Structure of PDB 5obm Chain D6 Binding Site BS01

Receptor Information
>5obm Chain D6 (length=97) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVR
DLSEASVYPEYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPP
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)		P2 K3 K4 R5 A6 S7 N8 G9 R10 N11 K13 R15 H17 K28 K32 K34 K37 R38 K70 V75 S76 I79 H80 I83 V84 R85 R87 S88 R89 R92 R95 P97
Binding residue
(residue number reindexed from 1)		P1 K2 K3 R4 A5 S6 N7 G8 R9 N10 K12 R14 H16 K27 K31 K33 K36 R37 K69 V74 S75 I78 H79 I82 V83 R84 R86 S87 R88 R91 R94 P96
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
UniProtP39939|RS26B_YEAST Small ribosomal subunit protein eS26B (Gene Name=RPS26B)

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