Structure of PDB 5nwy Chain q Binding Site BS01

Receptor Information

>5nwy Chain q (length=64) Species: 83333 (Escherichia coli K-12)

PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVS
KGDLGLVIACLPYA

Ligand information

>5nwy Chain N (length=2897)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacuuaccaacccgau
gcaaacugcgaauaccggagaauguuaucacgggagacacacggcgggug
cuaacguccgucgugaagagggaaacaacccagaccgccagcuaaggucc
caaagucaugguuaagugggaaacgaugugggaaggcccagacagccagg
auguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacug
gucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaa
gcugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaag
ccugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaug
cugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacc
aaggguuccuguccaacguuaaucggggcagggugagucgaccccuaagg
cgaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuu
gguguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgg
uugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaau
caaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugc
ccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguaccc
caaaccgacacagguggucagguagagaauaccaaggcgcuugagagaac
ucgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcac
gcugauauguaggugaggucccucgcggauggagcugaaaucagucgaag
auaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacac
gaaaguggacguauacggugugacgccugcccggugccggaagguuaauu
gaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcg
gccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguu
ccgaccugcacgaauggcguaaugauggccaggcugucuccacccgagac
ucagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacg
gaaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuu
gauguguaggauaggugggaggcuuugaaguguggacgccagucugcaug
gagccgaccuugaaauaccacccuuuaauguuugauguucuaacguugac
ccguaauccggguugcggacagugucugguggguaguuugacuggggcgg
ucuccuccuaaagaguaacggaggagcacgaagguuggcuaauccugguc
ggacaucaggagguuagugcaauggcauaagccagcuugacugcgagcgu
gacggcgcgagcaggugcgaaagcaggucauagugauccggugguucuga
auggaagggccaucgcucaacggauaaaagguacuccggggauaacaggc
ugauaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugu
cggcucaucacauccuggggcugaaguaggucccaaggguauggcuguuc
gccauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguuc
ggucccuaucugccgugggcgcuggagaacugaggggggcugcuccuagu
acgagaggaccggaguggacgcaucacugguguucggguugucaugccaa
uggcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucu
aagcacgaaacuugccccgagaugaguucucccugacccuuuaagggucc
ugaaggaacguugaagacgacgacguugauaggccggguguguaagcgca
gcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nwy The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): P2 K3 I4 K5 T6 R8 G9 K12 R13 T17 G18 K19 K23 H26 A27 N28 R30 H31 I32 L33 T34 K35 T38 K39 R40 R42 H43 R45 K47 M49 S51 K52 G53 D54 Y64
• Binding residue (residue number reindexed from 1): P1 K2 I3 K4 T5 R7 G8 K11 R12 T16 G17 K18 K22 H25 A26 N27 R29 H30 I31 L32 T33 K34 T37 K38 R39 R41 H42 R44 K46 M48 S50 K51 G52 D53 Y63

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• 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

External links

• PDB: RCSB:5nwy, PDBe:5nwy, PDBj:5nwy
• PDBsum: 5nwy
• PubMed: 28556777
• UniProt: P0A7Q1|RL35_ECOLI Large ribosomal subunit protein bL35 (Gene Name=rpmI)