Structure of PDB 6vwm Chain j Binding Site BS01

Receptor Information
>6vwm Chain j (length=117) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFA
AQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITD
VTPIPHNGCRPPKKRRV
Ligand information
>6vwm Chain 1 (length=1508) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaguuugaucauggcucagauugaacgcuggcggcaggccuaacacaug
caagucgaacgguaacaggaagcuuugcugacgaguggcggacgggugag
uaaugucugggaaacugccugauggagggggauaacuacuggaaacggua
gcuaauaccgcauaacgucgcaagaccaaagagggggaccuucgggccuc
uugccaucggaugugcccagaugggauuagcuaguaggugggguaacggc
ucaccuaggcgacgaucccuagcuggucugagaggaugaccagccacacu
ggaacugagacacgguccagacuccuacgggaggcagcaguggggaauau
ugcacaaugggcgcaagccugaugcagccaugccgcguguaugaagaagg
ccuucggguuguaaaguacuuucagcggggaggaagggaguaaaguuaau
accuuugcucauugacguuacccgcagaagaagcaccggcuaacuccgug
ccagcagccgcgguaauacggagggugcaagcguuaaucggaauuacugg
gcguaaagcgcacgcaggcgguuuguuaagucagaugugaaauccccggg
cucaaccugggaacugcaucugauacuggcaagcuugagucucguagagg
gggguagaauuccagguguagcggugaaaugcguagagaucuggaggaau
accgguggcgaaggcggcccccuggacgaagacugacgcucaggugcgaa
agcguggggagcaaacaggauuagauacccugguaguccacgccguaaac
gaugucgacuuggagguugugcgcguggcuuccggagcuaacgcguuaag
ucgaccgccuggggaguacggccgcaagguuaaaacucaaaugaauugac
gggggcccgcacaagcgguggagcaugugguuuaauucgaugcaacgcga
agaaccuuaccuggucuugacauccacggaaguuuucagagaugagaaug
ugccuucgggaaccgugagacaggugcugcauggcugucgucagcucgug
uugugaaauguuggguuaagucccgcaacgagcgcaacccuuauccuuug
uugccagcgguccggccgggaacucaaaggagacugccagugauaaacug
gaggaagguggggaugacgucaagucaucauggcccuuacgaccagggcu
acacacgugcuacaauggcgcauacaaagagaagcgaccucgcgagagca
agcggaccucauaaagugcgucguaguccggauuggagucugcaacucga
cuccaugaagucggaaucgcuaguaaucguggaucagaaugccacgguga
auacguucccgggccuuguacacaccgcccgucacaccaugggagugggu
ugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacuuugu
gauucaugacuggggugaagucguaacaagguaaccguagggaaaccugc
gguuggau
.<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<.<<
<..<<<..<<.<...<<<<<<..>>>.>>>.>..>>>>>......<<...
....<<<<<<<..<<...<<<<<<<.<.<<.....<<<<<<....>>>>>
>......>>.>.....<<<....>>>....<<<<<<..<<....>>>>>>
>>.>>>>>>>..>>.>>>>>>><<<....<<<..<<<<<<<.........
>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<<
<<<.<.........>>>>>>.<<<<<..>>>>>...>>>>>>........
.<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<<
<<....>>>>.....>>>>..<<.<<<<<......<.<<<<<<<<.....
..>>>>>>>>.>........>>>>>....>>.<<<<<(((...<<<<<..
...<<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<
<<((.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<
.....>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<
<<<<<....<<<<<<<<...<<<......>>>......>>>>>>>>....
.......<<....>>.>>>>>>>..>>>.>>>>>...>>>...>>>>...
.<<<<<<...<<...<<<<.<.....>.>>>>...>>>>>>>>.......
...<<<<<<.<<<<<<<<<<<..>>>>>>>>>>>..<<..))>>.....>
>>>>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<
<.<<<<<<<.<<.<<<<<<..<<<<<<<<<<......<<........>>.
.........<<<<<<<......<<<<<<<..<<<<<<<....>>>>>>>.
..<<....>>..>>>>>.>>.<<<.<<<..<<<<<<.......<<<<<<<
<<....>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<
...<<..<<<.....>>>>>....>>>>>>>.....<<<<<.....>>>>
>........>>>>.........>>>...>>>>>>>>>...>>>>>>>...
>>.>>>>>>>>.....<<<<<<<.....<<<..<<...<<<....>>>..
.>>....>>>.....>>>>>>>......<....<<<<<<<........>>
>>>>>....>.....>>>>>>....<<<<<<<.........>>>>>>>..
....>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<
<<<<<<....<<<<<<.<<<<..<<....>>.>>>>>>>>>>...>>>>>
>>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>
>>>>....
Receptor-Ligand Complex Structure
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PDB6vwm mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		H21 N27 N28 I30 G38 N39 A40 W43 T45 G47 G48 G53 S54 K56 I115 P116 H117 N118 G119 C120 R121 P123 K124 R126 R127 V128
Binding residue
(residue number reindexed from 1)		H10 N16 N17 I19 G27 N28 A29 W32 T34 G36 G37 G42 S43 K45 I104 P105 H106 N107 G108 C109 R110 P112 K113 R115 R116 V117
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0070181 small ribosomal subunit rRNA binding
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vwm, PDBe:6vwm, PDBj:6vwm
PDBsum6vwm
PubMed32427100
UniProtP0A7R9|RS11_ECOLI Small ribosomal subunit protein uS11 (Gene Name=rpsK)

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