Structure of PDB 8r8m Chain f Binding Site BS02

Receptor Information
>8r8m Chain f (length=177) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLD
NAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFE
RLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRG
LDITITTTAKSDEEGRALLAAFDFPFR
Ligand information
>8r8m Chain a (length=2738) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggccaacccgaugcaaacugc
gaauaccggagaauguuaucacgggagacacacggcgggugcuaacgucc
gucgugaagagggaaacaacccagaccgccagcuaaggucccaaagucau
gguuaagugggaaacgaugugggaaggcccagacagcgucgagucggccu
gcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcga
cgcgcguuguuggguaggggagcguucuguaagccugcgaaggugugcug
ugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaacgau
aaagcgggugaaaagcccgcucgccggaagaccaaggguuccuguccaac
guuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggcgua
gucgaugggaaacagguuaauauuccuguacuugguguuacugcgaaggg
gggacggagaaggcuauguuggccgggcgacgguugucccgguuuaagcg
uguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgugau
gacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaaaag
ccucuaagcaucagguaacaucaaaucguaccccaaaccgacacaggugg
ucagguagagaauaccaaggcgcuugagagaacucgggugaaggaacuag
gcaaaauggugccguaacuucgggagaaggcacgcugauauguaggugag
gucccucgcggauggagcugaaaucagucgaagauaccagcuggcugcaa
cuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguauacg
gugugacgccugcccggugccggaagguuaauugaugggguuagcgcaag
cgaagcucuugaucgaagccccgguaaacggcggccguaacuauaacggu
ccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaugg
cguaaugauggccaggcugucuccacccgagacucagugaaauugaacuc
gcugugaagaugcaguguacccgcggcaagacggaaagaccccgugaacc
uuuacuauagcuugacacugaacauauguucuaacguugacccguaaucc
ggguugcggacagugucugguggguaguuugacuggggcggucuccuccu
aaagaguaacggaggagcacgaagguuggcuaauccuggucggacaucag
gagguuagugcaauggcauaagccagcuugacugcgagcgugacggcgcg
agcaggugcgaaagcaggucauagugauccggugguucugaauggaaggg
ccaucgcucaacggauaaaagguacuccggggauaacaggcugauaccgc
ccaagaguucauaucgacggcgguguuuggcaccucgaugucggcucauc
acauccuggggcugaaguaggucccaaggguauggcuguucgccauuuaa
agugguacgcgagcuggguuuagaacgucgugagacaguucggucccuau
cugccgugggcgcuggagaacugaggggggcugcuccuaguacgagagga
ccggaguggacgcaucacugguguucggguugucaugccaauggcacugc
ccgguagcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaa
acuugccccgagaugaguucucccugacccuuuaaggguccugaaggaac
guugaagacgacgacguugauaggccggguguguaagcgcagcgaugcgu
ugagcuaaccgguacuaaugaaccgugaggcuuaaccu
<<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<...
...<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>...
...>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<
<<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>
>......>>>>>.>.........<<....>>..<<<<<<.....<<....
.>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...
<<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>
>>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>.
.....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]].....
..........<<....>>....]].........<<<<.....>>>>....
..............>>>>>>>>>>>.......<<<<..<<<<<<....>>
>>>>..>>>>...<............>.<<<<<<....<<<<<<<<<<<<
<..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>
.....>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<
<<....<<<<<<......>>>>>>.....>>>...<<<.<<<<<......
..>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>.
.....>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<
<<<<<<.....<<<...<<<.<<<<...<<.>>...>>>>.>>>..>>.>
.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<......>>>>
>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<<<
<<<...........<<..<<<<<..<<........<..>....>>..>>>
>>.>>...........))).....>>>>>>.>>>...>>>>>>><<<<<<
<<..>>>>>>>>....>>>>>>..<<<<<...<<<......<<<<<<<<.
...>>>>>>>>...>>>..>>>>>........>>>>>><......<<...
..<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<
<.....>>.>>>>>>....((<<<.<<<...<<<...<<<....>>>...
>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<<...<<<
<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>><<..<<<
<...<<<<<<<<<<<<.<<.....>>>>>>>>>>..>>>>...>>>>...
>><..<<<<<....>>>>>...>>>>>>...>>>...>>>>.........
>>>>...>>....>>>>>>>>>>>.>>>..>>.....<<......>>>>>
>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<.......
........<<<<<...............>>>>><<<<<<.....<<<...
<<<<.....>>>>...>>>...>>>>>>............<<<<<<<<<.
.<<<.........>>>..<<<<<<<.....<<<....>>>.......>>>
>>>>.<<<<<.<<<..<<<<<<<..<<<....<...<<<<<..<<....>
>...>>>>>..>.....>>>>>>>>..>>>>><<<<<<.......>>>>>
>........<...........<<<<<<.....>>>>>>.....>....>>
>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>.....<
<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[[<<<
<..<<<<<.<<<.<<<<<.<<<<<..>>>>>...<<<.<<<<<<.....>
>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.
..........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>
>>.....<<...(((>>....>>>>>>>...<<<<..<<<<....>>>>.
.>>>>.<<<....>>>.>>))).......<<<<<<<.((..>>>>..))>
>>>>>>.............>>>>..]]>>>>.......<<<<...<<<<<
<...<<.......>>...>>>>>>....>>>.>.......<<<<<.<<<<
<<..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>....
.>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]..)
))>>>>>>>>....<<<<<<<...<<<<..<<<<<<<.............
..>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>..>>
>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>>...
.>>>.>>>>.......>>>>>>>..<<<<<.....>>>>><....<<..<
<<<<.......>>>>>....<<<<<<<<..<<....<<<<<....>>>>>
...>>...>>>>>.>>>.....>>..>..>>>>>>>>.
Receptor-Ligand Complex Structure
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PDB8r8m Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
K33 T35 N37 M38 G39 G41 T68 A70 R71 K72 F77 I79 I85 K88 S121 F122 D123 R125 S129 M130 G131 R150 G151 L152 D153 T155 T157
Binding residue
(residue number reindexed from 1)
K32 T34 N36 M37 G38 G40 T67 A69 R70 K71 F76 I78 I84 K87 S120 F121 D122 R124 S128 M129 G130 R149 G150 L151 D152 T154 T156
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0008097 5S rRNA 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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8r8m, PDBe:8r8m, PDBj:8r8m
PDBsum8r8m
PubMed38826346
UniProtP62399|RL5_ECOLI Large ribosomal subunit protein uL5 (Gene Name=rplE)

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