Structure of PDB 5hl7 Chain W Binding Site BS01

Receptor Information

>5hl7 Chain W (length=57) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

AKLQITLTRSVIGRPETQRKTVEALGLKKTNSSVVVEDNPAIRGQINKVK
HLVTVEE

Ligand information

>5hl7 Chain X (length=2705)

auuaaguuauuaagggcgcacgguggaugccuuggcacuagaagccaaug
aaggacguuacuaacgacgauaugcuuuggggagcuguaaguaagcuuug
auccagagauuuccgaauggggaaacccagcaugaguuaugucauguuau
cgauauguauacauagcauaucagaaggcacacccggagaacugaaacau
cuuaguacccggaggaagagaaagaaaauucgauucccuuaguagcggcg
agcgaaacgggaagagcccaaaccaacaagcuugcuuguugggguuguag
gacacucuaugaguuacaaaggacgacauuagacgaaucaucuggaaaga
ugaaucaaagaagguaauaauccuguagucgaaaauguugucucucuuga
guggauccugaguacgacggagcacgugaaauuccgucggaaucugggag
gaccaucuccuaaggcuaaauacucucuagugaccgauagugaaccagua
ccgugagggaaaggugaaaagcaccccggaaggggagugaaauagaaccu
gaaaccgugugcuuacaaguagucagagcccguuaaugggugauggcgug
ccuuuuguagaaugaaccggcgaguuacgauuugaugcaagguuaagcag
uaaauguggagccguagcgaaagcgagucugaauagggcguuuaguauuu
ggucguagacccgaaaccaggugaucuacccuuggucagguugaaguuca
ggcugaauggaggaccgaaccgacuuacguugaaaagugagcggaugaac
ugaggguagcggagaaauuccaaucgaaccuggagauagcugguucucuc
cgaaauagcuuuagggcuagccucaagugaugauuauuggagguagagca
cuguuuggacgaggguuaccgaauucagacaaacuccgaaugccaauuaa
uuuaacuugggagucagaacaugggugauaagguccguguucgaaaggga
aacagcccagaccaccagcuaaggucccaaaauauauguuaaguggaaaa
ggauguggcguugcccagacaacuagcucacuagucgagugacacugcgc
cgaaaauguaccggggcuaaacauauuaccgaagcuguggauuguccuug
gacaaugguaggagagcguucuaagggcguugaagcaugaucguaaggac
auguggagcgcuuagaagugagaaugccggugugaguagcgaaagacggg
ugagaaucccguccaccgauugacuaagguuuccagaggaaggcucgucc
gcucuggguuagucggguccuaagcugaggccgacaggcguaggcgaugg
auaacagguugauauuccuguaccaccuacguaucgauggggggacgcag
uaggauaggcgaagcgugcgauuggauugcacgucuaagcaguaggcgag
uaauccgguacucguggcugagcugugauggggagaagagagucguugau
uucacacugccgagaaaagccucuagauagaauaggugcccguaccgcaa
accgacacagguagucaagaugagaauucuaaggugagcgagcgaacucu
cguuaaggaacucggcaaaaugaccccguaacuucgggagaaggggugcu
cuuuaggguuaacgcccagaagagccgcagugaauaggcccaagcgacug
uuuaucaaaaacacaggucucugcuaaaccguaaggugauguauaggggc
ugacgccugcccgugcuggaagguuaagaggagugguuagcugcgaagcu
acgaaucgaagccccaguaaacggcggcuaagguagcgaaauuccuuguc
ggguaaguuccgacccgcacgaaaggcguaacgauuugggcacugucuca
acgagagacucggugaaaucauaguaccugugaagaugcagguuacccgc
gacaggacggaaagaccccguggagcuuuacuguagccugauauugaaau
ucgggcuuucuaacccgcaccacuuaucguggugggagacagugucaagc
gggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcuca
aagguucccucagaaugguugaaaucauucauagaguguaaaggcauaag
ggagcuugacugcgagaccuacaagucgagcagggucgaaagacggacuu
agugauccggugguuccgcauggaagggccaucgcucaacggauaaaagc
uaccccggggauaacaggcuuaucucccccaagaguucacaucgacgggg
agguuuggcaccucgaugucggcucaucgcauccuggggcuguagucggu
cccaaggguugggcuguucgcccauuaaagcgguacgcgagcuggguuca
gaacgucgugagacaguucggucccuauccgucgugggcguaggaaauuu
gagaggagcuguccuuaguacgagaggaccgggauggacauaccucuggu
guaccaguugucgugccaacggcauagcuggguagcuauguguggacggg
auaagugcugaaagcaucuaagcaugaagccccccucaagaugagauuuc
ccaacuugguuauaagaucccucaaagaugaugagguuaauagguucgag
guggaagcauggugacauguggagcugacgaauacuaaucgaucgaagac
uuaau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5hl7 A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.
• Resolution: 3.55 Å
• Binding residue (original residue number in PDB): S11 I13 G14 E17 R20 K21 T22 A25 K29 K30 T31 N32 A42 G45 Q46 K49
• Binding residue (residue number reindexed from 1): S10 I12 G13 E16 R19 K20 T21 A24 K28 K29 T30 N31 A41 G44 Q45 K48

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

External links

• PDB: RCSB:5hl7, PDBe:5hl7, PDBj:5hl7
• PDBsum: 5hl7
• PubMed: 27958389
• UniProt: P0A0G2|RL30_STAA8 Large ribosomal subunit protein uL30 (Gene Name=rpmD)