Structure of PDB 5hl7 Chain A Binding Site BS01

Receptor Information

>5hl7 Chain A (length=269) Species: 93061 (Staphylococcus aureus subsp. aureus NCTC 8325)

IKKYKPITNGRRNMTSLDFAEITKTTPEKSLLKPLPKKAGRNNQGKLTVR
HHGGGHKRQYRVIDFKRNKDGINAKVDSIQYDPNRSANIALVVYADGEKR
YIIAPKGLEVGQIVESGAEADIKVGNALPLQNIPVGTVVHNIELKPGKGG
QIARSAGASAQVLGKEGKYVLIRLRSGEVRMILSTCRATIGQVGNLQHEL
VNVGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAPIGRPSPMSPWGK
PTLGKKTRRGKKSSDKLIV

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): P8 I9 T10 N11 R14 N15 L37 K40 R43 N44 N45 Q46 G47 K48 L49 T50 V51 H53 H54 G56 H58 K59 R60 P85 G99 G149 Q153 A155 R156 S157 A158 G159 Y171 L176 S178 E180 R182 H200 E201 N204 V205 G206 K207 A208 S211 R212 W213 R217 P218 T219 V220 R221 G222 S223 V224 M225 N226 N228 D229 H232 G235 E236 G237 R238 P240 I241 G242 R243 P244 P246 M247 S248 P249 W250 T254 G256 K257 K258 T259 R260 S266
• Binding residue (residue number reindexed from 1): P6 I7 T8 N9 R12 N13 L35 K38 R41 N42 N43 Q44 G45 K46 L47 T48 V49 H51 H52 G54 H56 K57 R58 P83 G97 G147 Q151 A153 R154 S155 A156 G157 Y169 L174 S176 E178 R180 H198 E199 N202 V203 G204 K205 A206 S209 R210 W211 R215 P216 T217 V218 R219 G220 S221 V222 M223 N224 N226 D227 H230 G233 E234 G235 R236 P238 I239 G240 R241 P242 P244 M245 S246 P247 W248 T252 G254 K255 K256 T257 R258 S264

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• 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: P60430|RL2_STAA8 Large ribosomal subunit protein uL2 (Gene Name=rplB)