Structure of PDB 5ndw Chain S5 Binding Site BS01

Receptor Information

>5ndw Chain S5 (length=206) Species: 559292 (Saccharomyces cerevisiae S288C)

FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIF
VAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLD
IINVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVN
QAIALLTIGAREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELER
VAKSNR

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): H72 A78 R81 K84 R92 N95 L97 M98 M99 N100 G101 R102 N103 N104 G105 K106 K107 L108 K109 R112 R166 N169 R180 F184 R185 N186 I187 T189 I190
• Binding residue (residue number reindexed from 1): H53 A59 R62 K65 R73 N76 L78 M79 M80 N81 G82 R83 N84 N85 G86 K87 K88 L89 K90 R93 R147 N150 R161 F165 R166 N167 I168 T170 I171

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000054 ribosomal subunit export from nucleus
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006450 regulation of translational fidelity
• GO:0030490 maturation of SSU-rRNA

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P26783|RS5_YEAST Small ribosomal subunit protein uS7 (Gene Name=RPS5)