Structure of PDB 5jvg Chain Q Binding Site BS01

Receptor Information

>5jvg Chain Q (length=93) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

SHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVI
GISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQ

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): S2 S13 E14 K15 T34 K35 S54 T55 M56 N57 P59 K61 R62 K63 V65 F68 I69 Q71 N73 K76 K77 I79 R81
• Binding residue (residue number reindexed from 1): S1 S12 E13 K14 T33 K34 S53 T54 M55 N56 P58 K60 R61 K62 V64 F67 I68 Q70 N72 K75 K76 I78 R80

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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: Q9RXK0|RL23_DEIRA Large ribosomal subunit protein uL23 (Gene Name=rplW)