Structure of PDB 5zeb Chain V Binding Site BS01

Receptor Information

>5zeb Chain V (length=97) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

MKVHKGDTVLVISGKDKGAKGKVLVAYPDRNKVLVEGVNRIKKHTAVSGG
IVTQEAPIHVSNVMVVDSDGKPTRVGYRIDDETGKKVRIAKTNGKDI

Ligand information

>5zeb Chain A (length=3102)

aaguguuuaagggcgcaugguggaugccuuggcacugggagccgaugaag
gacguaggaggcugcgauaagccucggggagcugucaaccgagcguugau
ccgaggauguccgaauggggaaacccggcacgagugaugucgugucacca
ggcgcugaauauauaggcgucuggggggaacgcggggaagugaaacaucu
caguacccguaggaagagaaaacaaaaugugauuccgugaguaguggcga
gcgaaagcggaggauggcuaaaccguaugcaugugauaccggguaggggu
ugugugugcgggguugugggaccuaucuuuccggcucugcuggagggcag
ugagaaaauguugugguuagcggaaauggcuugggauggccugccguaga
cggugagagcccgguacgugaaaacccgacgucugucuugaugguguucc
cgaguagcagcgggcccguggaaucugcugugaaucugccgggaccaccc
gguaagccugaauacuucccagugaccgauagcggauuaguaccgugagg
gaauggugaaaaguaccccgggaggggagugaaagaguaccugaaaccgu
gcgcuuacaauccgucagagcccucgaucguggggugauggcgugccuuu
ugaagaaugagccugcgagucagggacaugucgcgagguuaacccgggug
ggguagccgcagcgaaagcgagucugaauagggcguauccacacaagagu
gugugguguagugguguguucuggacccgaagcggagugaucuacccaug
gccagggugaagcgcggguaagaccgcguggaggcccgaacccacuuagg
uugaagacugaggggaugagcuguggguaggggugaaaggccaaucaaac
uccgugauagcugguucuccccgaaaugcauuuaggugcagcgucgcaug
uuucuugccggagguagagcuacuggauggccgaugggccccaggguuac
ugacgucagccaaacuccgaaugccgguaaguccaagagugcggcaguga
gacggcgggggauaagcuccgugcgucgagagggaaacagcccagaucgc
cggcuaaggccccuaagcgugugcuaaguggaaaaggaugugcagucgcg
aagacaaccaggagguuggcuuagaagcagccacccuugaaagagugcgu
aauagcucacuggucaagugauugugcgccgauaauguagcggggcucaa
gcacaccgccgaagccgcggcagccaacguguuggcuggguaggggagcg
uccugcauccggugaagccgccgagugaucgagugguggaggguguggga
gugagaaugcaggcaugaguagcgauuaggcaagugagaaccuugcccgc
cgaaagaccaaggguuccugggccaggccaguccgcccagggugagucgg
gaccuaaggcgaggccgacaggcguagucgauggacaacggguugauauu
cccguacccguguaugugcguccaugaugaaucagcgguacuaaccaucc
aaaaccaccgugaccgcaccuuucgggguguggcguugguggggcugcau
gggaccuucguugguaguagucaagcgauggggugacgcaggaagguagc
cguaccggucagugguaauaccgggguaagccuguagggagucagauagg
uaaauccgucuggcauauauccugagaggugaugcauagccgagaggcga
auucggugauccuaugcugccgagaaaagccucuagcgaggacauacacg
gcccguaccccaaaccaacacagguggucagguagagaauacuaaggcgu
acgagugaacuaugguuaaggaacucggcaaaaugcccccguaacuucgg
gagaagggggacccacauggcguguaagccucggcccaagcgugaguggg
uggcacaaaccagugagaagcgacuguuuacuaaaaacacagguccgugc
gaagucgcaagacgauguauacggacugacgccugcccggugcuggaagg
uuaagaggacccguuaacucccuuugggggugaagcggagaauuuaagcc
ccaguaaacggcggugguaacuauaaccauccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaauggcguaacgacuucucaacugu
cucaaccauagacucggcgaaauugcacuacgaguaaagaugcucguuac
gcgcggcaggacgaaaagaccccgggaccuucacuacaacuugguauugg
ugcucgauacgguuuguguaggauaggugggagacugugaagcucacacg
ccaguguggguggagucguuguugaaauaccacucugaucguauugggcc
ucuaaccucggaccguauauccgguucagggacagugccugguggguagu
uuaacuggggcgguugccuccuaaaauguaacggaggcgcccaaagguuc
ccucaaccuggacggcaaucagguguugaguguaagugcacaagggagcu
ugacugcgagacggacaugucgagcagggacgaaagucgggacuagugau
ccggcaccucugaguggaaggggugucgcucaacggauaaaagguacccc
ggggauaacaggcugaucuuccccaagaguccauaucgacgggaugguuu
ggcaccucgaugucggcucgucgcauccuggggcuggagcaggucccaag
gguugggcuguucgcccauuaaagcggcacgcgagcuggguuuagaacgu
cgugagacaguucggucucuauccgccgcgcgcgucagaagcuugaggaa
accugucccuaguacgagaggaccgggacggacgaaccucugguauacca
guugucccaccaggggcacggcuggauagccacguucggacaggauaacc
gcugaaagcaucuaagcgggaaaccucuuccaagaccaggcuucucaccc
ucuaggagggauaaggccccccgcagaccacgggauugauagaccagacc
uggaagccuaguaauaggugcagggaacuggcacuaaccggccgaaaacu
ua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5zeb Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): H4 K5 I12 G14 K15 A26 P28 I41 K42 K43 H44 T45 A46 G58 H67 S69 N70 M72 P80 R82 Y85 K99
• Binding residue (residue number reindexed from 1): H4 K5 I12 G14 K15 A26 P28 I41 K42 K43 H44 T45 A46 G50 H59 S61 N62 M64 P72 R74 Y77 K91

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:5zeb, PDBe:5zeb, PDBj:5zeb
• PDBsum: 5zeb
• PubMed: 30206241
• UniProt: A0QSG0|RL24_MYCS2 Large ribosomal subunit protein uL24 (Gene Name=rplX)