Structure of PDB 6by1 Chain AP Binding Site BS01

Receptor Information
>6by1 Chain AP (length=82) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGT
RLDLDRIAHWVGQGATISDRVAALIKEVNKAA
Ligand information
>6by1 Chain AA (length=1540) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
caagguaaccguaggggaaccugcgguuggaucaccuccu
........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<....
.<<<.<<<..<<<..<<.<....<<<<<<<<......>>>>>>.>>..>.
.>>>>>......<<.......<<<<<<<..<<...<<<<<<<.<.<<...
.<.<<<<......>>>>..>....>>.>.....<<<....>>>.....<<
<<<..<<....>>>>>>>..>>>>>>>..>>.>>>>>>><<<....<<<.
.<<<<<<<.........>>>>>>>>>>......>>>..<<<<<<<<....
>>>>...>>>>.>>.<<<<.<<.........>>>>>>.<<<.<..>.>>>
...>>>>>>.........<<<...<<<<<....>>>>.>>>>..>>.>>>
>>>..<<<<.......<<<....>>>......>>>>...<.<<<<<....
..<.<<<<<<<<.......>>>>>>>>.>........>>>>>....>..<
<<<<(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>
>>>>>>..........<<<((.....<<<<...<<<.<<<<<<<.<<<<<
<<<.<......<<<<<<.....>>>>>>....>.>>>>>>..>>>>>>>>
>...<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.
.....>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>
>...>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>.
..>>>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>
>>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<<<<...
.>>>>....>>>..)))).]<<<<<.<<<<<<<.<<..<<<<<..<<<<<
<<<<<......<<........>>..........<<<<<<<........<<
<<<..<<<<.<<....>>.>>>>...<<<..>>>..>>>>>....<<<.<
<<..<<<<<<.......<<<<<<<<<....>>>..<<<<......>>>>.
.>>>>>>.....<<<<.<<<<.<...<<...<<<.....>>>.>..>..>
.>>>>.....<<<<<.....>>>>>........>>>>.........>>>.
..>>>>>>>>>...>>>>>>>...>>.>>>>>>>>.....<<<<<<<...
..<<<..<<...<<<....>>>...>>....>>>.....>>>>>>>....
.......<<<<<<<........>>>>>>>..........>>>>>.....<
<<<<<<.........>>>>>>>......>>...>>>>>>>>>>.>>....
<..<<.<.<<<<.<<<..<<<<<<<<<<<<....<<<<<<.<<<<..<<.
...>>.>>>>>>>>>>...>>>>>>>>>>>>..>>>.>>>>..>.>>...
>.....<<<<<<<<<....>>>>>>>>>............
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6by1 Structural evidence for product stabilization by the ribosomal mRNA helicase.
Resolution3.94 Å
Binding residue
(original residue number in PDB)		M1 T3 R5 L6 R8 H9 K12 K13 R14 F16 R25 N26 R28 R31 F32 R35 F38 Q63 G64 S68 R70 A73 K76
Binding residue
(residue number reindexed from 1)		M1 T3 R5 L6 R8 H9 K12 K13 R14 F16 R25 N26 R28 R31 F32 R35 F38 Q63 G64 S68 R70 A73 K76
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000400 four-way junction DNA binding
GO:0003735 structural constituent of ribosome
GO:0004519 endonuclease activity
GO:0004520 DNA endonuclease activity
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006259 DNA metabolic process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
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:6by1, PDBe:6by1, PDBj:6by1
PDBsum6by1
PubMed30552154
UniProtP0A7T3|RS16_ECOLI Small ribosomal subunit protein bS16 (Gene Name=rpsP)

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