Structure of PDB 5ndw Chain c4 Binding Site BS01

Receptor Information

>5ndw Chain c4 (length=128) Species: 559292 (Saccharomyces cerevisiae S288C)

NSQVFGVARIYASFNDTFVHVTDLSGKETIARVTGGMKVKADRDESSPYA
AMLAAQDVAAKCKEVGITAVHVKIRATGGTRTKTPGPGGQAALRALARSG
LRIGRIEDVTPVPSDSTRKKGGRRGRRL

Ligand information

>5ndw Chain 6 (length=1736)

uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguuccucuacaugguauaacugug
guaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagau
guauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucaua
auaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauu
ucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaa
cggguaacggggaauaaggguucgauuccggagagggagccugagaaacg
gcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaau
ucagggagguagugacaauaaauaacgauacagggcccauucgggucuug
uaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggaggg
caagucuggugccagcagccgcgguaauuccagcuccaauagcguauauu
aaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguuggc
cggucacuggauuuccaacggggccuuuccuucuggcuaacgaaccagga
cuuuuacuuugaaaaaauuagaguguucaaagcaggcguauugcucgaau
auauuagcauggaauaauagaauaggacguuugguucuauuuuguugguu
ucuaggaccaucguaaugauuaauagggacggucgggggcaucaguauuc
aauugucagaggugaaauucuuggauuuauugaagacuaacuacugcgaa
agcauuugccaaggacguuuucauuaaucaagaacgaaaguuaggggauc
gaagaugaucagauaccgucguagucuuaaccauaaacuaugccgacuag
ggaucgggugguguuuuuuuaaugacccacucggcaccuuacgagaaauc
aaagucuuuggguucuggggggaguauggucgcaaggcugaaacuuaaag
gaauugacggaagggcaccaccaggaguggagccugcggcuuaauuugac
ucaacacggggaaacucaccagguccagacacaauaaggauugacagauu
gagagcucuuucuugauuuugugggugguggugcauggccguucuuaguu
gguggagugauuugucugcuuaauugcgauaacgaacgagaccuuaaccu
acuaaauaguggugcuagcauuugcugguuauccacuucuuagagggacu
aucgguuucaagccgauggaaguuugaggcaauaacaggucugugaugcc
cuuagacguucugggccgcacgcgcgcuacacugacggagccagcgaguc
uaaccuuggccgagaggucuugguaaucuugugaaacuccgucgugcugg
ggauagagcauuguaauuauugcucuucaacgaggaauuccuaguaagcg
caagucaucagcuugcguugauuacgucccugcccuuuguacacaccgcc
cgucgcuaguaccgauugaauggcuuagugaggccucaggaucugcuaga
gcggagaauuuggacaaacuuggucauuuagaggaacuaaaagucguaac
aagguuuccguaggugaaccugcggaaggaucauua

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

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): R18 N24 D25 F27 H29 G35 K36 E37 T38 R41 T43 G45 M46 D51 R52 E54 G88 V121 P122 S123 D124 S125 T126 R127 K129 G130 G131 R132 R133 R135 R136
• Binding residue (residue number reindexed from 1): R9 N15 D16 F18 H20 G26 K27 E28 T29 R32 T34 G36 M37 D42 R43 E45 G79 V112 P113 S114 D115 S116 T117 R118 K120 G121 G122 R123 R124 R126 R127

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P39516|RS14B_YEAST Small ribosomal subunit protein uS11B (Gene Name=RPS14B)