Structure of PDB 8vtu Chain 11 Binding Site BS01

Receptor Information
>8vtu Chain 11 (length=97) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRV
RVAGQEITFRVAASHIPKVYELVERAKGLKLEGLSPKEIKKELLKLL
Ligand information
>8vtu Chain 1A (length=2871) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcagcggccgcaaaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguggcuuagaagcagccauccu
uuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaaug
aucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccca
ggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcg
gcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagaggg
ugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguca
gcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagg
gcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcu
cuaggcuagggggaccggagccauggacgagcccggccagaagcgcaggg
ugggagguaggcaaauccgccucccaacaagcucugcgugguggggaagc
ccgggugacaaccccccgaagccagggagccaagaaaagccucuaagcac
aaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaaga
gcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcc
ccguaacuucgggagaaggggugcucccuggggugaugagccccggggag
ccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugc
gaacucguaagaggagguauagggagcgacgcuugcccggugccggaagg
ucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggcc
guaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
accugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccg
gugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaa
agaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccu
gcguaggauaggugggagccugugaacccccgccuccgggugggggggag
gcgccggugaaauaccacccuggcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccacggcagccgguaaggacccgggaagacc
acccgguggaugggccggggguguaagcgccgcgaggcguugagccgacc
ggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>......
...<<....>>...<<<<<.....<<.....>>....>>>>>...<<<..
..<<<<<<<<.....>>>>>>>>......<<<<<<<<<..<<<...<<<<
<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>>>
...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<<.
......>>>>>>>>>......<<<<<..((((>>>>>..>>>......>>
.>>>>>>.>>...............<<....>>....>>.........<<
<<....>>>>..................>>>>>>>>>>>.......<<<<
<<<<<<<..>>>>>>>>>>>...<............>.<<<<<<....<<
<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>..<
<<<.....>>>>...<<<..>>>...>>>>>>>>>>>>>..<<.<...<<
<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>>>.....
>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<....
<<<<........>>>..>...>>>>>>>>..>>.>...>>>>>>>>>...
..>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<..
....>>>...<<<<.<<<...<<<(((.....<<<<<<...........<
<..<<<<<<<<<........<<<<<.<<<..<<<.......>>>...>>>
.........<<......>>...>>>>>....>>>>>>>>>.>>.......
...)))......>>>>>>.>>>...>>>>>>><<<<<<<<.....>>>>>
>>>....>>>>>><.<<<<<...<<<......<<<<<.<<<....>>>>>
>>>...>>>..>>>>>..>.....>>>>>><......<<.....<<<<<<
.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>
.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>
...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<<
<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<...<<<<<<<<
<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>>..>>><...<<
<..>>>.....>>>>>>...>>>..>>>>>.........>>>>...>>..
.>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<<....
>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<.....<<<
<<...............>>>>><<<<<<<<<<<<.....>>>>>>>>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<
<...<<...<<<<<....>>>>>...>>...>>>>>>>>..>>>>><<<<
<<.......>>>>>>........<...........<<<<<<.....>>>>
>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>
>>.....>.....<<<<<........>>>>>..<<<<<<<<.<<<.....
....<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<<<<<<.
..........<<<<<..<<<.......<<<<<<<....>>>>>>>....>
>>............>>>>>..>>>>>>>>>>>>>>>>...<<<<<....>
>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.....
......>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>..
...<....(((.>....>>>>>>>...<<<<..<<<......>>>..>>>
>.<<<....>>>.>>))).......<<<<<<<.<<..))))..>>>>>>>
>>.............>>>>..>>>>>>.......<<<<.<.<<<<<<...
<<.......>>...>>>>>>...>>>>.>.......<<<<<.<<<<<<..
<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.....>>>
>>..>...>>>.>>....<<<<<<<....>>>.>>>>........>>>>>
>>>>>>....<<<<<<<...<<<<..<<<<<<<...............>>
>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...>>>>>
...>>>>.>>>>>...<<<....<<<<<...........>>>>>....>>
>.>>>>.......>>>>>>>..<<<<.>>>>....<<<<<<<<<......
.>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>
>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vtu Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
S2 K3 K10 I13 V14 A15 N16 Q19 R20 R21 A24 K25 G28 G29 V30 G31 K32 K33 T34 T35 K39 R40 R41 Q42 Y43 P44 N45 Q47 K48 R50 R52 R61 H66 K69 R76 G79
Binding residue
(residue number reindexed from 1)
S1 K2 K9 I12 V13 A14 N15 Q18 R19 R20 A23 K24 G27 G28 V29 G30 K31 K32 T33 T34 K38 R39 R40 Q41 Y42 P43 N44 Q46 K47 R49 R51 R60 H65 K68 R75 G78
External links
PDB RCSB:8vtu, PDBe:8vtu, PDBj:8vtu
PDBsum8vtu
PubMed39039256
UniProtP60494|RL28_THET8 Large ribosomal subunit protein bL28 (Gene Name=rpmB)

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