Structure of PDB 5jvh Chain D Binding Site BS01

Receptor Information

>5jvh Chain D (length=177) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDK
AAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEK
LINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGM
DITIVTTAKTDEEARALLQSMGLPFRK

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): K33 V35 N37 G39 S42 S43 T68 K69 K71 S75 F77 V85 K88 F122 D123 R125 N127 N129 L130 G131 I132 K133 R150 D153 T155
• Binding residue (residue number reindexed from 1): K31 V33 N35 G37 S40 S41 T66 K67 K69 S73 F75 V83 K86 F120 D121 R123 N125 N127 L128 G129 I130 K131 R148 D151 T153

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA 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:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RXJ0|RL5_DEIRA Large ribosomal subunit protein uL5 (Gene Name=rplE)