Structure of PDB 5l3p Chain d Binding Site BS01

Receptor Information
>5l3p 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
>5l3p Chain a (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
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PDB5l3p The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		A1 R2 L4 P6 K7 L8 K9 R12 R13 K32 Q39 H40 S48 Y50 L54 Q58 R61 E68 R69 Q70 R80 K82 T109 R114 Q115 H119 K120 V129 N130 I131 E201 S204 K205
Binding residue
(residue number reindexed from 1)		A1 R2 L4 P6 K7 L8 K9 R12 R13 K32 Q39 H40 S48 Y50 L54 Q58 R61 E68 R69 Q70 R80 K82 T109 R114 Q115 H119 K120 V129 N130 I131 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:5l3p, PDBe:5l3p, PDBj:5l3p
PDBsum5l3p
PubMed27226493
UniProtP0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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