Structure of PDB 6n8k Chain C Binding Site BS01

Receptor Information

>6n8k Chain C (length=361) Species: 559292 (Saccharomyces cerevisiae S288C)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

Ligand information

>6n8k Chain 1 (length=3201)

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
aacggcgggaguuaugacucucuuaagguagccaaaugccucgucaucua
auuagugacgcgcaugaauggauuaacgagauucccacugucccuaucua
cuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggg
gaaagaagacccuguugagcuugacucuaguuugacauugugaagagaca
uagaggguguagaauaagugggagcuucggcgccagugaaauaccacuac
cuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuuc
cacguucuagcauucaaggucccauucggggcugauccggguugaagaca
uugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacg
cagauguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggu
gccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguuca
uagcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccg
aagcagaauucgguaagcguuggauuguucacccacuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
uguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgg
auaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccau
ccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgc
ggugauuucuuugcuccacacaauauagauggauacgaauaaggcguccu
uguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaa
ggccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaa
aucauuuguauacgacuuagauguacaacgggguauuguaagcaguagag
uagccuuguuguuacgaucugcugagauuaagccuuuguugucugauuug
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n8k Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): I34 H36 T40 N45 K46 R47 Q48 Y50 V52 S53 E54 A56 G57 H58 Q59 T60 S61 T67 G68 R69 V71 R73 P75 G80 T82 R84 N92 M93 R95 G96 R98 M99 F100 A101 P102 K104 W106 R107 K108 K112 N114 H115 N116 K118 R119 R138 R141 T162 K163 L179 K183 K186 L187 R188 A189 K191 K193 Y194 R195 R197 W199 R202 R203 Y209 K217 R220 N221 T227 S232 N234 G241 H243 K271 V272 T287 N291 R300 G303 Q304 A305 Q307 K308 R309 V312 L313 K315 N320 K321 Q322 R326 A331 K332 F334 A335 S341 K342 K343 T347 T349 L359 K360
• Binding residue (residue number reindexed from 1): I33 H35 T39 N44 K45 R46 Q47 Y49 V51 S52 E53 A55 G56 H57 Q58 T59 S60 T66 G67 R68 V70 R72 P74 G79 T81 R83 N91 M92 R94 G95 R97 M98 F99 A100 P101 K103 W105 R106 K107 K111 N113 H114 N115 K117 R118 R137 R140 T161 K162 L178 K182 K185 L186 R187 A188 K190 K192 Y193 R194 R196 W198 R201 R202 Y208 K216 R219 N220 T226 S231 N233 G240 H242 K270 V271 T286 N290 R299 G302 Q303 A304 Q306 K307 R308 V311 L312 K314 N319 K320 Q321 R325 A330 K331 F333 A334 S340 K341 K342 T346 T348 L358 K359

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:6n8k, PDBe:6n8k, PDBj:6n8k
• PDBsum: 6n8k
• PubMed: 30814529
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)