Structure of PDB 5jvh Chain O Binding Site BS01

Receptor Information

>5jvh Chain O (length=94) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

IQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKY
TVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGI

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): Q6 T7 R21 V22 R65 G66 K67 K68 Y70 I71 K73 Y74 G77 V78 Q79 Y80 R81 R82 R83 T84 G85 H86 R87 Q88 F90
• Binding residue (residue number reindexed from 1): Q2 T3 R17 V18 R61 G62 K63 K64 Y66 I67 K69 Y70 G73 V74 Q75 Y76 R77 R78 R79 T80 G81 H82 R83 Q84 F86

Gene Ontology

Molecular Function

• GO:0003723 RNA 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RY64|RL21_DEIRA Large ribosomal subunit protein bL21 (Gene Name=rplU)