Structure of PDB 5jvg Chain 1 Binding Site BS01

Receptor Information

>5jvg Chain 1 (length=53) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

AKDGPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAKKHVVFR
EKK

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

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): A2 K3 D4 R7 I8 I9 F20 Y22 T25 K26 R28 N30 T31 E36 K38 K39 K46 H47
• Binding residue (residue number reindexed from 1): A1 K2 D3 R6 I7 I8 F19 Y21 T24 K25 R27 N29 T30 E35 K37 K38 K45 H46

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:0005737 cytoplasm
• 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: Q9RSS4|RL33_DEIRA Large ribosomal subunit protein bL33 (Gene Name=rpmG)