Structure of PDB 5ndw Chain C6 Binding Site BS01

Receptor Information

>5ndw Chain C6 (length=141) Species: 559292 (Saccharomyces cerevisiae S288C)

AVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPL
LLVGLDKFSNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSK
NELKKAFTSYDRTLLIADSRRPEPKKFGGKGARSRFQKSYR

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): Q8 T9 F10 K12 K14 S15 V19 H21 K26 L28 R66 R68 G71 G72 G73 H74 V75 S76 Q77 I118 R122 R123 P124 E125 P126 K127 K128 F129 K132 R135 S136 R137 F138 Q139 K140 S141 Y142
• Binding residue (residue number reindexed from 1): Q6 T7 F8 K10 K12 S13 V17 H19 K24 L26 R64 R66 G69 G70 G71 H72 V73 S74 Q75 I116 R120 R121 P122 E123 P124 K125 K126 F127 K130 R133 S134 R135 F136 Q137 K138 S139 Y140

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 translation
• GO:0006413 translational initiation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• 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: P0CX51|RS16A_YEAST Small ribosomal subunit protein uS9A (Gene Name=RPS16A)