Structure of PDB 6q97 Chain O Binding Site BS01

Receptor Information

>6q97 Chain O (length=115) Species: 562 (Escherichia coli)

KKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAAS
TVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGR
VQALADAAREAGLQF

Ligand information

>6q97 Chain 1 (length=2903)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaacccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugauguguaggauaggugggaggcuuugaaguguggacgccaguc
ugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

<<<<<<<<......<<<<<<<<<<<....{[[..[[<<<<<<<[[<<...
...<<.<<<....(((.>>>.....<<<<<<<..<<.))).....>>...
...>>>>>>>....>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<...........>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>...<<<<<.....<<....
.>>....>>>>>...(((.....<.......<...<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>...>....>...........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<......>....]].........<<.........>>....
.........}....>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<.....<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<.<.....>.>>
.....>>>>>>>>>>>>...<<.<...<<<<<<.....<<<<<<<<...<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<.<<......
..>>.>>>>>.....>>>>>>>>...<<<.....>>>......>>>>>>.
......>>>..<<<<......<<<<<....>>>>>.<.<<<<<<...<<<
<<.<.<<....<......<<.<<<<...<<..<.........>...>>..
.>>>>.>>......>.....>>.>>>.>>>...>>>>>>..>...<<<<<
..<<<......>>>..>>>>>....<<<......>>>...<<<<.<<<..
.<<<((......<<.<<<...........<<..<<<<<...<........
.<.....<.....................>....................
......>.....>...>>>>>.>>............)).....>>>.>>.
>>>...>>>>>>><<<.<<<<......>>>>.>>>......>>>>..<<<
<<...<<<<.....<<<<<<<<....>>>>>>>>..>>>>..>>>>>...
.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<..
..<<<<..<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<
.<..<<<...<<<....>>>...>>>...>>>...<<<<........>>>
>.))<<<<<<<<<<.<<...<<<<....<<<<..<<<..<<<<<<<<<<<
....(((...>>>>>><<..<<<..<.<<<<<<<<<<<<..........>
>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>
>...>>>...>>>.>........>>>>...>>.....>>>>>>>>>>.>>
>..>>.....<<......>>.>>>>.<<<<.....>>>>..>>>>..<<<
<....<<<<<<<...<...............<<<<<....<<..>>....
.>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<......>>.......>>>>>>>..<<<<..<<..<<<<<<<..<<
<........<...<<.<<....>>..>>...>........>>>>>>>>..
>>>>.<<<<<<.......>>>>>>....................<<<<<.
......>>>>>..........>>>>...>>.>>>>>>>.....>...>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.(((.[[......<<<<.[.<<<<..<<<<..<<<.<<<<<.<<<<<<.<
<<<..<<............<<<<...<<.......<<.<<<<......>>
>>.>>....>>.............>>>.>..>.>.>>>>.>>>>>>...<
<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>...>>>>..<<<<.
....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<
<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<
..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<
<.((..>>>>..))>>>>>>>.............>>>>...]>>>>....
...<<<<.<.<<<<<<...<<.......>>...>>>>>>...>>>>.>..
.....<<<<<.<<<<<<..<<<<<.<<<......>>>.>>>..>>.<<<<
<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>
>.>>>>....]]..)))>>>>>>>>....<<.<<<<...<<<<..<<<<<
<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<.<
.)))..>.>>>..>>>>>...>>>>.>>>>>...<<<.<..<<<<<....
.......>>>>>...>>>>.>>>>.......>>>>..>>.<<<<<.....
>>>>>.....<<..<<<<.........>>>>....<<.<<..<..<<...
.<<<<<....>>>>>...>>....>.>>..>>.....>>.....>>>>>>
>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6q97 How a circularized tmRNA moves through the ribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R9 R10 K17 S91 F92 R94 Y99 F117
• Binding residue (residue number reindexed from 1): R7 R8 K15 S89 F90 R92 Y97 F115

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6q97, PDBe:6q97, PDBj:6q97
• PDBsum: 6q97
• PubMed: 30765567
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)