Structure of PDB 6by1 Chain BG Binding Site BS01

Receptor Information

>6by1 Chain BG (length=132) Species: 83333 (Escherichia coli K-12)

PRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLA
QRSGKSELEAFEVALENVRPTRPVRRNALAMRWIVEAARKRGDKSMALRL
ANELSDAAENKGTAVKKREDVHRMAEANKAFA

Ligand information

>6by1 Chain BA (length=1541)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccu
ucgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaa
caagguaaccguaggggaaccugcgguuggaucaccuccuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
• Resolution: 3.94 Å
• Binding residue (original residue number in PDB): P1 R2 R3 V5 R9 N27 L29 M30 V31 D32 G33 K34 T37 R94 R101 K113 S114 M115
• Binding residue (residue number reindexed from 1): P1 R2 R3 V5 R9 N27 L29 M30 V31 D32 G33 K34 T37 R75 R82 K94 S95 M96

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0016020 membrane
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6by1, PDBe:6by1, PDBj:6by1
• PDBsum: 6by1
• PubMed: 30552154
• UniProt: P02359|RS7_ECOLI Small ribosomal subunit protein uS7 (Gene Name=rpsG)