Structure of PDB 8r8m Chain v Binding Site BS02

Receptor Information

>8r8m Chain v (length=78) Species: 679895 (Escherichia coli BW25113)

GSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDH
TLFAKADGKVKFEVKGPKNRKFISIEAE

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): G8 S9 R11 N12 R14 D15 S16 E17 A18 K19 R20 K24 R25 F26 G27 E29 A33 G34 S35 I36 R41 G42 T43 H46 G54 R55 D56 H57 T58 F60 F69 K75 R77 K78
• Binding residue (residue number reindexed from 1): G1 S2 R4 N5 R7 D8 S9 E10 A11 K12 R13 K17 R18 F19 G20 E22 A26 G27 S28 I29 R34 G35 T36 H39 G47 R48 D49 H50 T51 F53 F62 K68 R70 K71

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding
• GO:0043022 ribosome binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0001558 regulation of cell growth
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042256 cytosolic ribosome assembly
• GO:0090070 positive regulation of ribosome biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005737 cytoplasm
• 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: P0A7L8|RL27_ECOLI Large ribosomal subunit protein bL27 (Gene Name=rpmA)