Structure of PDB 8r8m Chain D Binding Site BS01

Receptor Information

>8r8m Chain D (length=205) Species: 679895 (Escherichia coli BW25113)

ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDY
GVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNV
VYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKK
QSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIV
ELYSK

Ligand information

>8r8m Chain A (length=1519)

aauugaagaguuugaucauggcucagauugaacgcuggcggcaggccuaa
cacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacga
guggcggacgggugaguaaugucugggaaacugccugauggagggggaua
acuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagagg
gggccucuugccaucggaugugcccagaugggauuagcuaguaggugggg
uaacggcucaccuaggcgacgaucccuagcuggucugagaggaugaccag
ccacacuggaacugagacacgguccagacuccuacgggaggcagcagugg
ggaauauugcacaaugggcgcaagccugaugcagccaugccgcguguaug
aagaaggccuucggguuguaaaguacuuucagcggggaggaagggaguaa
aguuaauaccuuugcucauugacguuacccgcagaagaagcaccggcuaa
cuccgugccagcagccgcgguaauacggagggugcaagcguuaaucggaa
uuacugggcguaaagcgcacgcaggcgguuuguuaagucagaugugaaau
ccccgggcucaaccugggaacugcaucugauacuggcaagcuugagucuc
guagagggggguagaauuccagguguagcggugaaaugcguagagaucug
gaggaauaccgguggcgaaggcggcccccuggacgaagacugacgcucag
gugcgaaagcguggggagcaaacaggauuagauacccugguaguccacgc
cguaaacgaugucgacuuggagguugugccggcguggcuuccggagcuaa
cgcguuaagucgaccgccuggggaguacggccgcaagguuaaaacucaaa
ugaauugacgggggcccgcacaagcgguggagcaugugguuuaauucgau
gcaacgcgaagaaccuuaccuggucuugacauccacggaaguuuucagag
augagaaugugccuucgggaaccgugagacaggugcugcauggcugucgu
cagcucguguugugaaauguuggguuaagucccgcaacgagcgcaacccu
uauccuuuguugccagcgguccggccgggaacucaaaggagacugccagu
gauaaacuggaggaagguggggaugacgucaagucaucauggcccuuacg
accagggcuacacacgugcuacaauggcgcauacaaagagaagcgaccuc
gcgagagcaagcggaccucauaaagugcgucguaguccggauuggagucu
gcaacucgacuccaugaagucggaaucgcuaguaaucguggaucagaaug
ccacggugaauacguucccgggccuuguacacaccgcccgucacaccaug
ggaguggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuua
ccacuuugugauucaugacuggggugaagucguaacaagguaaccguagg
ggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8r8m Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): A2 R3 P7 K8 L9 K10 R13 R14 K22 S23 R26 K31 C32 Q36 G39 Q40 H41 R44 Y51 L55 R56 Q59 R62 L68 E69 R70 Q71 N74 R81 K83 T110 E113 R115 Q116 S119 H120 K121 N131 I132 S134 Q152 R154 E202 S205 K206
• Binding residue (residue number reindexed from 1): A1 R2 P6 K7 L8 K9 R12 R13 K21 S22 R25 K30 C31 Q35 G38 Q39 H40 R43 Y50 L54 R55 Q58 R61 L67 E68 R69 Q70 N73 R80 K82 T109 E112 R114 Q115 S118 H119 K120 N130 I131 S133 Q151 R153 E201 S204 K205

Gene Ontology

Molecular Function

• GO:0000900 mRNA regulatory element binding translation repressor activity
• 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

External links

• PDB: RCSB:8r8m, PDBe:8r8m, PDBj:8r8m
• PDBsum: 8r8m
• PubMed: 38826346
• UniProt: P0A7V8|RS4_ECOLI Small ribosomal subunit protein uS4 (Gene Name=rpsD)