Structure of PDB 5zeb Chain T Binding Site BS01

Receptor Information

>5zeb Chain T (length=114) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

EFPSATAKARYVRVSATKARRVIDLVRGKSVEEALDILRWAPQAASEPVA
KVIASAAANAQNNEGLDPSTLVVATVYADEGPTAKRIRPRAQGRAFRIRK
RTSHITVIVESRPP

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): K13 A14 R15 Y16 R18 S20 K23 R25 R26 R32 A49 K56 S60 A63 N64 N67 N68 Y82 D84 E85 K90 R91 R93 P94 R95 A96 Q97 G98 R99 A100 F101 R102 R104 K105 R106
• Binding residue (residue number reindexed from 1): K8 A9 R10 Y11 R13 S15 K18 R20 R21 R27 A44 K51 S55 A58 N59 N62 N63 Y77 D79 E80 K85 R86 R88 P89 R90 A91 Q92 G93 R94 A95 F96 R97 R99 K100 R101

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5zeb, PDBe:5zeb, PDBj:5zeb
• PDBsum: 5zeb
• PubMed: 30206241
• UniProt: A0QSD6|RL22_MYCS2 Large ribosomal subunit protein uL22 (Gene Name=rplV)