Structure of PDB 8cep Chain P Binding Site BS01

Receptor Information

>8cep Chain P (length=80) Species: 679895 (Escherichia coli BW25113)

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGT
RLDLDRIAHWVGQGATISDRVAALIKEVNK

Ligand information

>8cep Chain A (length=1046)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaaugcugacgaguggcggacgggu
gaguaaugucugggaaacugccugauggagggggauaacuacuggaaacg
guagcuaauaccgcauaacgucgcaagaccaaagagggggccucuugcca
ucggaugugcccagaugggauuagcuaguaggugggguaacggcucaccu
aggcgacgaucccuagcuggucugagaggaugaccagccacacuggaacu
gagacacgguccagacuccuacgggaggcagcaguggggaauauugcaca
augggcgcaagccugaugcagccaugccgcguguaugaagaagcccuucg
gguuguaaaguacuuucagcggggaggaagggaguaaaguuaauaccuuu
gcucauugacguuacccgcagaagaagcaccggcuaacuccgugccagca
gccgcgguaauacggagggugcaagcguuaaucggaauuacugggcguaa
agcgcacgcaggcgguuuguuaagucagaugugaaauccccgggcucaac
cugggaacugcaucugauacuggcaagcuugagucucguagaggggggua
gaauuccagguguagcggugaaaugcguagagaucuggaggaauaccggu
ggcgaaggcggcccccuggacgaagacugacgcucaggugcgaaagcgug
gggagcaaacaggauuagauacccugguaguccacgccguaaacgauguc
gacuuggagguugugccggcguggcuuccggagcuaacgcguuaagucga
ccgccuggggaguacggccgcaagguuaaaacucaaaugaauugacgggg
guuguacacaccgcccgucacaccaugggaguggguugcaaaagaaguag
guagcuuaaccuucgggagggcgcuuaccacuuugugauucaugacuggg
gugaagucguaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cep Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): M1 V2 R5 L6 R8 G10 K12 K13 R14 F16 Y17 Q18 D23 R25 R28 G30 R31 R35 F38 S44 K46 E47 R51 W60 Q63 G64 S68 R70
• Binding residue (residue number reindexed from 1): M1 V2 R5 L6 R8 G10 K12 K13 R14 F16 Y17 Q18 D23 R25 R28 G30 R31 R35 F38 S44 K46 E47 R51 W60 Q63 G64 S68 R70

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

External links

• PDB: RCSB:8cep, PDBe:8cep, PDBj:8cep
• PDBsum: 8cep
• PubMed: 37550453
• UniProt: P0A7T3|RS16_ECOLI Small ribosomal subunit protein bS16 (Gene Name=rpsP)