Structure of PDB 5obm Chain c2 Binding Site BS01

Receptor Information

>5obm Chain c2 (length=124) Species: 559292 (Saccharomyces cerevisiae S288C)

AEVTIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEA
NIIKLVEGLANDPENKVPLIKVADAKQLGEWAGLGKIDREGNARKVVGAS
VVVVKNWGAETDELSMIMEHFSQQ

Ligand information

>5obm Chain 6 (length=1739)

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

Structure summary

• PDB: 5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): R43 G44 R46 E47 V66 V116 G117 A118 S119
• Binding residue (residue number reindexed from 1): R24 G25 R27 E28 V47 V97 G98 A99 S100

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0030490 maturation of SSU-rRNA
• GO:0042274 ribosomal small subunit biogenesis
• GO:1990145 maintenance of translational fidelity

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5obm, PDBe:5obm, PDBj:5obm
• PDBsum: 5obm
• PubMed: 29208708
• UniProt: P48589|RS12_YEAST Small ribosomal subunit protein eS12 (Gene Name=RPS12)