Structure of PDB 5zeb Chain J Binding Site BS01

Receptor Information

>5zeb Chain J (length=133) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

LIKLQIQAGQANPAPPVGPALGQHGVNIMEFCKAYNAATESQRGNVIPVE
ITVYEDRSFTFALKTPPAAKLLLKAAGVQKGSGEPHKTKVAKVTWDQVRE
IAETKKADLNANDIDAAAKIIAGTARSMGITVE

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): K12 L13 Q14 P76 A78 S91 G92 P94 L118 N119 A120 A125 K128 I129 G132 T133 S136 M137
• Binding residue (residue number reindexed from 1): K3 L4 Q5 P67 A69 S82 G83 P85 L109 N110 A111 A116 K119 I120 G123 T124 S127 M128

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5zeb, PDBe:5zeb, PDBj:5zeb
• PDBsum: 5zeb
• PubMed: 30206241
• UniProt: A0QS45|RL11_MYCS2 Large ribosomal subunit protein uL11 (Gene Name=rplK)