Structure of PDB 5obm Chain d2 Binding Site BS01

Receptor Information
>5obm Chain d2 (length=129) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFE
YIDDHRSGKIVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGY
VILTTSAGIMDHEEARRKHVSGKILGFVY
Ligand information
>5obm Chain 6 (length=1739) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaucugguugauccugccaguagucauaugcuugucucaaagauuaagcc
augcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcuca
uuaaaucaguuaucguuuauuugauaguucccuacaugguauaacugugg
uaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagagaug
uauuuauuagauaaaaaaucaaugucuucggacucuuugaugauucauaa
uaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaauuu
cugcccuaucaacuuucgaugguaggauaguggccuaccaugguuucaac
ggguaacggggaauaaggguucgauuccggagagggagccugagaaacgg
cuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccuaauu
cagggagguagugacaauaaauaacgauacaguuguaauuggaaugagua
caauguaaauaccuuaacgaggaacaauuggagggcaagucuggugccag
cagccgcgguaauuccagcuccaauagcguauauuaaaguuguugcaguu
aaaaagcucguaguugaacuuugggcccgguuggccgguacuggauuucc
aacggggccuuuccuucuggcuaacuggcgaaccaggacuuuuacuuuga
aaaaauuagaguguucaaagcaggcguauugcucgaauauauuagcaugg
aauaauagaauaggacguuugguucuauuuuguugguuucuaggaccauc
guaaugauuaauagggacggucgggggcaucaguauucaauugucagagg
ugaaauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaa
ggacguuuucauuaaucaagaacgaaaguuaggggaucgaagaugaucag
auaccgucguagucuuaaccauaaacuaugccgacuagggaucggguggu
guuuuuuuaaugacccacucggcaccuuacgagaaaucaaagucuuuggg
uucuggggggaguauggucgcaaggcugaaacuuaaaggaauugacggaa
gggcaccaccaggaguggagccugcggcuuaauuugacucaacacgggga
aacucaccagguccagacacaauaaggauugacagauugagagcucuuuc
uugauuuugugggugguggugcauggccguucuuaguugguggagugauu
ugucugcuuaauugcgauaacgaacgagaccuuaaccuacuaaauagugg
ugcuagcauuugcugguuauccacuucuuagagggacuaucgguuucaag
ccgauggaaguuugaggcaauaacaggucugugaugcccuuagacguucu
gggccgcacgcgcgcuacacugacggagccagcgagucuaaccuuggccg
agaggucuugguaaucuugugaaacuccgucgugcuggggauagagcauu
guaauuauugcucuucaacgaggaauuccuaguaagcgcaagucaucagc
uugcguugauuacgucccugcccuuuguacacaccgcccgucgcuaguac
cgauugaauggcuuagugaggccucaggaucugcuuagagaagccaucuc
agagcggagaauuuggacaaacuuggucauuuagaggaacuaaaagucgu
aacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<<.{.[[[[>>>>><<<<.<<<<<<...<.<...<......<<<
.<<<..<<....<<....<<..........>>...>>.>>......<<..
......<<<..<<..<<....<<<..............<.....<<.<<.
......>>.>>......>.........<<<<<..<<....>>..>>>>>.
...<<<<<<......(((((((....<..>.................>>>
>>>.........<<<<..<<<.....>>>.>>>>....>>>...>>>>..
>>>.<<<....<<<....<<<<<<<<.......>>>>>>>>>>>......
>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<..........>
>>.>>.<.<<....>>.>...>>>>>>.........<<<....<<<....
.>>>..>>>..>....>.>.....<<<<<<<..>>>>.>>.>.....<<.
.<...........>..>>.........<<<<<((....<.<<<<.....<
<..))>>.......>>>>>>>>>>..>>>>>>>>>>.........<<<[[
.....<.<<...<<<.<<....<<<<<<.<<<..<<<<..>>>>......
>>>.>>>>>>....<<<<<<............>>>>>>...<<<<<.<<.
......<<...<.......>..<<<.....>>>....>>......>>.>>
..>>>.........<<<..<<<<<<<<.....))))))).>>>>>>>>.>
>>.....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<.
.....>>>......>.>>>>>>..>>......<<<....>>>..>>>>..
.>>>>>.>>>...>>>...>>.>....<<<<<<<...<...<<<<.....
....>>>>...>>>>>>>>..........<<<.<<.<<<..<<<<<<<<.
<<<<.....>.>>>>>>>>>>>..>>>...<<..]]>>...>>.....>>
>.>>>.<<<......<<<......>>>....>>>..]]]].}<<<<<.<<
<<<<<..<<.<<<<<<..<<<.<<<<<<......<<........>>....
......<<<<<.<....<<<<<........<<.<<<........>>>.>>
......>>>>>...<<.<<<..<<.<<<<<<....<<<.<<<<<....>>
>...<<<......>>>...>>.>>>....<<<<<.<<..<<<<..<<<<<
.<<<<<<....>>>>>>...>>>>>..>>>>.>>....<<<<<<.....>
>>>>>.......>>>>>....>>>.>>>.....>>>>>>>.....>.>>>
>>...>>.>>>>.>>>.....<<<<<<<......<<.....<<..<<<<.
...>>>>..>>....>>.......>>>>>>>...........<<<<<<..
........>>>>>>..........>>>>>>....<<<<<<<<.......>
>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<..<<<<.<
<....<<<<<<<<.<<<..<.<<......<<<<<<<.<<<<.....>>>>
.>>>>>>>......>>.>..>>>.>>>>>>>>...>>.>>>>...>.>>.
..>.....<<<<<<<<<....>>>>>>>>>.........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		T2 R3 S4 S5 A8 D9 N12 N16 T20 R28 S31 K32 H56 R57 S58 K71 V74 I75 S76 R78 N80 K82 I83 T105 T106 S107 R118 K119 H120 S122 K124
Binding residue
(residue number reindexed from 1)		T1 R2 S3 S4 A7 D8 N11 N15 T19 R27 S30 K31 H55 R56 S57 K70 V73 I74 S75 R77 N79 K81 I82 T104 T105 S106 R117 K118 H119 S121 K123
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

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
UniProtP0C0W1|RS22A_YEAST Small ribosomal subunit protein uS8A (Gene Name=RPS22A)

[Back to BioLiP]