Structure of PDB 5jvg Chain U Binding Site BS01

Receptor Information
>5jvg Chain U (length=74) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENG
QVKTVWLSANALRTLSKGPYKGIE
Ligand information
>5jvg Chain X (length=2710) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

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PDB5jvg Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
Resolution3.428 Å
Binding residue
(original residue number in PDB)
Y6 L7 V15 V18 I19 R20 R21 D27 R32 K33 T34 T35 G36 I37 T38 V41 R43 N45 L46 H47 K48 K49 A64 R68
Binding residue
(residue number reindexed from 1)
Y1 L2 V10 V13 I14 R15 R16 D22 R27 K28 T29 T30 G31 I32 T33 V36 R38 N40 L41 H42 K43 K44 A59 R63
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:5jvg, PDBe:5jvg, PDBj:5jvg
PDBsum5jvg
PubMed27791159
UniProtQ9RRG8|RL28_DEIRA Large ribosomal subunit protein bL28 (Gene Name=rpmB)

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