Structure of PDB 6by1 Chain CW Binding Site BS01

Receptor Information
>6by1 Chain CW (length=75) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLF
AKADGKVKFEVKGPKNRKFISIEAE
Ligand information
>6by1 Chain CA (length=2867) [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
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugaugggugggaggcuuguguauggagccgaaccacccuuuaaug
uuugauguucuaacguugacccguaauccggguugcggacagugucuggu
ggguaguuugacuggggcggucuccuccuaaagaguaacggaggagcacg
aagguuggcuaauccuggucggacaucaggagguuagugcaauggcauaa
gccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcagguca
uagugauccggugguucugaauggaagggccaucgcucaacggauaaaag
guacuccggggauaacaggcugauaccgcccaagaguucauaucgacggc
gguguuuggcaccucgaugucggcucaucacauccuggggcugaaguagg
ucccaaggguauggcuguucgccauuuaaagugguacgcgagcuggguuu
agaacgucgugagacaguucggucccuaucugccgugggcgcuggagaac
ugaggggggcugcuccuaguacgagaggaccggaguggacgcaucacugg
uguucggguugucaugccaauggcacugcccgguagcuaaaugcggaaga
gauaagugcugaaagcaucuaagcacgaaacuugccccgagaugaguucu
cccugacccuuuaaggguccugaaggaacguugaagacgacgacguugau
aggccggguguguaagcgcagcgaugcguugagcuaaccgguacuaauga
accgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>...<<<<<.....<<....
.>>....>>>>>...(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
..>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<....<<<<<<.....>>>>>.>...
.>>>>.>>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<
<<<<<......>>>>>>>>>>....<<<......>>>...<<<<.<<<..
.<<<(((.....<<<<<<...........<<..<<<<<..<<........
<<<<<.<<...<<<.........>>>...>>........<..........
>..>>>>>....>>..>>>>>.>>...........))).....>>>>>>.
>>>...>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>><<<<<
<<...<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.>>
.....>>>>>><......<<.....<<<<<<.......>>>>>><<<<..
..<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<
<...<<<...<<<....>>>...>>>...>>>..<<<<<........>>>
>>))<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<
....(((...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>
>>>>>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>
>...>>>...>>>>.........>>>.>..>>....>>>>>>>>>>>.>>
>..>>.....<<......>>>>>>>.<<<.......>>>..>>>>..<<<
<....<<<<<<<<.<<...............<<<<<....<<..>>....
.>>>>><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>
>............<<<<<<<<<..<<<.........>>>..<<<<<<<..
...<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<
<<.......<<<<<..<<....>>...>>>>>.......>>>>>>>>>..
>>>>><<<<<<.......>>>>>>........<...........<<<<<<
.....>>>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>
>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<
.(((.[[......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<
<<..<<<<.<<<<<<...<<..<<..>>...>>....>>>>>>.>>>>..
>>>>>>>>>>...<<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>
..>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<.
..<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....
>>>>>>>...<<<<..<<<<....>>>>..>>>>.<<<....>>>.>>))
).......<<<<<<<.((..>>>>..))>>>>>>>.............>>
>>..]]>>>>.......<<<<.<.<<<<<<...<<.......>>...>>>
>>>...>>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>
>>>>..>>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>...
.<<<<<<<....>>>.>>>>....]]..)))>>>>>>>>....<<<<<<<
...<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<
<...<<<<<<<<<<<))).>>>>>>..>>>>>...>>>>.>>>>>...<<
<....<<<<<...........>>>>>....>>>.>>>>.......>>>>>
>>..<<<<<.....>>>>><....<<..<<<<<.......>>>>>....<
<<<<<<<..<<....<<<<<....>>>>>...>>...>>>>>.>>>....
.>>..>..>>>>>>>>.
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]
PDB6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
Resolution3.94 Å
Binding residue
(original residue number in PDB)
N12 R14 S16 E17 A18 K19 R20 K24 R25 F26 G27 G28 E29 A33 G34 S35 I36 R41 G42 T43 K44 F45 H46 R55 D56 T58 F60 F69 R77 K78
Binding residue
(residue number reindexed from 1)
N2 R4 S6 E7 A8 K9 R10 K14 R15 F16 G17 G18 E19 A23 G24 S25 I26 R31 G32 T33 K34 F35 H36 R45 D46 T48 F50 F59 R67 K68
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6by1, PDBe:6by1, PDBj:6by1
PDBsum6by1
PubMed30552154
UniProtP0A7L8|RL27_ECOLI Large ribosomal subunit protein bL27 (Gene Name=rpmA)

[Back to BioLiP]