Structure of PDB 6vyw Chain y Binding Site BS01

Receptor Information

>6vyw Chain y (length=114) Species: 562 (Escherichia coli)

SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIR
NRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLR
ERTGKAARIKERLN

Ligand information

>6vyw Chain a (length=2880)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugaaaaa
uuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggagau
agcugguucuccccgaaagcuauuuagguagcgccucgugaauucaucuc
cggggguagagcacuguuucggcaagggggucaacccgacuuaccaaccc
gaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcgg
ggcuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggu
cccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcca
ggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucac
uggucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccg
aagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucugua
agccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaa
ugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaaga
ccaaggguuccuguccaacguuaaucggggcagggugagucgaccccuaa
ggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguac
uugguguuacugcgaaggggggacggagaaggcuauguuggccgggcgac
gguugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaa
aucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaau
gcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguac
cccaaaccgacacgguggucagguagagaauaccaaggcgcuugagagaa
cucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggca
cgcugauauguaggugaggucccucgcggauggagcugaaaucagucgaa
gauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaaca
cgaaaguggacguauacggugugacgccucccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccgaacaaacgguccuaagguagcgaaauccuugucggguaaguuccga
cugcacgaauggcguaaugauggccaggcugucuccacccgagacucagu
gaaauugaacucgcugugagaugcaguguacccgcggcaagacggaaaga
ccccguaaccuuacuauagcuugacacugaacauugagccuugaugugua
ggauaggugggaggcuuugaaguguggacgccagucugcauggagccgac
cuugaaauaccacccuuuaauguuugauguucuaacguugacccguaauc
cggguugcggacagugucugguggguaguuugacugggcggucuccuccu
aaagaguaacggaggagcacgaagguuggcuaauccuggucggacaucag
gagguuagugcaauggcauaagccagcuugacugcgagcgugacggcgcg
agcaggugcgaaagcaggucauagugauccggugguucugaauggaaggg
ccaucgcucaacggauaaaagguacuccgggauaacaggcgauaccgccc
aagaguucauaucgacggcgguguuuggcacucggucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcguucgccauuuaaaguggu
acgcgagcggguuuagaacgucgugagacagucggucccuaucugccgug
ggcgcuggagaacugaggggggcugcuccuaguacgagaggaccggagug
gacgcaucacugguguucggguugucaugccaauggcacugcccgguagc
uaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuugccc
cgagaugaguucucccugacccuuuaaggguccugaaggaacguugaaga
cgacgacguugauaggccggguguguaagcgcagcgaugcguugagcuaa
ccgguacuaaugaaccgugaggcuuaaccu

<<<<<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<<...
...<<<<<<.[..(((.>>>.....<<<<<<<..<<<)))..].>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..<<<..<<<<.<....<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>..>>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..((((>>>>>..>>>......>>.>>>>>>>.>>.....
..........<<....>>....>>.........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<.....>
>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>....
..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<<<<
<<<.....<<<...<<<.<<<<...<<.<<<<.....>>>>..>>...>>
>>.>>>..>>.>.....>>>>>>>.>>...>>>>>>>.>...<<<<<<<<
<.......>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<
(((.....<<<<<<...........<<..<<<<<..<<........<<<<
<.<<...<<<<.......>>>>...>>........<<<......>>>..>
>>>>....>>..>>>>>.>>...........))).....>>>>>>.>>>.
..>>>>>>><<<<<<<<<....>>>>>>>>>....>>>>>>..<<<<<..
.<<<......<<<<<<<<....>>>>>>>>...>>>..>>>>>.......
.>>>>>><......<<.....<<<<<<.......>>>>>><<<<....<<
<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...
<<<...<<<....>>>...>>>...>>>..<<<<<........>>>>>))
<<<<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....
[[[...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>
>>>..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...
>>>...>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>
>.....<<.....>>>>>>>.<<<<.....>>>>..>>>>..<<<<....
<<<<<<<<.<<.........<.....<<<<<...............>>>>
><<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>....
........<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<
<....>>>.......>>>>>>>.<<<<<.<<..<<<<<<<..<<<....<
...<<<<<..<<....>>...>>>>>.>......>>>>>>>>..>>>>..
<<<<......>>>>.........<..........<<<<<<.....>>>>>
>....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>
.....>.....<<<<<.......>>>>>..<<<<<<<<.<<<.<<.....
.<.<<..<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<<......
.....<<<<<..<<.......<<<<<<<<....>>>>>>>>....>>...
.........>>>>>..>>>>.>>>>>>>>>>>...<<<.<<<<<<.....
>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<....>>>><<<<<<.
..........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>
>>.....<<...(((>>....>>>>>>>...<<<<..<<<<....>>>>.
.>>>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..>>>
>>>>>>..............>>>....>>>........<<...<<<<<<.
..<<.......>>...>>>>>>.....>>......<<.<<.<<<<<<..<
<<<<<<<<......>>>>>>>..>>.<<<<<....>>>>>.....>>>>>
..>...>>.>>....<.<<<<<....>>>.>>>....>>..>>>>>>>>>
>>....<<<<<<<...<<<<..<<<<<<<...............>>>>>>
>.<<<<<...<<<<...<<<<<<<<<<<]]].>>>>>>..>>>>>...>>
>>.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>
>.......>>>>>>>..<<<<<.....>>>>><....<<..<<<<<....
...>>>>>....<<<<<<<<..<<....<<<<<....>>>>>...>>...
>>>>>.>>>.....>>..>..>>>>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vyw Structural basis of transcription-translation coupling.
• Resolution: 7.0 Å
• Binding residue (original residue number in PDB): S2 R21 R51 N52 R53 H56 Q75 R93 K94 A95 K96 Y98 Y99 R103
• Binding residue (residue number reindexed from 1): S1 R20 R50 N51 R52 H55 Q74 R92 K93 A94 K95 Y97 Y98 R102

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:6vyw, PDBe:6vyw, PDBj:6vyw
• PDBsum: 6vyw
• PubMed: 32820061
• UniProt: P0A7K6|RL19_ECOLI Large ribosomal subunit protein bL19 (Gene Name=rplS)