Structure of PDB 3jbu Chain D Binding Site BS01

Receptor Information
>3jbu Chain D (length=205) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK
Ligand information
>3jbu Chain A (length=1530) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaacac
augcaagucgaacgguaacaggaagaagcuugcuucuuugcugacgagug
gcggacgggugaguaaugucugggaaacugccugauggagggggauaacu
acuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagaggggg
accuucgggccucuugccaucggaugugcccagaugggauuagcuaguag
gugggguaacggcucaccuaggcgacgaucccuagcuggucugagaggau
gaccagccacacuggaacugagacacgguccagacuccuacgggaggcag
caguggggaauauugcacaaugggcgcaagccugaugcagccaugccgcg
uguaugaagaaggccuucggguuguaaaguacuuucagcggggaggaagg
gaguaaaguuaauaccuuugcucauugacguuacccgcagaagaagcacc
ggcuaacuccgugccagcagccgcgguaauacggagggugcaagcguuaa
ucggaauuacugggcguaaagcgcacgcaggcgguuuguuaagucagaug
ugaaauccccgggcucaaccugggaacugcaucugauacuggcaagcuug
agucucguagagggggguagaauuccagguguagcggugaaaugcguaga
gaucuggaggaauaccgguggcgaaggcggcccccuggacgaagacugac
gcucaggugcgaaagcguggggagcaaacaggauuagauacccugguagu
ccacgccguaaacgaugucgacuuggagguugugcccuugaggcguggcu
uccggagcuaacgcguuaagucgaccgccuggggaguacggccgcaaggu
uaaaacucaaaugaauugacgggggcccgcacaagcgguggagcaugugg
uuuaauucgaugcaacgcgaagaaccuuaccuggucuugacauccacgga
aguuuucagagaugagaaugugccuucgggaaccgugagacaggugcugc
auggcugucgucagcucguguugugaaauguuggguuaagucccgcaacg
agcgcaacccuuauccuuuguugccagcgguccggccgggaacucaaagg
agacugccagugauaaacuggaggaagguggggaugacgucaagucauca
uggcccuuacgaccagggcuacacacgugcuacaauggcgcauacaaaga
gaagcgaccucgcgagagcaagcggaccucauaaagugcgucguaguccg
gauuggagucugcaacucgacuccaugaagucggaaucgcuaguaaucgu
ggaucagaaugccacggugaauacguucccgggccuuguacacaccgccc
gucacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucgg
gagggcgcuuaccacuuugugauucaugacuggggugaagucguaacaag
guaaccguaggggaaccugcgguuggauca
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<
.<<<..<<<..<<.<<...<<<.<<<........>>>.>.>>.>>..>>>
>>......<<.......<<<<<<<..<.....<<<<<<.<.<<.....<<
<<<......>>>>>......>>.>.....<<<....>>>....<<<<<..
.<<....>>.>>>>>.>>>>>>....>.>>>>>>><<<....<<<...<<
<<<<.........>>>>>>.>>>......>>>..<<<<<<<<....>>>>
...>>>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>
>>>>>.........<<.......<<....>>.....>>..>>.>>>>>>.
.<<<<.......<<<<..>>>>......>>>>...<.<<<<<......<.
.<<<<<.<.......>.>>>>>..>........>>>>>....>..<<<<<
(((...<<<<<.....<<.)))>>.......>>>>>>>>>>..>>>>>>>
>>..........<<<((.....<<<<...<<<.<<<.<<<.<<<<<<<<<
<......<<<<<<.....>>>>>>....>>>>>>>>..>>>>>.>>>...
<<<<<<<<...<<<<<<<....<<<<<<<<...<<<......>>>.....
.>>>>>>>>...........<<....>>.>>>>>>>..>>>>.>>>>...
>>>...>>>>....<<<<<<...<<...<<<<.<.....>.>>>>...>>
>>>>>>..........<<<<<<.<<<<<<<<<<<<<.....>>>>>>>>>
>>>>..<<..))>>.....>>>>>>.>>>.<<<.......<<<....>>>
.....>>>..))))..].<<<.<<<<<<<.<<.<<<.....<<<<<<<<.
.......<<........>>..........<<<<<<<......<<<<<<<.
.<<<<<<<....>>>>>>>...<<....>>..>>>>>.>>.<<<.<<...
<<<<<<..<....<<<<<<<<<....>>>..<<<<......>>>>..>>>
>>>.....<<<<.<<<<<<<...<...<<<.....>>>.>....>>>>>>
>.....<<<<<.....>>>>>........>>>>.....>...>>>...>>
>.>>>>>...>>>>>>>......>>>>>>>>.....<<<<<<<.....<<
<..<<...<<<....>>>...>>....>>>.....>>>>>>>......<.
...<<<<<<<........>>>>>>>....>........>>>....<<<<<
<...........>>>>>>......>>...>>>>>>>>>>..........<
<.<.<<<<.<<<..<<<<<<<<<<<<....<<<<<..<<<<..<<....>
>.>>>>.>>>>>...>>>>>>>>>>>>..>>>.>>>>..>.>>.......
..<<<<<<<<<....>>>>>>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3jbu Mechanisms of ribosome stalling by SecM at multiple elongation steps
Resolution3.64 Å
Binding residue
(original residue number in PDB)		A1 R2 L4 P6 K7 L8 K9 R13 K21 G23 R25 K32 Q35 P37 G38 H40 R43 S48 Y50 L54 L67 E68 R69 Q70 N73 R80 G83 T109 E112 S118 H119 R127 V129 N130 I131 Y134 Q151 E201 S204 K205
Binding residue
(residue number reindexed from 1)		A1 R2 L4 P6 K7 L8 K9 R13 K21 G23 R25 K32 Q35 P37 G38 H40 R43 S48 Y50 L54 L67 E68 R69 Q70 N73 R80 G83 T109 E112 S118 H119 R127 V129 N130 I131 Y134 Q151 E201 S204 K205
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0048027 mRNA 5'-UTR binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0002181 cytoplasmic translation
GO:0006353 DNA-templated transcription termination
GO:0006412 translation
GO:0006417 regulation of translation
GO:0031564 transcription antitermination
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0045947 negative regulation of translational initiation
GO:0046677 response to antibiotic
GO:1990145 maintenance of translational fidelity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0015935 small ribosomal subunit
GO:0022627 cytosolic small ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3jbu, PDBe:3jbu, PDBj:3jbu
PDBsum3jbu
PubMed26670735
UniProtP0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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