Structure of PDB 8r8m Chain p Binding Site BS01

Receptor Information

>8r8m Chain p (length=117) Species: 679895 (Escherichia coli BW25113)

ARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRR
QRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVF
DKVAFTALVEKAKAALA

Ligand information

>8r8m Chain a (length=2738)

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

Structure summary

• PDB: 8r8m Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): A2 R3 V4 K5 R6 V8 I9 R11 R13 H14 K15 K16 K19 K22 G23 Y24 Y25 G26 A27 R28 R30 V31 Y32 R33 V34 Q37 K41 A42 Y45 Y47 R48 D49 R50 R51 Q52 R53 K54 R55 Q56 F57 R58 Q59 W61 I62 N66 R70 S75 Y76 S77 N81 K84 D91 R92 K93
• Binding residue (residue number reindexed from 1): A1 R2 V3 K4 R5 V7 I8 R10 R12 H13 K14 K15 K18 K21 G22 Y23 Y24 G25 A26 R27 R29 V30 Y31 R32 V33 Q36 K40 A41 Y44 Y46 R47 D48 R49 R50 Q51 R52 K53 R54 Q55 F56 R57 Q58 W60 I61 N65 R69 S74 Y75 S76 N80 K83 D90 R91 K92

Gene Ontology

Molecular Function

• GO:0000900 mRNA regulatory element binding translation repressor activity
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0017148 negative regulation of 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:8r8m, PDBe:8r8m, PDBj:8r8m
• PDBsum: 8r8m
• PubMed: 38826346
• UniProt: P0A7L3|RL20_ECOLI Large ribosomal subunit protein bL20 (Gene Name=rplT)