Structure of PDB 8ekc Chain R Binding Site BS02

Receptor Information

>8ekc Chain R (length=114) Species: 562 (Escherichia coli)

SNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIR
NRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLR
ERTGKAARIKERLN

Ligand information

>8ekc Chain A (length=2845)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gcgucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccg
aagcugcggcagcgacgcgcguuguuggguaggggagcguucuguaagcc
ugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugcu
gacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagaccaa
ggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggcg
aggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuugg
uguuacugcgaaggggggacggagaaggcuauguuggccgggcgacgguu
gucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauca
aggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugccc
ugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccca
aaccgacacagguggucagguagagaauaccaaggcgcuugagagaacuc
gggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacgc
ugauauguaggugaggucccucgcggauggagcugaaaucagucgaagau
accagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacga
aaguggacguauacggugugacgccugcccggugccggaagguuaauuga
ugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaauggcguaaugauggccaggcugucuccacccgagacuc
agugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgga
aagaccccgugaaccuuuacuauagcuugacacugaacauugagccuuga
uguguaggauaggugggaggcuuugaaguguggacgccagucugcaugga
gccgaccuugaaauaccacccuuuaauguuugauguucuaacguugaccc
guaauccggguugcggacagugucugguggguaguuugacuggggcgguc
uccuccuaaagaguaacggaggagcacgaagguuggcuaauccuggucgg
acaucaggagguuagugcaauggcauaagccagcuugacugcgagcguga
cggcgcgagcaggugcgaaagcaggucauagugauccggugguucugaau
ggaagggccaucgcucaacggauaaaagguacuccggggauaacaggcug
auaccgcccaagaguucauaucgacggcgguguuuggcaccucgaugucg
gcucaucacauccuggggcugaaguaggucccaaggguauggcuguucgc
cauuuaaagugguacgcgagcuggguuuagaacgucgugagacaguucgg
ucccuaucugccgugggcgcuggagaacugaggggggcugcuccuaguac
gagaggaccggaguggacgcaucacugguguucggguugucaugccaaug
gcacugcccgguagcuaaaugcggaagagauaagugcugaaagcaucuaa
gcacgaaacuugccccgagaugaguucucccugacccuuuaaggguccug
aaggaacguugaagacgacgacguugauaggccggguguguaagcgcagc
gaugcguugagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ekc Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): S2 R21 R51 N52 R53 H56 R93 K94 A95 K96 R103
• Binding residue (residue number reindexed from 1): S1 R20 R50 N51 R52 H55 R92 K93 A94 K95 R102

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8ekc, PDBe:8ekc, PDBj:8ekc
• PDBsum: 8ekc
• PubMed: 36546783
• UniProt: P0A7K6|RL19_ECOLI Large ribosomal subunit protein bL19 (Gene Name=rplS)