Structure of PDB 5obm Chain S1 Binding Site BS01

Receptor Information
>5obm Chain S1 (length=214) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVC
LADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQT
LIEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVIS
EILTKEVQGSTLAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLK
QPKFDVGALMALHG
Ligand information
>5obm Chain 2 (length=1712) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguucacaugguauaacugugguaa
uucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagauguau
uuauuagauaaaaaaucaaugucuucggacucuuugaugauucauaauaa
cuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuucug
cccuaucaacuuucgaugguaggauaguggccuaccaugguuucaacggg
uaacggggaauaaggguucgauuccggagagggagccugagaaacggcua
ccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauucag
ggagguagugacaauaaauaacgauacagggucuuguaauuggaaugagu
acaauguaaauaccuuaacgaggaacaauuggagggcaagucuggugcca
gcagccgcgguaauuccagcuccaauagcguauauuaaaguuguugcagu
uaaaaagcucguaguugaacuuugggcccgguuggccggucggauuucca
acggggccuuuccuucuggcuaccaggacuuuuacuuugaaaaaauuaga
guguucaaagcaggcguauugcucgaauauauuagcauggaauaauagaa
uaggacguuugguucuauuuuguugguuucuaggaccaucguaaugauua
auagggacggucgggggcaucaguauucaauugucagaggugaaauucuu
ggauuuauugaagacuaacuacugcgaaagcauuugccaaggacguuuuc
auuaaucaagaacgaaaguuaggggaucgaagaugaucagauaccgucgu
agucuuaaccauaaacuaugccgacuagggaucgggugguguuuuuuuaa
ugacccacucggcaccuuacgagaaaucaaagucuuuggguucugggggg
aguauggucgcaaggcugaaacuuaaaggaauugacggaagggcaccacc
aggaguggagccugcggcuuaauuugacucaacacggggaaacucaccag
guccagacacaauaaggauugacagauugagagcucuuucuugauuuugu
gggugguggugcauggccguucuuaguugguggagugauuugucugcuua
auugcgauaacgaacgagaccuuaaccuacuaaauaguggugcuagcauu
ugcugguuauccacuucuuagagggacuaucgguuucaagccgauggaag
uuugaggcaauaacaggucugugaugcccuuagacguucugggccgcacg
cgcgcuacacugacggagccagcgagucuaaccuuggccgagaggucuug
guaaucuugugaaacuccgucgugcuggggauagagcauuguaauuauug
cucuucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugau
uacgucccugcccuuuguacacaccgcccgucgcuaguaccgauugaaug
gcuuagugaggccucaggaucugccagagcggagaauuuggacaaacuug
gucauuuagaggaacuaaaagucguaacaagguuuccguaggugaaccug
cggaaggaucau
...<<<<<...[[[[>>>>>[[[[.((((((................[[[
.[[[..<<....<<....<<..........>>...>>.>>......{{..
......[[[..{{..{{....[[[...........<.....<<.<<....
...>>.>>......>.........<<<<<..<......>..>>>>>[...
((((((......<<<<<<<<<<<....>>>..............))))))
.....]...<<<<..<<<.....>>>.>>>>....]]]...}}}}..]]]
.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>......>>>
...<<<.<<<<....>>>>....>>>.}}.<<.<<<..........>>>.
>>.<.<<....>>.>...]]]]]].........<<<....<<<.....>>
>..>>>...............<<<<<..<....>..>>.>>>......<<
<.<...........>>.>>.........<<<<<((......<<<<.....
<<..))>>.......>>>>.>>>>>..))))))]]]].........[[[{
{.......{{...[[[.[[....<<<<<<.<<<<<....<..>....>>>
>>.>>>>>>....<<<<<<...>>>>>>...<<<<<.<<.......<<..
.<.......>..<<<.....>>>....>>......>>.>>..>>>.....
....[[...((((((((....>>>>>>>>.))))))))..]].....]].
...<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<......>>>..
....>.>>>>>>..>>.......<<....>>...>>>>...>>>>>.>>>
...]]]...}}......<<<<<<<...<...<<<<.........>>>>..
.>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.<<<.......
.>>>>>>>>>>>..>>>...<<..}}>>...>>.....>>>.]]].<<<.
.....<<<......>>>....>>>..]]]]..<<<<<.<<<<<<<..<<.
<<<<<<..<<<.<<<<<.......<<........>>..........<<<<
<......<<<<<........<<.<<<........>>>.>>......>>>>
>...<<.<<<..<<.<<<<<<....<<<.<<<<<....>>>...<<<...
...>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<.<<<<<<...
.>>>>>>...>>>>>..>>>>.>>....<<<<<<.....>>>>>>.....
..>>>>>....>>>.>>>.....>>>>>>>.......>>>>>....>.>>
>>.>>>.....<<<<<<<......<<.....<<..<<<<....>>>>..>
>....>>.......>>>>>>>......<....<<<<<<..........>>
>>>>....>.....>>>>>>....<<<<<<<<.......>>>>>>>>...
...>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<<....<<<<<
<<<.<<<..<.<<......<<<<......>>>>......>>.>..>>>.>
>>>>>>>...>>.>>>>...>.>>...>.....<<<<<<<<<....>>>>
>>>>>.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		P23 V114 K116 W117 Q118 T119 L120 N124 R136 Q146 N148 Q149 V150 K151 H153 Y155 Q157 S158 S159 H160 R165 K202 D203 I204 F205 P206 K216
Binding residue
(residue number reindexed from 1)		P4 V95 K97 W98 Q99 T100 L101 N105 R117 Q127 N129 Q130 V131 K132 H134 Y136 Q138 S139 S140 H141 R146 K183 D184 I185 F186 P187 K197
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5obm, PDBe:5obm, PDBj:5obm
PDBsum5obm
PubMed29208708
UniProtP33442|RS3A1_YEAST Small ribosomal subunit protein eS1A (Gene Name=RPS1A)

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