Structure of PDB 5hkv Chain P Binding Site BS01

Receptor Information
>5hkv Chain P (length=112) 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]
MEAKAVARTIRIAPRKVRLVLDLIRGKNAAEAIAILKLTNKASSPVIEKV
LMSALANAEHNYDMNTDELVVKEAYANEGPTLKRFRPRAQGRASAINKRT
SHITIVVSDGKE
Ligand information
>5hkv Chain X (length=2695) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
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]
PDB5hkv Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
Resolution3.66 Å
Binding residue
(original residue number in PDB)		V6 R8 R11 R15 K16 R18 R25 N40 K41 S53 A56 N57 H60 N61 Y62 N77 E78 P80 K83 R84 R86 P87 R88 A89 Q90 G91 R92 A93 S94 A95 N97 R99 H102
Binding residue
(residue number reindexed from 1)		V6 R8 R11 R15 K16 R18 R25 N40 K41 S53 A56 N57 H60 N61 Y62 N77 E78 P80 K83 R84 R86 P87 R88 A89 Q90 G91 R92 A93 S94 A95 N97 R99 H102
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
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:5hkv, PDBe:5hkv, PDBj:5hkv
PDBsum5hkv
PubMed28973455
UniProtQ2FW11|RL22_STAA8 Large ribosomal subunit protein uL22 (Gene Name=rplV)

[Back to BioLiP]