Structure of PDB 6y69 Chain O Binding Site BS01

Receptor Information

>6y69 Chain O (length=116) Species: 83333 (Escherichia coli K-12)

DKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAA
STVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHG
RVQALADAAREAGLQF

Ligand information

>6y69 Chain A (length=2887)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucacgacuuaccaaccc
gaugcaaacugcgaauaccggagaauguuaucacgggagacacacggcgg
gugcuaacguccgucgugaagagggaaacaacccagaccgccagcuaagg
ucccaaagucaugguuaagugggaaacgaugugggaaggcccagacagcc
aggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagcuca
cuggucgagucggccugcgcggaagauguaacggggcuaaaccaugcacc
gaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguucugu
aagccugcgaaggugugcugugaggcaugcuggagguaucagaagugcga
augcugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaag
accaaggguuccuguccaacguuaaucggggcagggugagucgaccccua
aggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccugua
cuugguguuacugcgaaggggggacggagaaggcuauguuggccgggcga
cgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaa
aaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaa
ugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaaucgua
ccccaaaccgacacagguggucagguagagaauaccaaggcgcuugagag
aacucgggugaaggaacuaggcaaaauggugccguaacuucgggagaagg
cacgcugauauguaggugaggucccucgcggauggagcugaaaucagucg
aagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaa
cacgaaaguggacguauacggugugacgccugcccggugccgggagguua
auugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaaacg
gcggcguccuaagguagcgaaauuccuugucggguaaguuccgaccugca
cgaauggcguaaugauggccaggcugucuccacccgagacucagugaaau
ugaacucgcugugaagaugcaguguacccgcggcaagacggaaagacccc
guaaaccuuuacuauagcuugacacugaacauugagccuugauguguagg
auaggugggaggcuuugaaguguggacgccagucugcauggagccgaccu
ugaaauaccacccuuuaauguuugauguucuaacguugacccguaauccg
gguugcggacagugucugguggguaguuugacuggggcggucuccuccua
aagaguaacggaggagcacgaagguuggcuaauccuggucggacaucagg
agguuagugcaauggcauaagccagcuugacugcgagcgugacggcgcga
gcaggugcgaaagcaggucauagugauccggugguucugaauggaagggc
caucgcucaacggauaaaagguacuccggggauaacaggcugauaccgcc
caagaguucauaucgacggcgguguuuggcaccucgaugucggcucauca
cauccuggggcugaaguaggucccaaggguauggcuguucgccauuuaaa
gugguacgcgagcuggguuuagaacgucgugagacaguucggucccuauc
ugccgugggcgcuggagaacugaggggggcugcuccuaguacgagaggac
cggaguggacgcaucacugguguucggguugucaugccaauggcacugcc
cgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaa
cuugccccgagaugaguucucccugacccuuuaaggguccugaaggaacg
uugaagacgacgacguugauaggccggguguguaagcgcagcgaugcguu
gagcuaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6y69 Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.
• Resolution: 2.86 Å
• Binding residue (original residue number in PDB): R9 R10 T12 R13 R16 K17 L21 S91 F92 R94 Y99 R111 F117
• Binding residue (residue number reindexed from 1): R8 R9 T11 R12 R15 K16 L20 S90 F91 R93 Y98 R110 F116

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• 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:6y69, PDBe:6y69, PDBj:6y69
• PDBsum: 6y69
• PubMed: 32601485
• UniProt: P0C018|RL18_ECOLI Large ribosomal subunit protein uL18 (Gene Name=rplR)