Structure of PDB 8r8m Chain 3 Binding Site BS01

Receptor Information
>8r8m Chain 3 (length=38) Species: 679895 (Escherichia coli BW25113) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG
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)
M1 K2 R4 A5 S6 V7 K8 L10 V17 R19 D20 R24 K32 K34 R36 Q37 G38
Binding residue
(residue number reindexed from 1)
M1 K2 R4 A5 S6 V7 K8 L10 V17 R19 D20 R24 K32 K34 R36 Q37 G38
Gene Ontology
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

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8r8m, PDBe:8r8m, PDBj:8r8m
PDBsum8r8m
PubMed38826346
UniProtP0A7Q6|RL36_ECOLI Large ribosomal subunit protein bL36A (Gene Name=rpmJ)

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