Structure of PDB 5t62 Chain F Binding Site BS01

Receptor Information

>5t62 Chain F (length=361) Species: 559292 (Saccharomyces cerevisiae S288C)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

Ligand information

>5t62 Chain A (length=3204)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaaugccucgucau
cuaauuagugacgcgcaugaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaagag
acauagaggguguagaauaagugggagcuucggcgccagugaaauaccac
uaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauu
uuccacguucuagcauucaaggucccauucggggcugauccggguugaag
acauugucagguggggaguuuggcuggggcggcacaucuguuaaacgaua
acgcagauguccuaaggggggcucauggagaacagaaaucuccaguagaa
caaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaacc
augaaaguguggccuaucgauccuuuagucccucggaauuugaggcuaga
ggugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcgu
ucauagcgacauugcuuuuugauucuucgaugucggcucuuccuaucaua
ccgaagcagaauucgguaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauu
cggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuac
cauccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaa
cgcggugauuucuuugcuccacacaauauagauggauacgaauaaggcgu
ccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcgg
aaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgugggga
uaaaucauuuguauacgacuuagauguacaacgggguauuguaagcagua
gaguagccuuguuguuacgaucugcugagauuaagccuuuguugucugau
uugu

.........................<<<<<.....<......>......>
>>>>...........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<.<<<<<..<<<...<<<<<<<<<....<<<<......>>
>>.((......<<<.....))>>>..>.>>>>>>>>.....>.>>.....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<<<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<..<....>..>>>..
.....>>>>>>.>>.>.>>>>>.>>>>>>>>>>........<<<....>>
>....>>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<....<<<<...<<<<<<.....>>>>>>.>>>>....>>>..>.>>...
..>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>
>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>
>>...<<<<<<<..<<<<(((.....<<<<<<.....<<..........<
<<.<<<<<<<<<<.......<<<<<.<<....<<.........>>....>
>.........<<......>>...>>>>>...>>>>>>>>>>>>>......
....))).>>...>>>>>>.>>>>..>>>>>>><<<<<<<<<........
.>>>>>>>>>....>>>>>><.<<<<<<<<.<<......<<<<.<<<<..
..>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<....
.<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<
<.....>>.>>>>>>....((<<<<<<...<<....<<<....>>>....
....<<<<<<<.....>.>>>>>>....>>....>>...<<<<<......
..>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<.
..<<<<.<<<<<<<.<<<<<<<<<<..{{{..>>>>>><...<<<<<...
.<<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<
<<<<......>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>
>..........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.......
..<.....<<<<<.....<..>......>>>>><<.<<<<<<<<<<....
..>>>>..>>>>>>.>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<.
.<<<..<<<<<<.<..<<<.....<<<<....>>>>.....>>>>>>>>.
.>>>>><<<<<<.......>>>>>>........<...........<<<<<
.......>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>
>>>>..>>>>>>....>>....<<<<<........>>>>>....[[[[[.
.{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<
<<<<<<.<............<<<<....<..>..............>>>>
....>>>>>.>>>>>>>>>>...<<<<<.....<<<<..<<<<<......
>>>>>...............<<<<<<....>>>>>>..>>>>..>>>>>.
....>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<.........
..>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<
<...(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<
<<....>>>.>>))).......((((((..((((.>>>>>>)))))))))
)..........]]]]..}}]]]].......<<.<.<.<<<<<<...<<..
.....>>...>>>>>>...>>..>>.......<<<<<.<<<<<<..<.<<
<<<<<......>>>>>>>...>.<<<.........>>>.....>>>>>..
>...>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]
....<<<<<<<<..<<<<.<.<<<<<<...............>>>>>>.>
<<<<<...<<<<....<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>.
.>>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>...
.>>>>>>>>.......<<<<<<.<<<.<<....<<..........<<<<<
<.....>>>>>>......>>.......<<<<<<...<<<<<.<..<<<..
....>>>..>.>>>>>.>>>>>>.............>>.>>>.>>>>>>.
.<<<<<.<.............>.....<<<<<<<<<.<<<....<<<<..
..<<<<<......>>>>>...>>>>...>>>....>>>>.>>>>>..>>>
>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): H36 T40 K44 K46 R47 Q48 Y50 V52 S53 Q59 T60 S61 T67 G68 A70 V71 R73 I74 P75 G80 G81 T82 R84 Q87 N92 M93 C94 R95 G96 R98 M99 F100 A101 P102 K104 W106 R107 K108 V111 K112 N114 H115 N116 E117 R119 R138 R141 T162 K183 K186 L187 R188 A189 K191 K193 Y194 R195 N196 R197 R202 R203 Y209 V216 K217 R220 N221 T227 L233 N234 P240 G241 H243 K271 V272 T287 I290 N291 G303 T306 Q307 K308 R309 V312 L313 K315 K319 N320 R326 N328 A331 K332 F334 A335 S341 K342 A344 T347 T349 P351
• Binding residue (residue number reindexed from 1): H35 T39 K43 K45 R46 Q47 Y49 V51 S52 Q58 T59 S60 T66 G67 A69 V70 R72 I73 P74 G79 G80 T81 R83 Q86 N91 M92 C93 R94 G95 R97 M98 F99 A100 P101 K103 W105 R106 K107 V110 K111 N113 H114 N115 E116 R118 R137 R140 T161 K182 K185 L186 R187 A188 K190 K192 Y193 R194 N195 R196 R201 R202 Y208 V215 K216 R219 N220 T226 L232 N233 P239 G240 H242 K270 V271 T286 I289 N290 G302 T305 Q306 K307 R308 V311 L312 K314 K318 N319 R325 N327 A330 K331 F333 A334 S340 K341 A343 T346 T348 P350

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)