Structure of PDB 5el5 Chain C5 Binding Site BS01

Receptor Information

>5el5 Chain C5 (length=105) Species: 300852 (Thermus thermophilus HB8)

RVKMHVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRV
SPKYPQGGFIEKEAPLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAK
CGGAL

Ligand information

>5el5 Chain 14 (length=2861)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuugcgcggggggaaccuggggaacugaaacaucucaguacccaga
ggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggac
cagccuaaaccguccggcuuguccgggcggggucguggggcccucggaca
ccgaauccccagccuagccgaagcuguugggaagcagcgccagagagggu
gaaagccccguaggcgaaagguggggggauaggugaggguacccgaguac
cccgugguucguggagccaugggggaaucugggcggaccaccgccuaagg
cuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggug
aaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuac
aagcagucacggccccgcaagggguuguggcgugccuauugaagcaugag
ccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcgua
gggaaaccgaguccgaacagggcgcaaacggcgaaaaguccgcggccgug
gacccgaaaccgggcgagcuagcccuggccagggugaagcuggggugaga
cccaguggaggcccgaaccggugggggaugcaaaccccucggaugagcug
gggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccccg
aaaugacuuuagggucagccucaggcgcugacuggggccuguagagcacu
gauagggcuaggaccaaacccugucaaacuccgaagggucccagguggag
ccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaaca
accgagaccgccagcuaaggcccccaagucugggcuaagugguaaaggau
guggcgccgcggacagccaggauguuggaagcagccaagagugcgagcuc
acuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgc
cgaagcugcgggucugggggaugaccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccguacgggugacaacccccc
gaagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgu
accgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggg
agaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaa
ggggugcucccuggggugaugagccccggggagccgcagugaacaggcuc
uggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggagg
uauagggagcgacgcuugcccggugccggaaggucaaggggaggggugca
agccccgaaccgaagccccggugaacggcggccguaacuauaacgguccu
aagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgu
aacgaccggagcgcugucucggcgagggacccggugaaauugaacuggcc
gugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuu
acugcagccugguguuggcucuuggucgcgccugcuaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaauaccacc
cuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaa
gguccccucaggcgggacggaaauccgccggagagcgcaaggguagaagg
gggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccua
gugaaccgguggucccguguggaagggccaucgaucaacggauaaaaguu
accccggggauaacaggcugaucucccccgagcguccacagcggcgggga
gguuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguc
ccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucag
aacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuug
aggggggcucuuccuaguacgagaggaccggaagggacgcaccucugguu
ucccagcugucccuccaggggcauaagcuggguagccaugugcggaaggg
auaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuc
ccacggcgucaagccgguaaggacccgggaagaccacccgguggaugggc
cggggguguaagcgccgcgaggcguugagccgaccggucccaaucguccg
aggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5el5 Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
• Resolution: 3.15 Å
• Binding residue (original residue number in PDB): R2 K4 H6 K8 K9 S17 G18 K19 V30 P32 Y35 I44 V45 K46 K47 V49 K54 F60 H68 S70 K71 R73 K81 T83 R84 V85
• Binding residue (residue number reindexed from 1): R1 K3 H5 K7 K8 S16 G17 K18 V29 P31 Y34 I43 V44 K45 K46 V48 K53 F59 H67 S69 K70 R72 K80 T82 R83 V84

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:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5el5, PDBe:5el5, PDBj:5el5
• PDBsum: 5el5
• PubMed: 26791911
• UniProt: Q5SHP9|RL24_THET8 Large ribosomal subunit protein uL24 (Gene Name=rplX)