Structure of PDB 8cgu Chain E Binding Site BS01

Receptor Information

>8cgu Chain E (length=156) Species: 679895 (Escherichia coli BW25113)

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAA
IQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGG
AMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK
SVEEIL

Ligand information

>8cgu Chain A (length=1047)

aaauugaagaguuugaucauggcucagauugaacgcuggcggcaggccua
acacaugcaagucgaacgguaacaggaauugcugacgaguggcggacggg
ugaguaaugucugggaaacugccugauggagggggauaacuacuggaaac
gguagcuaauaccgcauaacgucgcaagaccaaagagggggccucuugcc
aucggaugugcccagaugggauuagcuaguaggugggguaacggcucacc
uaggcgacgaucccuagcuggucugagaggaugaccagccacacuggaac
ugagacacgguccagacuccuacgggaggcagcaguggggaauauugcac
aaugggcgcaagccugaugcagccaugccgcguguaugaagaagcccuuc
ggguuguaaaguacuuucagcggggaggaagggaguaaaguuaauaccuu
ugcucauugacguuacccgcagaagaagcaccggcuaacuccgugccagc
agccgcgguaauacggagggugcaagcguuaaucggaauuacugggcgua
aagcgcacgcaggcgguuuguuaagucagaugugaaauccccgggcucaa
ccugggaacugcaucugauacuggcaagcuugagucucguagaggggggu
agaauuccagguguagcggugaaaugcguagagaucuggaggaauaccgg
uggcgaaggcggcccccuggacgaagacugacgcucaggugcgaaagcgu
ggggagcaaacaggauuagauacccugguaguccacgccguaaacgaugu
cgacuuggagguugugccggcguggcuuccggagcuaacgcguuaagucg
accgccuggggaguacggccgcaagguuaaaacucaaaugaauugacggg
gguuguacacaccgcccgucacaccaugggaguggguugcaaaagaagua
gguagcuuaaccuucgggagggcgcuuaccacuuugugauucaugacugg
ggugaagucguaacaagguaaccguaggggaaccugcgguuggauca

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cgu Structural conservation of antibiotic interaction with ribosomes.
• Resolution: 1.89 Å
• Binding residue (original residue number in PDB): N19 V21 S22 K23 T24 V25 K26 R29 T90 F95 Q97 A99 S100 T103 A107 G108 R112 L124 A125 K126 A127 Y128 S130 T131 N132 N135
• Binding residue (residue number reindexed from 1): N10 V12 S13 K14 T15 V16 K17 R20 T81 F86 Q88 A90 S91 T94 A98 G99 R103 L115 A116 K117 A118 Y119 S121 T122 N123 N126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• 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:8cgu, PDBe:8cgu, PDBj:8cgu
• PDBsum: 8cgu
• PubMed: 37550453
• UniProt: P0A7W1|RS5_ECOLI Small ribosomal subunit protein uS5 (Gene Name=rpsE)