Structure of PDB 5hkv Chain L Binding Site BS01

Receptor Information

>5hkv Chain L (length=109) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

ISKIDKNKVRLKRHARVRTNLSGTAEKPRLNVYRSNKHIYAQIIDDNKGV
TLAQASSKDSDIATTATKVELATKVGEAIAKKAADKGIKEIVFDRGGYLY
HGRVKALAE

Ligand information

>5hkv Chain X (length=2695)

gauuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaau
gaaggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuu
gauccagagauuuccgaauggggaaacccagcaugaguuaugucauguua
ucgauauguauacauagcauaucagaaggcacacccggagaacugaaaca
ucuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggc
gagcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguugua
ggacacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaag
augaaucaaagaagguaauaauccuguagucgaaaauguugucucucuug
aguggauccugaguacgacggagcacgugaaauuccgucggaaucuggga
ggaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagu
accgugagggaaaggugaaaagcaccccggaaggggagugaaauagaacc
ugaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgu
gccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagca
guaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauu
uggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuc
aggcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaa
cugaggguagcggagaaauuccaaucgaaccuggagauagcugguucucu
ccgaaauagcuuuagggcuagccucaagugaugauuauuggagguagagc
acuguuuggacgaggguuaccgaauucagacaaacuccgaaugccaauua
auuuaacuugggagucagaacaugggugauaagguccguguucgaaaggg
aaacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaa
aggauguggcguugcccagacaacuaguagucgagugacacugcgccgaa
aauguaccggggcuaaacauauuaccgaagcuguggauugucuggacaau
gguaggagagcguucuaagggcguugaagcaugaucguaaggacaugugg
agcgcuuagaagugagaaugccggugugaguagcgaaagacgggugagaa
ucccguccaccgauugacuaagguuuccagaggaaggcucguccgcucug
gguuagucggguccuaagcugaggccgacaggcguaggcgauggauaaca
gguugauauuccuguaccaccuauaaucguaucgauggggggacgcagua
ggauaggcgaagcgugcgauuggauugcacgucuaagcaguaggcgagua
auccgguacucgggcugagcugugauggggagaagagagucguugauuuc
acacugccgagaaaagccucuagauagaauaggugcccguaccgcaaacc
gacacagguagucaagaugagaauucuaaggugagcgagcgaacucucgu
uaaggaacucggcaaaaugaccccguaacuucgggagaaggggugcucuu
uaggguuaacgcccagaagagccgcagugaauaggcccaagcgacuguuu
aucaaaaacacaggucucugcuaaaccguaaggugauguauaggggcuga
cgccugcccgugcuggaagguuaagaggagugguuagcugcgaagcuacg
aaucgaagccccaguaaacggcgcuaagguagcgaaauuccuugucgggu
aaguuccgacccgcacgaaaggcguaacgauuugggcacugucucaacga
gagacucggugaaaucauaguaccugugaagaugcagguuacccgcgaca
ggacggaaagaccccguggagcuuuacuguagccugauauugaaauucgg
cuuucuaacccgcaccacuuaucgugugggagacagugucaagcgggcag
uuugacuggggcggucgccuccuaaaagguaacggaggcgcucaaagguu
cccucagaaugguuucauucauagaguguaaaggcauaagggagcuugac
ugcgagaccuacaagucgagcagggucgaaagacggacuuagugauccgg
ugguuccgcauggaagggccaucgcucaacggauaaaagcuaccccgggg
auaacaggcuuaucucccccaagaguucacaucgacggggagguuuggca
ccucgaugucggcucaucgcauccuggggcuguagucggucccaaggguu
gggcuguucgcccauuaaagcgguacgcgagcuggguucagaacgucgug
agacaguucggucccuauccgucgugggcguaggaaauuugagaggagcu
guccuuaguacgagaggaccgggauggacauaccucugguguaccaguug
ucgugccaacggcauagcuggguagcuauguguggacgggauaagugcug
aaagcaucuaagcaugaagccccccucaagaugagauuucccaacuuggu
uauaagaucccucaaagaugaugagguuaauagguucgagguggaagcau
ggugacauguggagcugacgaauacuaaucgaucgaagacuuaau

..<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>...
..>>>>>>>...>>>....<<<....>>><<<<<<<......>>>>>>>.
<<<<<<<<<.......>>>>>>>.>>.>>....<<<<<......<.....
.>.......>>>>.>.........<<....>>..<<<<<......<<...
..>>.....>>>>>..(((....<<<<<<<<....>>>>>>>>......<
<<<<<<<<..............<<<<<<<<<.<<<...<<<<<......>
>>>>((......<<<.....))>>>...>>>...>>>>>>>>.>.....>
>>>>..>>>>.....<<<<<<<<.........>>>>>>>>......<<<<
<..<<<<>>>>>..)))......]].>>>>>>>.]]..............
.<<....>>....]].........<<<<....>>>>..............
....>>>>>>>>>>>.......<<<<..<<<<......>>>>..>>>>..
.<.<........>.>.<<<<<<....<<<<<<<.<<<<<..<<<...<<.
......>>...>>>...<<....>>..<<<<.....>>>>.....>>>>>
.>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<
<<.>>>>>>.....>>>...<<<.<<<<<........>>>>>>>>....>
>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<
<<....<<<<<....>>>>><<<<<<<<<...<<<<<<<<<.....<<<.
..<<<<<<<<...<......>...>>>>>>>>..>>.>.....>>>>.>>
>>>..>>>>>>>.>>..<<<<<<<<<<......>>>>>>>>>>....<<<
......>>>...<<<<.<<<...<<<(((.....<<<<<<..........
.<<..<<<<.<<<<........<<<...>>>....>>>>.>>>>.>>...
........))).....>>>>>>.>>>...>>>>>>><<<<<....>>>>>
....>>>>>>..<<<<<<<.<<......<<<<<.<<....>>.>>>>>..
.>>.>>>>>>>........>>>>>><......<<....<<<<<<......
.>>>>>><<<<....<<<<<.<<<..<<<<<<...<<.....>>.>>>>>
>....((<<<<.<<.<.<<<...<<<....>>>...>>>..>>>...<<<
<<........>>>>>))<<<<<<<......<<<...<<<<....<<<<..
.<<...<....<.<<<...{.{...>>>.>.<....<<<<<.<<<<....
.........>...>>>..>>>>>.....>..............>....>>
...>>>>.........>>>.>.>>>...>>>>>>>>>>>.>>>.....<<
......>>>>>>>.<<<<....>.>>>..>>>>..<<<<....<<<<<<<
<.<<.........<.....<<<<<.....<..>......>>>>><<<<<<
<.<<<<....>>>>.>>>>>>>............<<<<<<<<<..<<<..
.......>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<
<<<<..<<.<<<<<<<..<<<...<<...<<<<<..<<.>>...>>>>>.
..>>...>>>>>>>>..>>>>..........<...........<<<<<<.
....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>
>>>.>>>>>>.....>.(...<<<<<.......)>>>>>..<<<<<<<<.
(((.[[......<<<<.[[<<<<..<<<<<.<<.<<<<<<.<<<<.....
.>>>>....<<.<<<.<<.....>>>>>>>.....>>>>>>.>>..>>>>
>..<<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<
<<<...<<<<<<..>>>>>>.....<<.[.(((>>....>>>>>>>...<
<<<..<<<......>>>..>>>>.<<<....>>>.>>)))]......<<<
<<<<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>.
......<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.
>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<
<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<...
.>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<
<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<
<<<<.}.}>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<.
..........>>>>>....>>>.>>>>.......>>>>>>>.<<<<.>>>
>....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<
<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hkv Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
• Resolution: 3.66 Å
• Binding residue (original residue number in PDB): S3 R17 L22 I89 K90 I92 R96
• Binding residue (residue number reindexed from 1): S2 R16 L21 I88 K89 I91 R95

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5hkv, PDBe:5hkv, PDBj:5hkv
• PDBsum: 5hkv
• PubMed: 28973455
• UniProt: Q2FW22|RL18_STAA8 Large ribosomal subunit protein uL18 (Gene Name=rplR)