Structure of PDB 5nwy Chain H Binding Site BS01

Receptor Information
>5nwy Chain H (length=55) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLP
YTDRH
Ligand information
>5nwy Chain 0 (length=1539) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggaccuucgggccucuugccaucggaugugcccagaugggauuagcuag
uaggugggguaacggcucaccuaggcgacgaucccuagcuggucugagag
gaugaccagccacacuggaacugagacacgguccagacuccuacgggagg
cagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugcc
gcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagga
agggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagc
accggcuaacuccgugccagcagccgcgguaauacggagggugcaagcgu
uaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucag
augugaaauccccgggcucaaccugggaacugcaucugauacuggcaagc
uugagucucguagagggggguagaauuccagguguagcggugaaaugcgu
agagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacu
gacgcucaggugcgaaagcguggggagcaaacaggauuagauacccuggu
aguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgug
gcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaa
gguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaug
ugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccac
ggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggugc
ugcauggcugucgucagcucguguugugaaauguuggguuaagucccgca
acgagcgcaacccuuauccuuuguugccagcgguccggccgggaacucaa
aggagacugccagugauaaacuggaggaagguggggaugacgucaaguca
ucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaa
agagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguagu
ccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaau
cguggaucagaaugccacggugaauacguucccgggccuuguacacaccg
cccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuu
cgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaac
aagguaaccguaggggaaccugcgguuggaucaccuccu
.......<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....
<<<.<<<..<<<..<<.<<..<<<<<<<<<<....>>>>>>>.>>>>>..
>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<....
.<<<<<......>>>>>......>>.>.....<<<....>>>....<<<<
<<..<<....>>>>>>>>.>>>>>>>..>>.>>>>>>><<<....<<<..
<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....>
>>>...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>.
..>>>>>>.........<<<....<<<<....>>>>..>>>..>>.>>>>
>>..<<<<......<<<<....>>>>.....>>>>..<<.<<<<<.....
.<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>>.<<
<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>>
>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<<
<<<<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>>>>>
...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>..
....>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>>
...>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>..
.>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>>
>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<....
>>>>....>>>..)))).]<<<<<.<<<<<<<.<<.<<<<<<..<<<<<<
<<<<......<<........>>..........<<<<<<<......<<<<<
<<...<<<.<<....>>>.>>....<<....>>..>>>>>.>>.<<<.<<
<..<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>..
>>>>>>.....<<<<.<<<<<<<...<<..<<<.....>>>>>....>>>
>>>>.....<<<<<.....>>>>>........>>>>.........>>>..
.>>>>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<....
.<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>.....
.<....<<<<<<<........>>>>>>>....>.....>>>>>>....<<
<<<<<.........>>>>>>>......>>...>>>>>>>>>>.>>....<
..<<.<.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<..
..>>.>>>>>>>>>>...>>>>>>>>>>>>..>>>.>>>>..>.>>...>
.....<<<<<<<<<....>>>>>>>>>............
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nwy The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		K38 I39 P41 S42 K50 Q52 R53 A56 K60 R61 R63 Y64 Y70 H74
Binding residue
(residue number reindexed from 1)		K19 I20 P22 S23 K31 Q33 R34 A37 K41 R42 R44 Y45 Y51 H55
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0048027 mRNA 5'-UTR 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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5nwy, PDBe:5nwy, PDBj:5nwy
PDBsum5nwy
PubMed28556777
UniProtP0A7T7|RS18_ECOLI Small ribosomal subunit protein bS18 (Gene Name=rpsR)

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