Structure of PDB 8cai Chain D Binding Site BS01

Receptor Information
>8cai Chain D (length=205) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK
Ligand information
>8cai Chain A (length=1114) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacagguugcugacgaguggcggacggguga
guaaugucugggaaacugccugauggagggggauaacuacuggaaacggu
agcuaauaccgcauaacgucgcaagaccaaagagcuugccaucggaugug
cccagaugggauuagcuaguaggugggguaacggcucaccuaggcgacga
ucccuagcuggucugagaggaugaccagccacacuggaacugagacacgg
uccagacuccuacgggaggcagcaguggggaauauugcacaaugggcgca
agccugaugcagccaugccgcguguaugaagaaggccuucggguuguaaa
guacuuucagcggggaggaagggaguaaaguuaauaccuuugcucauuga
cguuacccgcagaagaagcaccggcuaacuccgugccagcagccgcggua
auacggagggugcaagcguuaaucggaauuacugggcguaaagcgcacgc
aggcgguuuguuaagucagaugugaaauccccgggcucaaccugggaacu
gcaucugauacuggcaagcuugagucucguagagggggguagaauuccag
guguagcggugaaaugcguagagaucuggaggaauaccgguggcgaaggc
ggcccccuggacgaagacugacgcucaggugcgaaagcguggggagcaaa
caggauuagauacccugguaguccacgccguaaacgaugucgacuuggag
guuguuggcuuccggagcuaacgcguuaagucgaccgccuggggaguacg
gccgcaagguuaaaacucaaaugaauugacgggggcccggcauggcuguc
gucagcucguguugugaaauguuggguuaagucccgcaacgagcgcgacg
ucaaguggcuucccgggccuuguacacaccgcccgucacaccaugggagu
ggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuuaccacu
uugugauucaugacuggggugaagucguaacaagguaaccguaggggaac
cugcgguuggauca
.......<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....
<<<.<<<..<<<..<<.<<..<<<....>>>>>..>>>>>......<<..
.....<<<<<<<..<<...<<<<<<<.<.<<.....<<<<<......>>>
>>......>>.>.....<<<....>>>....<<<>>>.>>>>>>>..>>.
>>>>>>><<<....<<<..<<<<<<<.........>>>>>>>>>>.....
.>>>..<<<<<<<<....>>>>...>>>>.>>.<<<<<.<.........>
>>>>>.<<<<<..>>>>>...>>>>>>.........<<<....<<<<...
.>>>>..>>>..>>.>>>>>>..<<<<......<<<<....>>>>.....
>>>>...<.<<<<<......<.<<<<<<<<.......>>>>>>>>.>...
.....>>>>>....>..<<<<<(((...<<<<<.....<<.)))>>....
...>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<<<..
.<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>....
>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<<<<<
<<...<<<......>>>......>>>>>>>>...........<<....>>
.>>>>>>>..>>>>.>>>>...>>>...>>>>....<<<<<<...<<...
<<<<.........>>>>...>>>>>>>>..........<<<<<<.<<<<<
<<<<.>>>>>>>>>..<<..))>>.....>>>>>>.>>>.<<<......<
<<<....>>>>....>>>..)))).]<<<<<.<<<<<<.......<<...
....<<<<<<<<<....>>>..<<<<......>>>>..>>>>>>......
...>>.........>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<
<<<<<<<<<<....<<<<<<.<<<<..<<....>>.>>>>>>>>>>...>
>>>>>>>>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>
>>>>>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8cai Structural conservation of antibiotic interaction with ribosomes.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		A2 R3 L5 P7 K8 L9 K10 R13 R14 K22 S23 R26 K31 C32 K33 P38 G39 Q40 H41 R44 S49 Y51 L55 R56 K58 Q59 R62 R63 L68 E69 R70 Q71 N74 R81 K83 T110 E113 R115 Q116 S119 H120 K121 V130 N131 I132 S134 R154 E202 S205 K206
Binding residue
(residue number reindexed from 1)		A1 R2 L4 P6 K7 L8 K9 R12 R13 K21 S22 R25 K30 C31 K32 P37 G38 Q39 H40 R43 S48 Y50 L54 R55 K57 Q58 R61 R62 L67 E68 R69 Q70 N73 R80 K82 T109 E112 R114 Q115 S118 H119 K120 V129 N130 I131 S133 R153 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8cai, PDBe:8cai, PDBj:8cai
PDBsum8cai
PubMed37550453
UniProtP0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)

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