Structure of PDB 5ndv Chain C0 Binding Site BS01

Receptor Information
>5ndv Chain C0 (length=90) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLT
SKGYVKTQFSWQYYYYTLTEEGVEYLREYLNLPEHIVPGT
Ligand information
>5ndv Chain 2 (length=1712) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacu
gugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaaga
gauguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuc
auaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaa
auuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuu
caacggguaacggggaauaaggguucgauuccggagagggagccugagaa
acggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccu
aauucagggagguagugacaauaaauaacgauacagguuguaauuggaau
gaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucuggu
gccagcagccgcgguaauuccagcuccaauagcguauauuaaaguuguug
caguuaaaaagcucguaguugaacuuugggcccgguuggccggucggauu
uccaacggggccuuuccuucuggcaccaggacuuuuacuuugaaaaaauu
agaguguucaaagcaggcguauugcucgaauauauuagcauggaauaaua
gaauaggacguuugguucuauuuuguugguuucuaggaccaucguaauga
uuaauagggacggucgggggcaucaguauucaauugucagaggugaaauu
cuuggauuuauugaagacuaacuacugcgaaagcauuugccaaggacguu
uucauuaaucaagaacgaaaguuaggggaucgaagaugaucagauaccgu
cguagucuuaaccauaaacuaugccgacuagggaucgggugguguuuuuu
uaaugacccacucggcaccuuacgagaaaucaaagucuuuggguucuggg
gggaguauggucgcaaggcugaaacuuaaaggaauugacggaagggcacc
accaggaguggagccugcggcuuaauuugacucaacacggggaaacucac
cagguccagacacaauaaggauugacagauugagagcucuuucuugauuu
ugugggugguggugcauggccguucuuaguugguggagugauuugucugc
uuaauugcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagc
auuugcugguuauccacuucuuagagggacuaucgguuucaagccgaugg
aaguuugaggcaauaacaggucugugaugcccuuagacguucugggccgc
acgcgcgcuacacugacggagccagcgagucuaaccuuggccgagagguc
uugguaaucuugugaaacuccgucgugcuggggauagagcauuguaauua
uugcucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguu
gauuacgucccugcccuuuguacacaccgcccgucgcuaguaccgauuga
auggcuuagugaggccucaggaucuggagcggagaauuuggacaaacuug
gucauuuagaggaacuaaaagucguaacaagguuuccguaggugaaccug
cggaaggaucau
...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<............>...>>.>>......{{..
......[[[..{{..{{....[[[..................<.....<<
.<<<.....>>>.>>......>.........<<<<<..<......>..>>
>>>[...((((((......<<<<<<<<<<<....>>>.............
.)))))).....]...<<<<..<<<.....>>>.>>>>....]]]...}}
}}..]]].<<<....<<<....<<<<<<<<.......>>>>>>>>>>>..
....>>>...<<<.<<<<....>>>>....>>>.}}.<<.<<<.......
...>>>.>>.<.<<....>>.>...]]]]]].........<<<....<<<
.....>>>..>>>...............<<<<<.......>>.>>>....
..<<..<...........>..>>.........<<<<<((....<.<<<<.
....<<..))>>.......>>>>>>>>>>..))))))]]]].........
[[[{{.......{{...[[[.{{....<<<<<<.<<<<............
..>>>>.>>>>>>.....<<<<<..>>>>>....<<<<<.<<.......<
<...<.......>..<<<<...>>>>....>>......>>.>>..>>>..
.......[[[..((((((((....>>>>>>>>.)))))))).]]].....
}}....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>
>......>.>>>>>.>.>>.......<<....>>...>>>>..>.>>>>.
>>>...]]]...}}......<<<<<<<...<...<<<<.........>>>
>...>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.<<<....
....>>>>>>>>>>>..>>>...<<..}}>>...>>.....>>>.]]].<
<<......<<<<....>>>>....>>>..]]]]..<<<<<.<<<<<<<..
<<.<<<<<<..<<<.<<<<........<<........>>..........<
<<<<.<....<<<<<........<<.<<<........>>>.>>......>
>>>>.<.<<.<<<..<<<<<<<<.....<<<.<<<<<....>>>...<<<
......>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<<<<<<
....>>>>>>...>>>>>..>>>>.>>....<<<<<<.....>>>>>>..
.....>>>>>.....>>.>>>...>.>>>>>>>>....>.>>>>>.....
.>>>>.>>>.....<<<<<<<......<<.....<<..<<<<....>>>>
..>>....>>.......>>>>>>>...........<<<<<<.........
.>>>>>>..........>>>>>>....<<<<<<<<.......>>>>>>>>
......>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<
<<<<<<.<<<..<.<<......<<<.....>>>......>>.>..>>>.>
>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<....>>>>
>>>>>.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.3 Å
Binding residue
(original residue number in PDB)
M1 L2 M3 K25 F27 K44 Q47 S48 S51 F59 Y64
Binding residue
(residue number reindexed from 1)
M1 L2 M3 K25 F27 K44 Q47 S48 S51 F59 Y64
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
Biological Process
GO:0000054 ribosomal subunit export from nucleus
GO:0002181 cytoplasmic translation
GO:0034198 cellular response to amino acid starvation
GO:0045860 positive regulation of protein kinase activity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
PDBsum5ndv
PubMed29208708
UniProtQ08745|RS10A_YEAST Small ribosomal subunit protein eS10A (Gene Name=RPS10A)

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