Structure of PDB 5ndv Chain C7 Binding Site BS01

Receptor Information
>5ndv Chain C7 (length=115) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIA
GYTTHLMKRIQKGPVRGISFKLQEEERERKDQYVPEVSRSNGVLNVDNQT
SDLVKSLGLKLPLSV
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)		G2 R3 V4 R5 K7 K10 R11 F28 K32 R33 S43 K44 R45 L46 N48 K49 G52 K59 R60
Binding residue
(residue number reindexed from 1)		G1 R2 V3 R4 K6 K9 R10 F27 K31 R32 S42 K43 R44 L45 N47 K48 G51 K58 R59
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0000028 ribosomal small subunit assembly
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
UniProtP02407|RS17A_YEAST Small ribosomal subunit protein eS17A (Gene Name=RPS17A)

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