Structure of PDB 8bim Chain o Binding Site BS01

Receptor Information

>8bim Chain o (length=117) Species: 83333 (Escherichia coli K-12)

RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFA
AQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITD
VTPIPHNGCRPPKKRRV

Ligand information

>8bim Chain 2 (length=1534)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcccgcacaagcgguggagcau
gugguuuaauucgaugcaacgcgaagaaccuuaccuggucuugacaucca
cggaaguuuucagagaugagaaugugccuucgggaaccgugagacaggug
cugcauggcugucgucagcucguguugugaaauguuggguuaagucccgc
aacgagcgcaacccuuauccuuuguugccagcgguccggccgggaacuca
aaggagacugccagugauaaacuggaggaagguggggaugacgucaaguc
aucauggcccuuacgaccagggcuacacacgugcuacaauggcgcauaca
aagagaagcgaccucgcgagagcaagcggaccucauaaagugcgucguag
uccggauuggagucugcaacucgacuccaugaagucggaaucgcuaguaa
ucguggaucagaaugccacggugaauacguucccgggccuuguacacacc
gcccgucacaccaugggaguggguugcaaaagaaguagguagcuuaaccu
ucgggagggcgcuuaccacuuugugauucaugacuggggugaagucguaa
caagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8bim Modulation of translational decoding by m 6 A modification of mRNA.
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): N28 N29 T33 G39 A41 W44 T46 R53 K87 H118 N119 R122 K125 R127 R128 V129
• Binding residue (residue number reindexed from 1): N16 N17 T21 G27 A29 W32 T34 R41 K75 H106 N107 R110 K113 R115 R116 V117

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8bim, PDBe:8bim, PDBj:8bim
• PDBsum: 8bim
• PubMed: 37553384
• UniProt: P0A7R9|RS11_ECOLI Small ribosomal subunit protein uS11 (Gene Name=rpsK)