Structure of PDB 5ndv Chain C5 Binding Site BS01

Receptor Information

>5ndv Chain C5 (length=116) Species: 559292 (Saccharomyces cerevisiae S288C)

SYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKL
AAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHY
LGEFSITYTPVRHGRA

Ligand information

>5ndv Chain 2 (length=1712)

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

Structure summary

• PDB: 5ndv Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): P38 A39 R40 R42 R43 R44 R47 A54 K59 R77 T78 H79 R81 N82 Y97 G99 K100 Y115 G117 E118 T122 T124 V126 H128
• Binding residue (residue number reindexed from 1): P23 A24 R25 R27 R28 R29 R32 A39 K44 R62 T63 H64 R66 N67 Y82 G84 K85 Y100 G102 E103 T107 T109 V111 H113

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndv, PDBe:5ndv, PDBj:5ndv
• PDBsum: 5ndv
• PubMed: 29208708
• UniProt: Q01855|RS15_YEAST Small ribosomal subunit protein uS19 (Gene Name=RPS15)