Structure of PDB 8vty Chain 1N Binding Site BS01

Receptor Information
>8vty Chain 1N (length=140) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV
Ligand information
>8vty Chain 1A (length=2872) [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
gauguggcgccgcgaagacagccaggagguuggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccc
aggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggc
ggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagg
gugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguc
agcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaag
ggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgc
ucuaggcuagggggaccggagccauggacgagcccggccagaagcgcagg
gugggagguaggcaaauccgccucccaacaagcucugcgugguggggaag
cccgggugacaaccccccgaagccagggagccaagaaaagccucuaagca
caaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaag
agcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggc
cccguaacuucgggagaaggggugcucccuggggugaugagccccgggga
gccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucug
cgaacucguaagaggagguauagggagcgacgcuugcccggugccggaag
gucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggaccc
ggugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaa
aagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcc
ugcguaggauaggugggagccugugaacccccgccuccggguggggggga
ggcgccggugaaauaccacccuggcgcggcugggggccuaacccucggau
ggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaa
agguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccg
gagagcgcaaggguagaagggggccugacugcgaggccugcaagccgagc
aggggcgaaagccgggccuagugaaccgguggucccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agcguccacagcggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
ccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccg
gaagggacgcaccucugguuucccagcugucccuccaggggcauaagcug
gguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagc
ccgccccaagaugaggccucccacggcagccgguaaggacccgggaagac
cacccgguggaugggccggggguguaagcgccgcgaggcguugagccgac
cggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.>>>>>.>>...<<<<<<.....<......>......>>>>>.>......
...<<....>>...<<<<<.....<<.....>>....>>>>>...<<<..
..<<<<<<<<.....>>>>>>>>......<<<<<<<<<..<<<...<<<<
<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>>>
...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<<.
......>>>>>>>>>......<<<<<..((((>>>>>..>>>......>>
.>>>>>>.>>...............<<....>>....>>.........<<
<<....>>>>..................>>>>>>>>>>>.......<<<<
<<<<<<<..>>>>>>>>>>>...<............>.<<<<<<....<<
<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>..<
<<<.....>>>>...<<<..>>>...>>>>>>>>>>>>>..<<.<...<<
<<<<.....<<<<<<<<<..<<<....<<<<<<......>>>>>>.....
>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<...<
<<<<<......>>>>.>>...>>>>>>>>..>>.>...>>>>>>>>>...
..>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<..
....>>>...<<<<.<<<...<<<(((.....<<<<<<...........<
<..<<<<<<<<<........<<<<<.<<<...<<.........>>...>>
>.........<<......>>...>>>>>....>>>>>>>>>.>>......
....)))......>>>>>>.>>>...>>>>>>><<<<<<<<.....>>>>
>>>>....>>>>>>..<<<<<...<<<......<<<<<.<<<....>>>>
>>>>...>>>..>>>>>........>>>>>><......<<.....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>
>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<<....<<
<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<...<<<<<<<
<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>>..>>><...<
<<..>>>.....>>>>>>...>>>..>>>>>.........>>>>...>>.
..>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<<...
.>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<.....<<
<<<....<....>.....>>>>><<<<<<<<<<<<.....>>>>>>>>>>
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<
<<...<<...<<<<<....>>>>>...>>...>>>>>>>>..>>>>><<<
<<<.......>>>>>>........<...........<<<<<<.....>>>
>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>
>>>.....>.....<<<<<........>>>>>..<<<<<<<<.<<<....
.....<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<<<<<<
...........<<<<<..<<<......<<<<<<<<....>>>>>>>>...
>>>............>>>>>..>>>>>>>>>>>>>>>>...<<<<<....
>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<....
.......>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.
....<<...(((>>....>>>>>>>...<<<<..<<<......>>>..>>
>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..>>>>>>
>>>.............>>>>..>>>>>>.......<<<<.<.<<<<<<..
.<<.......>>...>>>>>>...>>>>.>.......<<<<<.<<<<<<.
.<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.....>>
>>>..>...>>>.>>....<<<<<<<....>>>.>>>>........>>>>
>>>>>>>....<<<<<<<...<<<<..<<<<<<<...............>
>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...>>>>
>...>>>>.>>>>>...<<<....<<<<<...........>>>>>....>
>>.>>>>.......>>>>>>>..<<<<.>>>>....<<<<<<<<<.....
..>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>
>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vty Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
K2 T3 V5 W13 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 R97 E100 H101 A102 G105 M106 P108 K109 P111 L112 R114 K118 K121 Q133
Binding residue
(residue number reindexed from 1)
K2 T3 V5 W13 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 K70 R74 Y75 S76 Y78 P79 G80 L82 K83 R97 E100 H101 A102 G105 M106 P108 K109 P111 L112 R114 K118 K121 Q133
External links
PDB RCSB:8vty, PDBe:8vty, PDBj:8vty
PDBsum8vty
PubMed39039256
UniProtP60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)

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