Structure of PDB 5ndw Chain E0 Binding Site BS01

Receptor Information

>5ndw Chain E0 (length=60) Species: 559292 (Saccharomyces cerevisiae S288C)

AKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVN
GKRRMNPGPS

Ligand information

>5ndw Chain 2 (length=1770)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccuacuacaugguauaacugu
gguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagaga
uguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucau
aauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaau
uucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuca
acggguaacggggaauaaggguucgauuccggagagggagccugagaaac
ggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaa
uucagggagguagugacaauaaauaacgauacagggcccauucgggucuu
guaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagg
gcaagucuggugccagcagccgcgguaauuccagcuccaauagcguauau
uaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguugg
ccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccuu
guggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuca
aagcaggcguauugcucgaauauauuagcauggaauaauagaauaggacg
uuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggga
cggucgggggcaucaguauucaauugucagaggugaaauucuuggauuua
uugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaauc
aagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuua
accauaaacuaugccgacuagggaucgggugguguuuuuuuaaugaccca
cucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaugg
ucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagug
gagccugcggcuuaauuugacucaacacggggaaacucaccagguccaga
cacaauaaggauugacagauugagagcucuuucuugauuuuguggguggu
ggugcauggccguucuuaguugguggagugauuugucugcuuaauugcga
uaacgaacgagaccuuaaccuacuaaauaguggugcuagcauuugcuggu
uauccacuucuuagagggacuaucgguuucaagccgauggaaguuugagg
caauaacaggucugugaugcccuuagacguucugggccgcacgcgcgcua
cacugacggagccagcgagucuaaccuuggccgagaggucuugguaaucu
ugugaaacuccgucgugcuggggauagagcauuguaauuauugcucuuca
acgaggaauuccuaguaagcgcaagucaucagcuugcguugauuacgucc
cugcccuuuguacacaccgcccgucgcuaguaccgauugaauggcuuagu
gaggccucaggaucugcuuagagaagccaucucagagcggagaauuugga
caaacuuggucauuuagaggaacuaaaagucguaacaagguuuccguagg
ugaaccugcggaaggaucau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): A2 R10 A11 G12 K13 V14 K15 Q17 T18 V21 K23 K26 K28 P30 K31 G32 R33 A34 R37 R43 R55 M56 N57
• Binding residue (residue number reindexed from 1): A1 R9 A10 G11 K12 V13 K14 Q16 T17 V20 K22 K25 K27 P29 K30 G31 R32 A33 R36 R42 R54 M55 N56

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0010494 cytoplasmic stress granule
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P0CX33|RS30A_YEAST Small ribosomal subunit protein eS30A (Gene Name=RPS30A)