Structure of PDB 5obm Chain SR Binding Site BS01

Receptor Information

>5obm Chain SR (length=318) Species: 559292 (Saccharomyces cerevisiae S288C)

ASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDD
QKFGVPVRSFKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQ
RFVGHKSDVMSVDIDKKASMIISGSRDKTIKVWTIKGQCLATLLGHNDWV
SQVRVVPNEAADDDSVTIISAGNDKMVKAWNLNQFQIEADFIGHNSNINT
LTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEVFSLAFSPNRYW
LAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQTL
FAGYTDNVIRVWQVMTAN

Ligand information

>5obm Chain 2 (length=1712)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguucacaugguauaacugugguaa
uucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagauguau
uuauuagauaaaaaaucaaugucuucggacucuuugaugauucauaauaa
cuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuucug
cccuaucaacuuucgaugguaggauaguggccuaccaugguuucaacggg
uaacggggaauaaggguucgauuccggagagggagccugagaaacggcua
ccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauucag
ggagguagugacaauaaauaacgauacagggucuuguaauuggaaugagu
acaauguaaauaccuuaacgaggaacaauuggagggcaagucuggugcca
gcagccgcgguaauuccagcuccaauagcguauauuaaaguuguugcagu
uaaaaagcucguaguugaacuuugggcccgguuggccggucggauuucca
acggggccuuuccuucuggcuaccaggacuuuuacuuugaaaaaauuaga
guguucaaagcaggcguauugcucgaauauauuagcauggaauaauagaa
uaggacguuugguucuauuuuguugguuucuaggaccaucguaaugauua
auagggacggucgggggcaucaguauucaauugucagaggugaaauucuu
ggauuuauugaagacuaacuacugcgaaagcauuugccaaggacguuuuc
auuaaucaagaacgaaaguuaggggaucgaagaugaucagauaccgucgu
agucuuaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaa
ugacccacucggcaccuuacgagaaaucaaagucuuuggguucugggggg
aguauggucgcaaggcugaaacuuaaaggaauugacggaagggcaccacc
aggaguggagccugcggcuuaauuugacucaacacggggaaacucaccag
guccagacacaauaaggauugacagauugagagcucuuucuugauuuugu
gggugguggugcauggccguucuuaguugguggagugauuugucugcuua
auugcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauu
ugcugguuauccacuucuuagagggacuaucgguuucaagccgauggaag
uuugaggcaauaacaggucugugaugcccuuagacguucugggccgcacg
cgcgcuacacugacggagccagcgagucuaaccuuggccgagaggucuug
guaaucuugugaaacuccgucgugcuggggauagagcauuguaauuauug
cucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugau
uacgucccugcccuuuguacacaccgcccgucgcuaguaccgauugaaug
gcuuagugaggccucaggaucugccagagcggagaauuuggacaaacuug
gucauuuagaggaacuaaaagucguaacaagguuuccguaggugaaccug
cggaaggaucau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): G63 H66 R102 Y281
• Binding residue (residue number reindexed from 1): G62 H65 R101 Y280

Gene Ontology

Molecular Function

• GO:0001965 G-protein alpha-subunit binding
• GO:0005080 protein kinase C binding
• GO:0005092 GDP-dissociation inhibitor activity
• GO:0043022 ribosome binding
• GO:0045182 translation regulator activity

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006521 regulation of cellular amino acid metabolic process
• GO:0007186 G protein-coupled receptor signaling pathway
• GO:0010629 negative regulation of gene expression
• GO:0017148 negative regulation of translation
• GO:0061157 mRNA destabilization
• GO:0070651 nonfunctional rRNA decay
• GO:0072344 rescue of stalled ribosome
• GO:1902660 negative regulation of glucose mediated signaling pathway
• GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process
• GO:1990145 maintenance of translational fidelity
• GO:2001125 negative regulation of translational frameshifting

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5obm, PDBe:5obm, PDBj:5obm
• PDBsum: 5obm
• PubMed: 29208708
• UniProt: P38011|GBLP_YEAST Small ribosomal subunit protein RACK1 (Gene Name=ASC1)