Structure of PDB 6yef Chain 2 Binding Site BS01

Receptor Information
>6yef Chain 2 (length=57) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVK
HLVTVEE
Ligand information
>6yef Chain A (length=2881) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccgauga
aggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuuga
uccagagauuuccgaauggggaaacccagcaugaguuaugucauguuauc
gauaugugaauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaaguuguugggguuguaggaca
cucggaguuacaaaggacgacauuagacgaaucaucuggaaagaugaauc
aaagaagguaauaauccuguagucgaaaauguugucucucuugaguggau
ccugaguacgacggagcacgugaaauuccgucggaaucugggaggaccau
cuccuaaggcuaaauacucucuagugaccgauagugaaccaguaccguga
gggaaaggugaaaagcaccccggaaggggagugaaauagaaccugaaacc
gugugcuuacaaguagucagagcccguuaaugggugauggcgugccuuuu
guagaaugaaccggcgaguuacgauuugaugcaagguuaagcaguaaaug
uggagccguagcgaaagcgagucugaauagggcguuuaguauuuggucgu
agacccgaaaccaggugaucuacccuuggucagguugaaguucagguaac
acugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaacu
gaggguagcggagaaauuccaaucgaaccuggagauagcugguucucucc
gaaauagcuuuagggcuagccucaagugaugauuauuggagguagagcac
uguuuggacgaggggccccucggguaccgaauucagacaaacuccgaaug
ccaauuaauuuaacuugggagucagaacaugggugauaagguccguguuc
gaaagggaaacagcccagaccaccagcuaaggucccaaaauauauguuaa
guggaaaaggauguggcguugcccagacaacuaggauguuggcuuagaag
cagccaucauuuaaagagugcguaauagcucacuagucgagugacacugc
gccgaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccu
ggacaaugguaggagagcguucuaagggcguugaagcaugaucguaagga
cauguggagcgcuuagaagugagaaugccggugugaguagcgaaagacgg
gugagaaucccguccaccgauugacuaagguuuccagaggaaggcucguc
cgcucuggguuagucggguccuaagcugaggccgacaggcguaggcgaug
gauaacagguugauauuccuguaccaccuauaaaucgauggggggacgca
guaggauaggcgaagcgugcgauuggauugcacgucuaagcaguaaggcu
gaguauuaggcaaauccgguacucguuaaggcugagcugugauggggaga
aguucgagucguugauuucacacugccgagaaaagccucuagauagaaaa
uaggugcccguaccgcaaaccgacacagguagucaagaugagaauucuaa
ggugagcgagcgaacucucguuaaggaacucggcaaaaugaccccguaac
uucgggagaaggggugcucuuuaggguuaacgcccagaagagccgcagug
aauaggcccaagcgacuguuuaucaaaaacacaggucucugcuaaaccgu
aaggugauguauaggggcugacgccugcccggugcuggaagguuaagagg
agugguuagcuucugcgaagcuacgaaucgaagccccaguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gacccgcacgaaaggcguaacgauuugggcacugucucaacgagagacuc
ggugaaaucauaguaccugugaagaugcagguuacccgcgacaggacgga
aagaccccguggagcuuuacuguagccugauauugaaauucggcacagcu
uguacaggauagguaggagccuuugaaacgugagcgcuagcuuacgugga
ggcgcuggugggauacuacccuagcuguguuggcuuucuaacccgcacca
cuuaucguggugggagacagugucaggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcucaaagguucccucagaaugguugg
aucauucauagaguguaaaggcauaagggagcuugacugcgagaccuaca
agucgagcagggucgaaagacggacuuagugauccggugguuccgcaugg
aagggccaucgcucaacggauaaaagcuaccccggggauaacaggcuuau
cucccccaagaguucacaucgacggggagguuuggcaccucgaugucggc
ucaucgcauccuggggcuguagucggucccaaggguugggcuguucgccc
auuaaagcgguacgcgagcuggguucagaacgucgugagacaguucgguc
ccuauccgucgugggcguaggaaauuugagaggagcuguccuuaguacga
gaggaccgggauggacauaccucugguguaccaguugucgugccaacggc
auagcuggguagcuauguguggacgggauaagugcugaaagcaucuaagc
augaagccccccucaagaugagauuucccaacugguuauaagaucccuca
aagaugaugagguuaauagguucgagguggaagcauggugacauguggag
cugacgaauacuaaucgaucgaagacuuaau
<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<.....
.<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....
>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.<<
<<<<<<<.........>>>>>>>.>>.>>....<<<<<......<<....
>>.......>>>>.>.........<<....>>..<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<.>>>>>>>......<<<<<<
<<<<<<<.......<<<<<<<<<<.<<<...<<<<<......>>>>>((.
.....<<<.....))>>>...>>>...>>>>>>>>>>>>>>.>>>>>..>
>>>.....<<<<<<<<.........>>>>>>>>......<<<<<..<<<<
>>>>>..)))......]].>>>>>>>.]]...............<<....
>>....]].........<<<<....>>>>..................>>>
>>>>>>>>.......<<<<..<<<<......>>>>..>>>>...<.<...
.....>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<<.....>>
>...>>>...<<....>>..<<<<.....>>>>.....>>>>>.>>>>>>
>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<.....
.>>>>>>.....>>>...<<<.<<<<<........>>>>>>>>....>>>
>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<
....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<.....<<<...
<<<<<<<<...<<...<.....>...>>...>>>>>>>>..>>.>.....
>>>>>.>>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>
....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<...
........<<..<<<<.<<<<........<<.....<...<<........
...>>...>..........................>>....>>>>.>>>>
.>>...........))).....>>>>>>.>>>...>>>>>>><<<<<<<.
>>>>>>>....>>>>>><.<<<<<<<.<<......<<<<<.<<....>>.
>>>>>...>>.>>>>>>>..>.....>>>>>><......<<....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<<.<<.<.<<<...<<<....>>>...>>>..>>
>...<<<<<........>>>>>))<<<<<<<..<<<...<<<<....<<<
<..<<...<<<<<.<.<<<.....{...>>>.>.<....<<<<...<<<.
<<<<<<..<<.....>>.>>>>>>......>>>...>>>>.....>....
........>>>>>....>>...>>>>.........>>>>..>>>.....>
>>>>>>>>>>..>>.....<<......>>>>>>>.<<<.......>>>..
>>>>..<<<<....<<<<<<<<.<<.........<.....<<<<<....<
<..>>.....>>>>><<<<<<<.<<<<....>>>>.>>>>>>>.......
.....<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<..
..>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<..
.<<<<<<.<<....>>..>>>>>>...>>...>>>>>>>>..>>>>><<<
<<<.......>>>>>>........<...........<<<<<.......>>
>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>
>>>.....>.....<<<<<........>>>>>..<<<<<<<<.(((.[[.
.....<<<<.[[<<<<..<<<<<.<<<<<<<<<.<<<<.<<<...<.<<<
...........<<<<<..<<<......<<<.<<<......>>>.>>>...
>>>............>>>>>..>>>.>...>>>.>>>>....<<.<<<<<
<.....>>>>>>>>.....>>>>>>>>>..>>>>>..<<<<.....>>>>
<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<....
.>>>>>>.....<<.[.(((>>....>>>>>>>...<<<<..<<<.....
.>>>..>>>>.<<<....>>>.>>)))]......<<<<<<<.((..>>>>
..))>>>>>>>.............>>>>..]]>>>>.......<<<<.<.
<<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<<<
.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>
>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....
]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<........
.......>>>>>>>.<<<<<...<<<<...<<<<<<<<<<..}...>>>>
>..>>>>>...>>>>.>>>>>...<<<.<..<<<<<...........>>>
>>...>>>>.>>>>.......>>>>>>>.<<<..>>>....<<<<<<<<<
.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>
>>..>>>>>.>>>...>>>>....>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yef Cryo-EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 angstrom resolution.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
S11 I13 G14 R15 P16 E17 R20 T22 A25 T31 A42 G45 Q46 K49
Binding residue
(residue number reindexed from 1)
S10 I12 G13 R14 P15 E16 R19 T21 A24 T30 A41 G44 Q45 K48
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:0015934 large ribosomal subunit
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:6yef, PDBe:6yef, PDBj:6yef
PDBsum6yef
PubMed32852796
UniProtP0A0G2|RL30_STAA8 Large ribosomal subunit protein uL30 (Gene Name=rpmD)

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