GLY337 GLN338 PRO339 LEU340 ARG341 ILE342 GLU343 LEU344 SER345 PHE346 ILE347 GLY348 THR349 ASP350 ALA351 LEU352 SER353 LYS354 SER355 MET356 ALA357 GLU358 ILE359 ILE360 GLN361 ALA362 ASP363 MET364 ARG365 GLN366 ILE367 GLY368 ALA369 ASP370 VAL371 SER372 LEU373 ILE374 GLY375 GLU376 GLU377 GLU378 SER379 SER380 ILE381 TYR382 ALA383 ARG384 GLN385 ARG386 ASP387 GLY388 ARG389 PHE390 GLY391 MET392 ILE393 PHE394 HIS395 ARG396 THR397 TRP398 GLY399 ALA400 PRO401 TYR402 ASP403 PRO404 HIS405 ALA406 PHE407 LEU408 SER409 SER410 MET411 ARG412 VAL413 PRO414 SER415 HIS416 ALA417 ASP418 PHE419 GLN420 ALA421 GLN422 GLN423 GLY424 LEU425 ALA426 ASP427 LYS428 PRO429 LEU430 ILE431 ASP432 LYS433 GLU434 ILE435 GLY436 GLU437 VAL438 LEU439 ALA440 THR441 HIS442 ASP443 GLU444 THR445 GLN446 ARG447 GLN448 ALA449 LEU450 TYR451 ARG452 ASP453 ILE454 LEU455 THR456 ARG457 LEU458 HIS459 ASP460 GLU461 ALA462 VAL463 TYR464 LEU465 PRO466 ILE467 SER468 TYR469 ILE470 SER471 MET472 MET473 VAL474 VAL475 SER476 LYS477 PRO478 GLU479 LEU480 GLY481 ASN482 ILE483 PRO484 TYR485 ALA486 PRO487 ILE488 ALA489 THR490 GLU491 ILE492 PRO493 PHE494 GLU495 GLN496 ILE497 LYS498 PRO499
Ligands
Unit 4 NI503 ACT504 ACT505 ACT506 ACT507 SO4508 CL509 CL510 HCT511 GOL512 GOL513 GOL514 GOL515
Unit 5 NI503 ACT504 ACT505 ACT506 ACT507 CL508 CL509 CL510 HCT511 GOL512 GOL513 GOL514 GOL515
Unit 6 NI503 ACT504 ACT505 ACT506 CL507 CL508 HCT509
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany