Structure of PDB 8p8m Chain LI Binding Site BS01

Receptor Information

>8p8m Chain LI (length=296) Species: 4932 (Saccharomyces cerevisiae)

AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRL
VVRFTNKDIICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYAT
GLLIARRTLQKLGLDETYKGVEEVEGEYELTEAVEDGPRPFKVFLDIGLQ
RTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEIDPELLRSYIFG
GHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTSAHEAIRADP
AFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Ligand information

>8p8m Chain A (length=3035)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucgguacgaucaacuuagaacug
guacggacaaggggaaucugacugucuaauuaaaacauagcauugcgaug
gucagaaagugauguugacgcaaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaccaagcgcggguaaacggcggaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggauuaacgagauuc
ccacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcu
uggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuug
acauugugaaguacuuauucaaugaagcggagcucacguucuagcauuca
aggucccauucggggcugauccggguugaagacauugucagguggggagu
uuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagggg
ggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccccc
uugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucg
auccuuuagucccucggaauuugaggcuagaggugccagaaaaguuacca
cagggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuu
ugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaa
gcguuggauuguucacccacuaauagggaacgugagcuggguuuagaccg
ucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauagua
auugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcg
gcugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcu
gaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcuc
cacacaauauagauggauacgaauaaggcguccuuguggcgucgcugaac
cauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugc
uggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgac
uuagauguacaacgggguauuguaagcaguagaguagccuuguuguuacg
aucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p8m Yeast 60S ribosomal subunit, RPL39 deletion
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): K8 R15 F16 Q17 R23 T28 D29 R35 L36 K43 Y44 P139 R140 F142 F145 I148 L150 R152 P174 H175 S176 R179
• Binding residue (residue number reindexed from 1): K7 R14 F15 Q16 R22 T27 D28 R34 L35 K42 Y43 P138 R139 F141 F144 I147 L149 R151 P173 H174 S175 R178

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic 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:8p8m, PDBe:8p8m, PDBj:8p8m
• PDBsum: 8p8m
• UniProt: P26321|RL5_YEAST Large ribosomal subunit protein uL18 (Gene Name=RPL5)