Structure of PDB 7afi Chain P Binding Site BS01

Receptor Information

>7afi Chain P (length=82) Species: 562 (Escherichia coli)

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGT
RLDLDRIAHWVGQGATISDRVAALIKEVNKAA

Ligand information

>7afi Chain A (length=1066)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcgccuugaacacacccaccau
gggaguggguugcaaaagaaguagguagcuuaaccuucgggagggcgcuu
accacuuugugauucaugacuggggugaagguaaccguaggggaaccugc
gguuggaucaccuccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7afi A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
• Resolution: 3.53 Å
• Binding residue (original residue number in PDB): M1 V2 R5 L6 R8 G10 K12 K13 R14 F16 R25 R28 G30 R31 K46 E47 R51 G64 S68 R70 K80
• Binding residue (residue number reindexed from 1): M1 V2 R5 L6 R8 G10 K12 K13 R14 F16 R25 R28 G30 R31 K46 E47 R51 G64 S68 R70 K80

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:7afi, PDBe:7afi, PDBj:7afi
• PDBsum: 7afi
• PubMed: 34088665
• UniProt: P0A7T3|RS16_ECOLI Small ribosomal subunit protein bS16 (Gene Name=rpsP)