Structure of PDB 3j5l Chain V Binding Site BS01

Receptor Information

>3j5l Chain V (length=94) Species: 83333 (Escherichia coli K-12)

MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNM
QAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA

Ligand information

>3j5l Chain A (length=2853)

gguuaacgacuaagcguacacgguggaugcccuggcagucagaggcgaug
aaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguua
uaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuauc
auuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacauc
uaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcga
gcgaacggggagcagcccagagccugaaucaguguguguguuaguggaag
cgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaugc
acaugcugugagcucgaugaguagggcgggacacgugguauccugucuga
auauggggggaccauccuccaaggcuaaauacuccugacugaccgauagu
gaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggaguga
aaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggcg
ugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguagc
aagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggcg
uuaaguugcaggguauagacccgaaacccggugaucuagccaugggcagg
uugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaaa
aauuagcggaugacuuguggcugggggugaaaggccaaucaaaccgggag
auagcugguucuccccgaaagcuauuuagguagcgccucgugaauucauc
uccggggguagagcacuguuucggcaagggggucacuuaccaacccgaug
caaacugcgaauaccggagaauguuaucacgggagacacacggcgggugc
uaacguccgucgugaagagggaaacaacccagaccgccagcuaagguccc
aaagucaugguuaagugggaaacgaugugggaaggcccagacagccagga
uguuggcuuagaagcagccaucauuuaaagaaagcguaauagcucacugg
ucgagucggccugcgcggaagauguaacggggcuaaaccaugcaccgaag
cugcggcagcgacgcuuaugcguuguuggguaggggagcguucuguaagc
cugcgaaggugugcugugaggcaugcuggagguaucagaagugcgaaugc
ugacauaaguaacgauaaagcgggugaaaagcccgcucgccggaagacca
aggguuccuguccaacguuaaucggggcagggugagucgaccccuaaggc
gaggccgaaaggcguagucgaugggaaacagguuaauauuccuguacuug
guguuacugcgaaggggggacggagaaggcuauguuggccgggcgacggu
ugucccgguuuaagcguguaggcugguuuuccaggcaaauccggaaaauc
aaggcugaggcgugaugacgaggcacuacggugcugaagcaacaaaugcc
cugcuuccaggaaaagccucuaagcaucagguaacaucaaaucguacccc
aaaccgacacagguggucagguagagaauaccaaggcgcuugagagaacu
cgggugaaggaacuaggcaaaauggugccguaacuucgggagaaggcacg
cugauauguaggugaggucccucgcggauggagcugaaaucagucgaaga
uaccagcuggcugcaacuguuuauuaaaaacacagcacugugcaaacacg
aaaguggacguauacggugugacgccugcccggugccggaagguuaauug
augggguuagcgcaagcgaagcucuugaucgaagccccgguaaacggcgg
ccguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuc
cgaccugcacgaauggcguaaugauggccaggcugucuccacccgagacu
cagugaaauugaacucgcugugaagaugcaguguacccgcggcaagacgg
aaagaccccgugaaccuuuacuauagcuugacacugaacauugagccuug
auggaaguguggacgccagucugcauggcuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<....
..<<<<<<....(((.>>>.....<<<<<<<..<<<)))....>>>....
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<......>
......>>>>>.>.........<<....>>..<<<<<<.....<<.....
>>....>>>>>>..(((..<<<<......<<<<<<<<<<<<<.<<<...<
<<<<......>>>>>((......<<<.....))>>>...>>>...>>>>>
>>>>>>>>...>>>>........<<<<<<<<.........>>>>>>>>..
....<<<<<..<<<<>>>>>..)))......]].>>>>>>>.]]......
.........<<....>>....]].........<<<<.....>>>>.....
.............>>>>>>>>>>>.......<<<<..<<<<<......>>
>>>..>>>>...<.<........>.>.<<<<<<....<<<<<<<<<<<<<
..<<<...<<.....>>...>>>...<<....>>..<<<<.....>>>>.
....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<
<<...<<<<<<......>>>>>>.>...>>>...<<<.<<<<<.......
.>>>>>>>>....>>>>>>>>>...<<<.....>>>......>>>>>>..
.>..>.>>..<<<<<<....<<<<<....>>>>>.<<<<<<<<...<<<<
<<<<<.....<<<...<<<.<<<<...<<<<<<.>>>>.>>...>>>>.>
>>..>>.>.....>>>>>>.>>>...>>>>>>>.>...<<<<<<<<<<..
....>>>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((
.....<<<<<<...........<<..<<<<<..<<........<<<<<.<
<...<<<.........>>>...>>........<<<......>>>..>>>>
>....>>..>>>>>.>>...........))).....>>>>>>.>>>...>
>>>>>><<<<<..<<....>>..>>>>>....>>>>>>..<<<<<...<<
<......<<<<<<<<....>>>>>>>>...>>>..>>>>>........>>
>>>>.......<<.....<<<<<<.......>>>>>><<<<....<<<<<
.<<...<<<<<<...<<.....>>.>>>>>>....((<<<.<<<...<<<
...<<<....>>>...>>>...>>>..<<<<<........>>>>>))<<<
<<<<<<<<<<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((
...>>>>>><<..<<<<...<<<<<<<<<<<<.<<.....>>>>>>>>>>
..>>>>...>>>>...>><..<<<<<....>>>>>...>>>>>>...>>>
...>>>>.........>>>>...>>....>>>>>>>>>>>.>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<
<<<<<<.<<...............<<<<<...............>>>>><
<<<<<.....<<<...<<<<.....>>>>...>>>...>>>>>>......
......<<<<<<<<<..<<<.........>>>..<<<<<<<.....<<<.
...>>>.......>>>>>>>.<<<<<.<<<..<<<<<<<..<<<......
..<<<<<..<<....>>...>>>>>........>>>>>>>>..>>>>><<
<<<<.......>>>>>>........<...........<<<<<<.....>>
>>>>.....>....>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>
>>>>...........<<<<<........>>>>>..<<<<<<<<.(((.[[
......<<<<.[[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<<<
<.....<<<<<<<......>>>>>>>....>>>>.>>>>>>>>>>>...<
<<.<<<<<<.....>>>>>>>>>....>>>>>.>>>..>>>>>..<<<<.
....>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<
<<<<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<
..<<<<....>>>>..>>>>.<<<....>>>.>>))).......<<<<<<
<.((..>>>>..))>>>>>>>.............>>>>..]]>>>>....
...<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>..
.....<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<
<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>
>.>>>>....]]..)))>>>>>>>>....<<<<<<<...<<<<..<<<<<
<<...............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<
<))).>>>>>>..>>>>>...>>>>.>>>>>...<<<....<<<<<....
.......>>>>>....>>>.>>>>.......>>>>>>>..<<<<<.....
>>>>>.....<<..<<<<<.......>>>>>....<<<<<<<<..<<...
.<<<<<....>>>>>...>>...>>>>>.>>>.....>>.....>.>>>>
>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3j5l Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide.
• Resolution: 6.6 Å
• Binding residue (original residue number in PDB): D45 N49 K83
• Binding residue (residue number reindexed from 1): D45 N49 K83

Gene Ontology

Molecular Function

• 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
• GO:0009314 response to radiation
• 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:3j5l, PDBe:3j5l, PDBj:3j5l
• PDBsum: 3j5l
• PubMed: 24662426
• UniProt: P68919|RL25_ECOLI Large ribosomal subunit protein bL25 (Gene Name=rplY)