Structure of PDB 5jvg Chain J Binding Site BS01

Receptor Information

>5jvg Chain J (length=136) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVM
SRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMF
EVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEA

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

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

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): F10 F14 G16 R17 M18 K23 G24 F30 N46 R57 Y66 F70 K77 K78 E81 T82 R83 M84 G85 K86 G87 R120 H124 K125 P127 K131 A141
• Binding residue (residue number reindexed from 1): F5 F9 G11 R12 M13 K18 G19 F25 N41 R52 Y61 F65 K72 K73 E76 T77 R78 M79 G80 K81 G82 R115 H119 K120 P122 K126 A136

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• 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: Q9RXJ5|RL16_DEIRA Large ribosomal subunit protein uL16 (Gene Name=rplP)