Structure of PDB 5zep Chain G Binding Site BS01

Receptor Information

>5zep Chain G (length=176) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

SRIGKQPVPVPSGVDVTINGQNLSVKGPKGTLTLDVAEPISVSRAEDGAI
VVTRPDDERRSRSLHGLSRTLIANLVTGVTEGYTQKMEIFGVGYRVQLKG
QNLEFALGYSHPVLIEAPEGITFAVESPTKFSVSGIDKQKVGQISAVIRR
LRRPDPYKGKGVRYEGEQIRRKVGKT

Ligand information

>5zep 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: 5zep 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): S2 R3 I4 R61 R63 S64 G67 L68 T71 N75 Y110 S111 H112 K139 Q140 G143 Q144 A147 R151 R154 P157 Y158 K159 K161 K173
• Binding residue (residue number reindexed from 1): S1 R2 I3 R60 R62 S63 G66 L67 T70 N74 Y109 S110 H111 K138 Q139 G142 Q143 A146 R150 R153 P156 Y157 K158 K160 K172

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5zep, PDBe:5zep, PDBj:5zep
• PDBsum: 5zep
• PubMed: 30206241
• UniProt: A0QSG4|RL6_MYCS2 Large ribosomal subunit protein uL6 (Gene Name=rplF)