Structure of PDB 5jvg Chain E Binding Site BS01

Receptor Information

>5jvg Chain E (length=171) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVER
PSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALE
MNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKP
DAYHGKGVRFVGEQIALKAGK

Ligand information

>5jvg Chain X (length=2710)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaac
cgaaacgcuugcguuucgggguuguaggaccaucaagccgaaguggcugg
aaagcuacaccucagaaggugagaguccuguaggcgaacgagccugagua
ggucguuguucgugaaacgaugacugaauccgcgcggaccaccgcgcaag
gcuaaauacucccagugaccgauagcgcauaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaagagaaccugaaaccguggacuuac
aagcagucauggcaccuuaugcguguuauggcgugccuauugaagcauga
gccggcgacuuagaccugacgugcgagcuuaaguugaaaaacggaggcgg
agcgaaagcgaguccgaauagggcggcauuaguacgucgggcuagacucg
aaaccaggugagcuaagcaugaccagguugaaacccccggggggcggagg
accgaaccggugccugcugaaacagucucggaugaguuguguuuaggagu
gaaaagcuaaccgaaccuggagauagcuaguucuccccgaaauguauuga
gguacagccucggauguugaccauguccuguagagcacucacaaggcuaa
accuuaugaaacuccgaaggggcacgcguuuaguccgggagugaggcugc
gagagcuaacuuccguagccgagagggaaacaacccagaccaucagcuaa
ggucccuaaaugaucgcucagugguuaaggaugugucgucgcauagacag
ccaggagguuggcuuagaagcagccacccuucaaagagugcguaauagcu
cacuggucgagugacgaugcgccgaaaaugaucggggcucaagugaucua
ccgaagcuauggauucaacucgcgaguugucugguaggggagcguucagu
ccgcggagaagccauaccggaaggagugguggagccgacugaagugcgga
ugccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaagg
acaaggguuccuggggaagggucguccgcccagggaaagucgggaccuaa
ggugaggccgaacggcgcagccgauggacagcaggucaagauuccugcac
cgaucauguggagugauggagggacgcauuacgcuauccaaugccaagcu
auggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuac
cggucaugccucagacguaucgggagcuuccucggaagcgaaguuggaaa
cgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccgua
ccgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcgaga
gaacccucguuaaggaacuuugcaaucucaccccguaacuucggaagaag
ggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacuguu
uaccaaaaucacagcacucugccaacacgaacaguggacguauagggugu
gacgccugcccggugccggaaggucaaguggagcggugcaagcugcgaaa
ugaagccccggugaacggcgaccgcuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaggcguaacgaucugggcgcugucucaacg
agggacucggugaaauugaauuggcuguaaagaugcggccuacccguagc
aggacgaaaagaccccguggagcuuuacuauagucuggcauugggauucg
gguugaaacuuggauuucuaaccugaaaaaucacuuucggggaccgugcu
uggcggguaguuugacuggggcggucgccucccaaaauguaacggaggcg
cccaaaggucaccucaagacgguuggaaaucgucuguagagcgcaaaggu
agaagguggcuugacugcgagacugacacgucgagcagggaggaaacucg
ggcuuagugaaccggugguaccguguggaagggccaucgaucaacggaua
aaaguuaccccggggauaacaggcugaucucccccgagaguccauaucgg
cggggagguuuggcaccucgaugucggcucgucgcauccuggggcugaag
aaggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugg
guucagaacgucgugagacaguucggucucuauccgcuacgggcgcagga
gaauugaggggaguugcuccuaguacgagaggaccggagugaacggaccg
cuggucucccugcugucguaccaacggcacaugcaggguagcuauguccg
gaacggauaaccgcugaaagcaucuaagcgggaagccagccccaagauga
guucucccacugagguaagacucccggaagaccaccggguuaagaggcca
ggcgugcacgcauagcaauguguucagcggacuggugcucaucagucgag
gucuugacca

.<<<<<<<......<<<<<<<<<<<....<<<..<<<<<<<<<<<<....
..<<<<<<<((..((>>>>.....<<<<<<...<<.))..))..>>....
..>>>>>>...>>>....<<<....>>><<<<<....>>>>><<<<....
>>>>>>...<<<<<<.....<......>......>>>>>.>.........
<<....>>...<<<<......<<.....>>.....>>>>...<<<....<
<<<<.<<....>>.>>>>>......<<<....<<..<<<...<<<<<...
...>>>>>((......<<<.....))>>>...>>>....>>.>>>.....
<<<<<<<<.........>>>>>>>>......<<<<<..((((>>>>>..>
>>......>>.>>>>>>.>>..............<<....>>....>>..
.......<<<<....>>>>.............>....>>>>>>>>>>>..
.....<<<<<<<<<<.......>>>>>>>>>>...<.<........>.>.
<<<<<<....<<<.<<<<<<<<<<..<<<...<<<....>>>...>>>..
.<<....>>...<<......>>.........>>>>>>>>>>>>>..<<.<
...<<<<<<.....<<<<<<<<<..<<<.....<<<<<.>>>>>......
>>>...<<<<.<.<<........>>.>>>>>....>>>>>>>>>...<<<
.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<...
.>>>>><<<<<<<<<...<<<..<<<<<<...<<<...<<<.<<<<....
.>>>>.>>>..>>.>...>>>>>>...>>>..>>>>>>>.>>..<<<<<<
<.<<......>>.>>>>>>>....<<<......>>>...<<<<.<<<...
<<<(((.....<<<<<<...........<<..<<<<<<<<<........<
<<<<.<<...<<<<.......>>>>...>>.........<<......>>.
..>>>>>....>>>>>>>>>.>>..........)))......>>>>>>.>
>>...>>>>>>><..<<<<......>>>>..>....>>>>>><.<<<<<<
<.<<......<<<<<.<<....>>.>>>>>...>>.>>>>>>>..>....
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...
<<<...<<<<..>>>>...>>>...>>...<<<<<........>>>>>))
<<<<<<<<<...<<...<<<<....<<<<..<<<..<<<<<.<<<<.<<.
.[[[....>>>>>><<<<<<<.<<..<<<<<<<<<<...<<.....>>.>
>>>>>..>>>>..>>>>>>>>>...<<<<<....>>>>>....>>>>>..
.>>>...>>>>.........>>>>...>>......>>>>>>>>>>>>>..
>>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<.
...<<<<<<<<.<<.........<.....<<<<<...............>
>>>><<<<<<<<...>>>>>>>>............<<<<<<<<<..<<..
.........>>..<<<<<<<.....<<<.....>>>.......>>>>>>>
.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>
>...>>>>>>>>..>>>>>.............<...........<<<<<<
.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<<
<<<<..>>>>>>>>>>>>...<<<<<<........>>>>>>....>>>>>
.>>>..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>.
.<<...<<<<<<<...<<<<<<<.....>>>>>>>.....<<...(((>>
....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.
>>))).......<<<<<<<.<<..))))..>>>>>>>>>...........
..>>>>..>>>>>>.......<<<<...<<<<<<...<<.......>>..
.>>>>>>....>>>.>.......<.<<<.<<<<<<..<<<<<<<<<....
..>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>...>>>..
>....<<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<
<<<<...<<<<..<<<<<<<...............>>>>>>>.<<<<<..
.<<<<...<<<<<<<<<<<.]]]>>>>>>...>>>>>...>>>>.>>>>>
....<<....<<<<<...........>>>>>....>>..>>>>.......
>>>>>>>..<<.>>....<<<<<<<<<.......>>>>>....<<<<<<<
<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>...
.>>>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jvg Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
• Resolution: 3.428 Å
• Binding residue (original residue number in PDB): G5 Q59 R62 A63 G66 L67 T70 G108 S110 H111 K138 Q139 G142 Q143 K150 K153 Y157 H158 K160 K172 K175
• Binding residue (residue number reindexed from 1): G1 Q55 R58 A59 G62 L63 T66 G104 S106 H107 K134 Q135 G138 Q139 K146 K149 Y153 H154 K156 K168 K171

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jvg, PDBe:5jvg, PDBj:5jvg
• PDBsum: 5jvg
• PubMed: 27791159
• UniProt: Q9RSL3|RL6_DEIRA Large ribosomal subunit protein uL6 (Gene Name=rplF)