Structure of PDB 6q97 Chain M Binding Site BS01

Receptor Information
>6q97 Chain M (length=136) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAAR
RAMTRAVKRQGKIWIRVFPDKPITEKPLAVRMGKGKGNVEYWVALIQPGK
VLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM
Ligand information
>6q97 Chain 1 (length=2903) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6q97 How a circularized tmRNA moves through the ribosome.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		K5 R6 K8 F9 K11 M12 H13 K14 G15 R16 R18 Q22 S27 F28 R40 R44 Q45 R55 K62 W64 R66 F68 E75 K76 A79 R81 M82 K84 G85 K86 L119 A122 K123 P125
Binding residue
(residue number reindexed from 1)		K5 R6 K8 F9 K11 M12 H13 K14 G15 R16 R18 Q22 S27 F28 R40 R44 Q45 R55 K62 W64 R66 F68 E75 K76 A79 R81 M82 K84 G85 K86 L119 A122 K123 P125
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6q97, PDBe:6q97, PDBj:6q97
PDBsum6q97
PubMed30765567
UniProtP0ADY7|RL16_ECOLI Large ribosomal subunit protein uL16 (Gene Name=rplP)

[Back to BioLiP]