Structure of PDB 8p8m Chain LL Binding Site BS01

Receptor Information

>8p8m Chain LL (length=233) Species: 4932 (Saccharomyces cerevisiae)

NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPP
TIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQ
DASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKM
GVPYAIVKGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFA
DKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

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): H28 S29 T30 P31 K32 N33 I36 Q38 Q41 P42 R44 L46 S47 R48 Y49 K51 P53 E54 Y55 R60 R68 E100 K105 R108 D124 S126 P129 K133 Y134 G135 L136 N137 H138 A141 L142 N145 V157 P159 L162 K183 A184 K193 T194 S195 G239 N240 K241 A242 K248 R249
• Binding residue (residue number reindexed from 1): H5 S6 T7 P8 K9 N10 I13 Q15 Q18 P19 R21 L23 S24 R25 Y26 K28 P30 E31 Y32 R37 R45 E77 K82 R85 D101 S103 P106 K110 Y111 G112 L113 N114 H115 A118 L119 N122 V134 P136 L139 K160 A161 K170 T171 S172 G216 N217 K218 A219 K225 R226

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing

Cellular Component

• 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: P17076|RL8A_YEAST Large ribosomal subunit protein eL8A (Gene Name=RPL8A)