Structure of PDB 6y69 Chain X Binding Site BS01

Receptor Information

>6y69 Chain X (length=77) Species: 83333 (Escherichia coli K-12)

SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRV
SAKGMRVIDKKGIDTVLAELRARGEKY

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): S1 R2 K9 T13 G14 N15 R17 S18 H19 A20 L21 N22 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 A52 K53 M55 R56 K60 K61
• Binding residue (residue number reindexed from 1): S1 R2 K9 T13 G14 N15 R17 S18 H19 A20 L21 N22 K25 R26 R27 F28 L29 P30 N31 H33 H35 R36 R49 A52 K53 M55 R56 K60 K61

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 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:6y69, PDBe:6y69, PDBj:6y69
• PDBsum: 6y69
• PubMed: 32601485
• UniProt: P0A7M2|RL28_ECOLI Large ribosomal subunit protein bL28 (Gene Name=rpmB)