Structure of PDB 6y69 Chain 2 Binding Site BS01

Receptor Information

>6y69 Chain 2 (length=46) Species: 83333 (Escherichia coli K-12)

MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

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): M1 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 H16 F18 R19 R21 K25 N26 Q29 R33 R34 K37 G38 R39 A40
• Binding residue (residue number reindexed from 1): M1 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 N13 R14 H16 F18 R19 R21 K25 N26 Q29 R33 R34 K37 G38 R39 A40

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• 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: P0A7P5|RL34_ECOLI Large ribosomal subunit protein bL34 (Gene Name=rpmH)