Structure of PDB 5ndv Chain d9 Binding Site BS01

Receptor Information
>5ndv Chain d9 (length=53) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFN
KFR
Ligand information
>5ndv Chain 6 (length=1683) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuuacaugguauaacugugg
uaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagaug
uauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucauaa
uaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuu
cugcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaac
ggguaacggggaauaaggguucgauuccggagagggagccugagaaacgg
cuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauu
cagggagguagugacaauaaauaacgauacaggggucuuguaauuggaau
gaguacaauguaaauaccuuaacgaggaacaauuggagggcaagucuggu
gccagcagccgcgguaauuccagcuccaauagcguauauuaaaguuguug
caguuaaaaagcucguaguugaacuuugggcccgguuaacggggccuuuu
uacuuugaaaaaauuagaguguucaaagcaggcguauugcucgaauauau
uagcauggaauaauagaauaggacguuugguucuauuuuguugguuucua
ggaccaucguaaugauuaauagggacggucgggggcaucaguauucaauu
gucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaagca
uuugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucgaag
augaucagauaccgucguagucuuaaccauaaacuaugccgacuagggau
cgggugguguuuuuuuaaugacccacucggcaccuuacgagaaaucaaag
ucuuuggguucuggggggaguauggucgcaaggcugaaacuuaaaggaau
ugacggaagggcaccaccaggaguggagccugcggcuuaauuugacucaa
cacggggaaacucaccagguccagacacaauaaggauugacagauugaga
gcucuuucuugauuuugugggugguggugcauggccguucuuaguuggug
gagugauuugucugcuuaauugcgauaacgaacgagaccuuaaccuacua
aauaguggugcuagcauuugcugguuauccacuucuuagagggacuaucg
guuucaagccgauggaaguuugaggcaauaacaggucugugaugcccuua
gacguucugggccgcacgcgcgcuacacugacggagccagcgagucuaac
cuuggccgagaggucuugguaaucuugugaaacuccgucgugcuggggau
agagcauuguaauuauugcucuucaacgaggaauuccuaguaagcgcaag
ucaucagcuugcguugauuacgucccugcccuuuguacacaccgcccguc
gcuaguaccgauugaauggcuuagugaggccucaggaucugcuuagagcg
gagaauuuggacaaacuuggucauuuagaggaacuaaaagucguaacaag
guuuccguaggugaaccugcggaaggaucauua
...<<<<..{.((((.>>>><<<<.<<<<<<.....<...<......<<<
.<<<..<<....<<....<<..........>>...>>.>>......<<..
......<<<..<<..<<....<<<..............<.....<<.<<<
.....>>>.>>......>.........<<<<<..<......>..>>>>>.
...<<<<<<......{..(((..<<......>>....<<......>>>>>
>>>.........<<<<..<<<.....>>>.>>>>....>>>...>>>>..
>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>......
>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<..........>
>>.>>.<.<<....>>.>...>>>>>>.........<<<....<<<....
.>>>..>>>..>....>.......<<<<<<<<<..>.>>>>>.>>>....
..<<..<...........>..>>.........<<<<<((......<<<<.
....<<..))>>.......>>>>.>>>>>..>>>>>>>>>>.........
<<<[[.....<.<<...<<<.<<....<<<<<<.<<..>>.>>>>>>..<
<<<<.<<.......<<...<.......>..<<<.....>>>....>>...
...>>.>>..>>>.........<<<..<<<<<<<.......)))..}..>
>>>>>>.>>>.....>>....<<<<<<.<<...<<<<..<<..<<<<<<.
<...<<<......>>>......>.>>>>>>..>>.......<<....>>.
..>>>>...>>>>>.>>>...>>>...>>.>....<<<<<<<...<...<
<<<.........>>>>...>>>>>>>>..........<<<.<<.<<<..<
<<<<<<<.<<<........>>>>>>>>>>>..>>>...<<..]]>>...>
>.....>>>.>>>.<<<......<<<<....>>>>....>>>..)))).}
<<<<<.<<<<<<<..<<.<<<<<<..<<<.<<<<<<......<<......
..>>..........<<<<<......<<<<<........<<.<<<......
..>>>.>>......>>>>>.<.<<.<<<..<<.<<<<<<....<<<.<<<
<<....>>>...<<<......>>>...>>.>>>....<<<<<.<<..<<<
<..<<<<<.<<<<<<<..>>>>>>>...>>>>>..>>>>.>>....<<<<
<<.....>>>>>>.......>>>>>....>>>.>>>.....>>>>>>>>.
.....>>>>>...>>.>>>>.>>>.....<<<<<<<......<<.....<
<..<<<<....>>>>..>>....>>.......>>>>>>>...........
<<<<<<..........>>>>>>..........>>>>>>....<<<<<<<<
.......>>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<
..<<<<.<<....<<<<<<<<.<<<..<.<<..<...<<<<<<...>>>>
>>...>..>>.>..>>>.>>>>>>>>...>>.>>>>...>.>>...>...
..<<<<<<<<<....>>>>>>>>>.........
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)		E4 N5 W7 F8 S9 H10 R12 R13 Y14 G15 K16 R19 C24 H27 G29 L30 I31 R32 Y34 R40 Q41 R44 E45 F55 R56
Binding residue
(residue number reindexed from 1)		E1 N2 W4 F5 S6 H7 R9 R10 Y11 G12 K13 R16 C21 H24 G26 L27 I28 R29 Y31 R37 Q38 R41 E42 F52 R53
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
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
UniProtP41057|RS29A_YEAST Small ribosomal subunit protein uS14A (Gene Name=RPS29A)

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