Structure of PDB 5jvh Chain L Binding Site BS01

Receptor Information

>5jvh Chain L (length=104) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

RRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQIIDDSRGQTLAAASSA
ALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAA
REGG

Ligand information

>5jvh Chain X (length=2658)

ggucaagauaguaaggguccacgguggaugcccuggcgcuggagccgaug
aaggacgcgauuaccugcgaaaagccccgacgagcuggagauacgcuuug
acucggggauguccgaauggggaaacccaccucguaagagguauccgcaa
ggaugggaacucagggaacugaaacaucucaguaccugaaggagaagaaa
gagaauucgauuccguuaguagcggcgagcgaacccggaucagcccaaac
ucaagccgaaguggcuggaaagcuacaccucagaaggugagaguccugua
ggcgaacgagcuaggucguuguucgugaaacgaugacugaauccgcgcgg
accaccgcgcaaggcuaaauacucccagugaccgauagcgcauaguaccg
ugagggaaaggugaaaagaaccccgggaggggagugaaagagaaccugaa
accguggacuuacaagcagucauggcaccuuaugcguguuauggcgugcc
uauugaagcaugagccggcgacuuagaccugacgugcgagcuuaaguuga
aaaacggaggcggagcgaaagcgaguccgaauagggcggcauuaguacgu
cgggcuagacucgaaaccaggugagcuaagcaugaccagguugaaacccc
cgugacagggggcggaggaccgaaccggugccugcugaaacagucucgga
ugaguuguguuuaggagugaaaagcuaaccgaaccuggagauagcuaguu
cuccccgaaauguauugagguacagccucggauguugaccauguccugua
gagcacucacaaggcuaaaccuuaugaaacuccgaaggggcacgcguuua
guccgggagugaggcugcgagagcuaacuuccguagccgagagggaaaca
acccagaccaucagcuaaggucccuaaaugaucgcucagugguuaaggau
gugucgucgcauagacagcuggcuuagaagcaugcguaauagcucacugg
ucgagugacgaugcgccgaaaaugaucggggcucaagugaucuaccgaag
cuauggauucaacucgcgaagcgaguugucugguaggggagcguucaguc
cgcggagaagccauaccggaaggagugguggagccgacugaagugcggau
gccggcaugaguaacgauaaaagaagugagaaucuucuucgccguaagga
caaggguuccuggggaagggucguccgcccagggaaagucgggaccuaag
gugaggccgaacggcgcagccgauggacagcaggucaagauuccugcacc
gaucauguggagugauggagggacgcauuacgcuauccaaugccaagcua
uggcuaugcugguugguacgcucaagggcgaucgggucagaaaaucuacc
ggucacaugccucagacguaucgggagcuuccucggaagcgaaguuggaa
acgcgacggugccaagaaaagcuucuaaacguugaaacaugauugcccgu
accgcaaaccgacacagguguccgagugucaaugcacuaaggcgcgcgag
agaacccucguuaaggaacuuugcaaucucaccccguaacuucggaagaa
gggguccccacgcuucgcguggggcgcagugaauaggcccaggcgacugu
uuaccaaaaucacagcacucugccaacacgaacaguggacguauagggug
ugacgccugcccggugccggaaggucaaguggagcggugcaagcugcgaa
augaagccccggugaacggcuaagguagcgaaauuccuugucggguaagu
uccgaccugcacgaaaggcguaacgaucugggcgcugucucaacgaggga
cucggugaaauugaauuggcuguaaagaugcggccuacccguagcaggac
gaaaagaccccguggagcuuuacuauagucuggcauugggauucggguuu
cugaaacuuggauuucuaaccugaaaaaucacuuucggggaccgugcuug
gcggguaguuugacuggggcggucgccucccaaaauguaacggaggcgcc
caaaggucaccucaagacgguuggaaaucgucuguagagcgcaaagguag
aagguggcuugacugcgagacugacacgucgagcagggaggaaacucggg
cuuagugaaccggugguaccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagaguccauaucggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgcuacgggcgcaggaga
auugaggggaguugcuccuaguacgagaggaccggagugaacggaccgcu
ggucucccugcugucguaccaacggcacaugcaggguagcuauguccgga
acggauaaccgcugaaagcaucuaagcgggaagccagccccaagaugagu
ucucccacugagguaagacucccggaagaccaccggguuaagaggccagg
cgugcacgcauagcaauguguucagcggacuggugcucaucagucgaggu
cuugacca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jvh Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
• Resolution: 3.58 Å
• Binding residue (original residue number in PDB): L11 T13 R15 V17 R18 R26 V88 F89 R91 K95 Y96
• Binding residue (residue number reindexed from 1): L4 T6 R8 V10 R11 R19 V81 F82 R84 K88 Y89

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RSL2|RL18_DEIRA Large ribosomal subunit protein uL18 (Gene Name=rplR)