Structure of PDB 5j4d Chain JA Binding Site BS01

Receptor Information

>5j4d Chain JA (length=258) Species: 83333 (Escherichia coli K-12)

LPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMS
ASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSA
CTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLP
TGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGS
GDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQA
DQLAALSE

Ligand information

>5j4d Chain A (length=1507)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcgggguuuuacuccguggucagcggcggac
gggugaguaacgcgugggugaccuacccggaagagggggacaacccgggg
aaacucgggcuaaucccccauguggacccgccccuugggguguguccaaa
gggcuuugcccgcuuccggaugggcccgcgucccaucagcuaguuggugg
gguaauggcccaccaaggcgacgacggguagccggucugagaggauggcc
ggccacaggggcacugagacacgggccccacuccuacgggaggcagcagu
uaggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuugga
ggaagaagcccuucgggguguaaacuccugaacccgggacgaaacccccg
aggaggggacugacgguaccgggguaauagcgccggccaacuccgugcca
gcagccgcgguaauacggagggcgcgagcguuacccggauucacugggcg
uaaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuc
aaccgugggggagcgugggauacgcucaggcuagacggugggagagggug
guggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgcc
gauggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagc
guggggagcaaaccggauuagauacccggguaguccacgcccuaaacgau
gcgcgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcg
cgccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacgg
gggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaag
aaccuuaccaggccuugacaugcuagggaacccgggugaaagccuggggu
gccccgcgaggggagcccuagcacaggugcugcauggccgucgucagcuc
gugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccgu
uaguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagc
gggaggaaggaggggacgacgucuggucagcauggcccuuacggccuggg
cgacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacgg
ggagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaaccc
gaccccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcgg
ugaauacguucccgggccuuguacacaccgcccgucacgccaugggagcg
ggcucuacccgaagucgccgggagccuacgggcaggcgccgaggguaggg
cccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcgg
cuggauc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j4d Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G118 T119 G121 R133 R183 Q185 Q193 R195 R303 Q314
• Binding residue (residue number reindexed from 1): G18 T19 G21 R33 R83 Q85 Q93 R95 R203 Q214

Gene Ontology

Molecular Function

• GO:0003747 translation release factor activity
• GO:0005515 protein binding
• GO:0016149 translation release factor activity, codon specific
• GO:0043022 ribosome binding

Biological Process

• GO:0006412 translation
• GO:0006415 translational termination

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5j4d, PDBe:5j4d, PDBj:5j4d
• PDBsum: 5j4d
• PubMed: 27107638
• UniProt: P0A7I0|RF1_ECOLI Peptide chain release factor RF1 (Gene Name=prfA)