Structure of PDB 6o8y Chain 5 Binding Site BS01

Receptor Information
>6o8y Chain 5 (length=64) Species: 1351 (Enterococcus faecalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKQKTHRGLAKRVKRTGGGGLKRGRAFTSHRFHGKTKKQRRQLRKASMVA
KGDYKRIRQQLARM
Ligand information
>6o8y Chain A (length=2897) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuaagugaauaagggcgcacgguggaugccuuggcacuaggagccgauga
aggacgggacuaacaccgauaugcuuuggggagcuguaaguaagcuauga
uccagagauuuccgaaugggggaacccaauaucuuuuauaggauauuacu
uuucagugaauacauagcugauuagagguagacgcagagaacugaaacau
cuuaguaccugcaggaagagaaagaaaauucgauucccugaguagcggcg
agcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguag
gacuccgauaugguagucuguuaguauaguugaaggauuuggaaaauucc
gcuaaagagggugaaagccccguagacgaaaugcugacaacaccuaggag
gauccugaguacggcggaacacgagaaauuccgucggaauccgcggggac
caucccgcaaggcuaaauacucccuagugaccgauagugaaccaguaccg
ugagggaaaggugaaaagcaccccggaaggggagugaaauagauccugaa
accgugugccuacaacaagucaaagcucguuaaugagugauggcgugccu
uuuguagaaugaaccggcgaguuacgauugcaugcgagguuaagucgaag
agacggagccgcagcgaaagcgagucugaauagggcgaaugaguauguag
ucguagacccgaaaccaugugaucuacccauguccagguugaaggugcgg
uaaaacgcacuggaggaccgaacccacguacguugaaaagugcggggaug
agguguggguagcggagaaauuccaaacgaacuuggagauagcugguucu
cuccgaaauagcuuuagggcuagccucggaauugagaaugauggagguag
agcacuguuuggacuaggggcccaucggguuaccgaauucagauaaacuc
cgaaugccauucauuuauauccgggagucagacugcgagugauaagaucc
guagucgaaagggaaacagcccagaccaccagcuaaggucccaaaauaua
uguuaaguggaaaaggaugugggguugcacagacaacuaggauguuggcu
uagaagcagccaccauuuaaagagugcguaauagcucacuagucgaguga
cccugcgccgaaaauguaccggggcuaaacauauuaccgaagcuguggac
uacaccauuagguguagugguaggagagcguucuaagggcguugaagguc
gaucgugaggacggcuggagcgcuuagaagugagaaugccgguaugagua
gcgaaagacaggugagaauccuguccaccguaugacuaagguuuccuggg
gaaggcucguccgcccaggguuagucgggaccuaagccgaggccgauagg
cguaggcgauggacaacagguugauauuccuguaccaguuguuuuuguuu
gagcaauggagggacgcaguaggcuaaggaaugcaugcgauuggaagugc
auguccaagcaaugagucuugaguagaguuaaaugcuuuacucuuuaagg
acaaguugugacggggagcgaaauaguagcgaaguuccugacgucacacu
gccaagaaaagcuucuagugagaaaacaacugcccguaccguaaaccgac
acagguagucgaggagaguauccuaaggugagcgagcgaacucucguuaa
ggaacucggcaaaaugaccccguaacuucgggagaaggggugcugacuuc
ggucagccgcagugaauaggcccaagcgacuguuuaucaaaaacacaggu
cucugcaaaaucguaagaugaaguauaggggcugacgccugcccggugcu
ggaagguuaagaggauggguuagcuucggcgaagcucagaauugaagccc
caguaaacggcggccguaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgacccgcacgaaaggcguaacgauuugggcacugucucaacg
agagacucggugaaauuuuaguaccugugaagaugcagguuacccgcgac
aggacggaaagaccccauggagcuuuacuguaguuugauauugaguguuu
guaccacauguacaggauagguaggagccgaugagaccggaacgcuaguu
ucggaggaggcgcuggugggauacuacccuuguguuaugaacccucuaac
ccgcaccacuaaucguggugggagacagugucagaugggcaguuugacug
gggcggucgccuccuaaaagguaacggaggcgcccaaagguucccucaga
augguuggaaaucauucgaagaguguaaaggcagaagggagcuugacugc
gagaccuacaagucgagcagggacgaaagucgggcuuagugauccggugg
uuccgcauggaagggccaucgcucaacggauaaaagcuacccuggggaua
acaggcuuaucucccccaagaguccacaucgacggggagguuuggcaccu
cgaugucggcucgucgcauccuggggcuguagucggucccaaggguuggg
cuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgugaga
caguucggucccuauccgucgcgggcguuggaaauuugagaggagcuguc
cuuaguacgagaggaccgggauggacuuaccgcugguguaccaguuguuc
ugccaagggcauugcuggguagcuauguagggaagggauaaacgcugaaa
gcaucuaagugugaagcccaccucaagaugagauuucccauuucuuuaag
aaaguaagaccccugagagaugaucagguagauagguuggaaguggaagg
cuagugauaguuggagcggaccaauacuaaucggucgaggacuuaac
<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
..<<<<<.........>>>>>..>>.>>....<<<<<......<......
>.......>>>>.>.........<<....>>..<<<<<......<<....
.>>.....>>>>>..(((....<<<<<<<......>>>>>>>......<<
<<<<<<.....<<<.<<.<<<<<<<<<.<<<...<<<.<......>.>>>
((......<<<.....))>>>...>>>...>>>>>>>>>>>>>>..>>>>
..>>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<
<<<>>>>>..)))......]].>>>>>>>.]]...............<<.
...>>....]].........<<<<....>>>>.............}....
>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...<.<
........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<.....
..>>...>>>...<<....>>...<<<.....>>>.......>>>>>>>>
>>>>>..<<.<...<<<.<<.....<<<<<<<<<..<<<....<<<<<<.
.....>>>>>>.....>>>...<<<.<<<<<........>>>>>>>>...
.>>>>>>>>>...<<<.....>>>......>>.>>>......>.>>..<<
<<<<....<<<<<....>>>>><<<<<<<<..<..<<<<<<<<<......
.....<<<<<<<<.......<<<...>>>........>>>>>>>>.....
......>>>>.>>>>>..>>>>>>>.>>..<<<<<<<.<<......>>.>
>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<
<<<...........<<..<<<<<<<<<........<<.....<...<...
..........>...>..........................>>....>>>
>>>>>>.>>...........))).....>>>>>>.>>>...>>>>>>><<
<<<<<<....>>>>>>>>....>>>>>><.<<<<<<<.<<......<<<<
<.<<....>>.>>>>>...>>.>>>>>>>..>.....>>>>>><......
<<....<<<<<<.......>>>>>><<<<....<<<<<.<<<..<<<<<<
...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>
>...>>>...>>...<<<<<........>>>>>))<<<<<<<........
..<<...<<<<....<<<<...<...<<<<<.........[.[.......
....<...<<<<<..<<<<.<<<<<<<<<.....>>>>>>>>>.....>>
>>..>>>>>....>...<<.........>>....>>>>>....>....>>
>>.........>>>>..>>......>>>>>>>>>>>.>>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<.........<.....<<<<<....<<..>>.....>>>>><<<<<<...
.>>>>>>............<<<<<<<<<..<<<.........>>>..<<<
<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<
<<..<<<...<<...<<<<<..<<....>>...>>>>>...>>...>>>>
>>>>..>>>>><<<<<...>>>>>........<...........<<<<<<
.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.(((.((......<<<<.((<<<<..<<<<<.<<<<<<<<<.<<<.<<<<
<<<.<<<<...........<<<<<..<<<.......<<<<<<<....>>>
>>>>....>>>............>>>>>..>>>>.>>>>>>>.>>>....
<<.<<<<<<.....>>>>>>>>.....>>>>>>>>>..>>>>>..<<<<.
....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<
<<<<.......>>>>>>.....<<.((.((>>....>>>>>>>...<<<<
..<<<......>>>..>>>>.<<<....>>>.>>))))......<<<<<<
<.((..>>>>..))>>>>>>>.............>>>>..))>>>>....
...<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>..
.....<.<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<
<.....>>>>>.....>>>>>..>...>>>..>....<<<<<<<....>>
>.>>>>....))..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<
<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<
<.].]>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<....
.......>>>>>....>>>.>>>>.......>>>>>>>..<<<......>
>>.....<<<<<<<<<.......>>>>>....<<<<<<<<..<<....<<
<<<....>>>>>...>>...>>>>>.>>>...>>>>....>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6o8y Cryo-electron microscopy structure of the 70S ribosome from Enterococcus faecalis.
Resolution4.14 Å
Binding residue
(original residue number in PDB)
P2 K3 Q4 K5 T6 H7 R8 K12 R13 T17 A27 F28 S30 H31 R32 F33 H34 K38 Q40 R42 Q43 R45 K46 K52 G53 D54 R57 R59 Q60 R64
Binding residue
(residue number reindexed from 1)
P1 K2 Q3 K4 T5 H6 R7 K11 R12 T16 A26 F27 S29 H30 R31 F32 H33 K37 Q39 R41 Q42 R44 K45 K51 G52 D53 R56 R58 Q59 R63
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
GO:0022625 cytosolic large 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:6o8y, PDBe:6o8y, PDBj:6o8y
PDBsum6o8y
PubMed33004869
UniProtA0A1B4XM73

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