Structure of PDB 5zeb Chain E Binding Site BS01

Receptor Information

>5zeb Chain E (length=207) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

LKVDVKTPAGKTDGSVELPAELFDVEPNIALMHQVVTAQLAAKRQGTHST
KTRGEVSGGGKKPYRQKGTGRARQGSTRAPQFTGGGTVHGPKPRDYSQRT
PKKMIAAALRGALSDRARNDRIHAVTELVEGQTPSTKSAKTFLGTLTENK
KVLVVIGRTDEVGAKSVRNLPGVHVISPDQLNTYDVLNADDVVFSVEALN
AYISANS

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): Q36 Q41 L42 K45 R46 Q47 T49 H50 S51 K53 R55 G56 V58 S59 G60 K63 K64 Q68 K69 G70 A74 R75 Q76 G77 R80 Q83 F84 T85 G86 T89 V90 H91 K94 R96 R101 T102 P103 K104 K105 M106 I107 P136 S137 T138 K139 K153 K167 R170 N171 H176 Q182 N184 D187
• Binding residue (residue number reindexed from 1): Q34 Q39 L40 K43 R44 Q45 T47 H48 S49 K51 R53 G54 V56 S57 G58 K61 K62 Q66 K67 G68 A72 R73 Q74 G75 R78 Q81 F82 T83 G84 T87 V88 H89 K92 R94 R99 T100 P101 K102 K103 M104 I105 P134 S135 T136 K137 K151 K165 R168 N169 H174 Q180 N182 D185

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5zeb, PDBe:5zeb, PDBj:5zeb
• PDBsum: 5zeb
• PubMed: 30206241
• UniProt: A0QSD2|RL4_MYCS2 Large ribosomal subunit protein uL4 (Gene Name=rplD)