Structure of PDB 7md7 Chain 1y Binding Site BS01

Receptor Information

>7md7 Chain 1y (length=97) Species: 83333 (Escherichia coli K-12)

TMNITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHIILSKEPQGFVAD
ATINTPNGVLVASGKHEDMYTAINELINKLERQLNKLQHKGEARRAA

Ligand information

>7md7 Chain 1a (length=1500)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag
uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg
ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu
gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug
gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca
ggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaau
cuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaa
gcccuucgggguguaaacuccugaacccgggacgaaacccccgacgaggg
gacugacgguaccgggguaauagcgccggccaacuccgugccagcagccg
cgguaauacggagggcgcgagcguuacccggauucacugggcguaaaggg
cguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgug
ggggagcgugggauacgcucaggcuagacggugggagagggugguggaau
ucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcg
aaggcagccaccugguccacccgugacgcugaggcgcgaaagcgugggga
gcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcu
aggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgcc
uggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccg
cacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuua
ccaggccuugacaugcuagggaacccgggugaaagccuggggugccccgc
gaggggagcccuagcacaggugcugcauggccgucgucagcucgugccgu
gagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugc
cagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggagga
aggaggggacgacgucuggucagcauggcccuuacggccugggcgacaca
cgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcua
aucgcaaaaaggugggcccaguucggauuggggucugcaacccgacccca
ugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauac
guucccgggccuuguacacaccgcccgucacgccaugggagcgggcucua
cccgaagucgccgggagccuacgggcaggcgccgaggguagggcccguga
cuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7md7 Binding and Action of Triphenylphosphonium Analog of Chloramphenicol upon the Bacterial Ribosome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): T2 N4 I5 T6 K8 Q9 R17 R23 K26 K29 W30 Q31 H33 P45 Q46 N55 V62 A63 S64 K80 R83 Q84 K87 H90 K91 E93 A94 R96
• Binding residue (residue number reindexed from 1): T1 N3 I4 T5 K7 Q8 R16 R22 K25 K28 W29 Q30 H32 P44 Q45 N54 V61 A62 S63 K79 R82 Q83 K86 H89 K90 E92 A93 R95

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0043024 ribosomal small subunit binding

Biological Process

• GO:0006417 regulation of translation
• GO:0009409 response to cold
• GO:0022611 dormancy process
• GO:0044238 primary metabolic process
• GO:0045900 negative regulation of translational elongation
• GO:0045947 negative regulation of translational initiation

Cellular Component

• GO:0005829 cytosol
• GO:0022627 cytosolic small ribosomal subunit

External links

• PDB: RCSB:7md7, PDBe:7md7, PDBj:7md7
• PDBsum: 7md7
• PubMed: 33916420
• UniProt: P0AD49|YFIA_ECOLI Ribosome-associated inhibitor A (Gene Name=raiA)