Structure of PDB 7bod Chain L Binding Site BS01

Receptor Information

>7bod Chain L (length=123) Species: 83333 (Escherichia coli K-12)

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRK
VCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGA
LDCSGVKDRKQARSKYGVKRPKA

Ligand information

>7bod Chain A (length=1078)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaagaagcuugcuucuuugcugacg
aguggcggacgggugaguaaugucugggaaacugccugauggagggggau
aacuacuggaaacgguagcuaauaccgcauaacgucgcaagaccaaagag
ggggaccuucgggccucuugccaucggaugugcccagaugggauuagcua
guaggugggguaacggcucaccuaggcgacgaucccuagcuggucugaga
ggaugaccagccacacuggaacugagacacgguccagacuccuacgggag
gcagcaguggggaauauugcacaaugggcgcaagccugaugcagccaugc
cgcguguaugaagaaggccuucggguuguaaaguacuuucagcggggagg
aagggaguaaaguuaauaccuuugcucauugacguuacccgcagaagaag
caccggcuaacuccgugccagcagccgcgguaauacggagggugcaagcg
uuaaucggaauuacugggcguaaagcgcacgcaggcgguuuguuaaguca
gaugugaaauccccgggcucaaccugggaacugcaucugauacuggcaag
cuugagucucguagagggggguagaauuccagguguagcggugaaaugcg
uagagaucuggaggaauaccgguggcgaaggcggcccccuggacgaagac
ugacgcucaggugcgaaagcguggggagcaaacaggauuagauacccugg
uaguccacgccguaaacgaugucgacuuggagguugugcccuugaggcgu
ggcuuccggagcuaacgcguuaagucgaccgccuggggaguacggccgca
agguuaaaacucaaaugaauugacgggggcgccuuguacacaccgcccgu
cacaccaugggaguggguugcaaaagaaguagguagcuuaaccuucggga
gggcgcuuaccacuuugugauucaugacuggggugaagucguaacaaggu
aaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bod A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit.
• Resolution: 2.88 Å
• Binding residue (original residue number in PDB): A2 N5 Q6 R9 R12 A13 R14 K15 V21 A26 C27 P28 Q29 K30 R31 K43 N46 S47 A48 L49 R50 T58 Y66 G68 G69 E70 R83 G84 R86 K88 X89 R94 R110 K111 Q112 A113 R114 S115 K116 G118 V119 K120 R121
• Binding residue (residue number reindexed from 1): A1 N4 Q5 R8 R11 A12 R13 K14 V20 A25 C26 P27 Q28 K29 R30 K42 N45 S46 A47 L48 R49 T57 Y65 G67 G68 E69 R82 G83 R85 K87 X88 R93 R109 K110 Q111 A112 R113 S114 K115 G117 V118 K119 R120

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0034336 misfolded RNA binding

Biological Process

• GO:0000372 Group I intron splicing
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0033120 positive regulation of RNA splicing
• GO:0034337 RNA folding
• 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:7bod, PDBe:7bod, PDBj:7bod
• PDBsum: 7bod
• PubMed: 34088665
• UniProt: P0A7S3|RS12_ECOLI Small ribosomal subunit protein uS12 (Gene Name=rpsL)