Structure of PDB 5j4d Chain OC Binding Site BS02

Receptor Information

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

LPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMS
ASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSA
CTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLP
TGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGS
GDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQA
DQLAALSE

Ligand information

>5j4d Chain GB (length=2880)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcgaagacagccaggagguuggcuuagaagcagccauc
cuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaa
ugaucggggcucaagcccagcgccgaagcugcgggucugggggaugaccc
caggcgguaggggagcguucccgaugccgaugaaggccgacccgcgaggg
cggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagag
ggugagaaucccucucgccguaagcccaaggguuccuacgcaauggucgu
cagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaa
gggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacg
cucuaggcuagggggaccggagccauggacgagcccggccagaagcgcag
ggugggagguaggcaaauccgccucccaaaagcucugcgugguggggaag
cccguacgggugacaaccccccgaagccagggagccaagaaaagccucua
agcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgggug
caagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaagu
uggccccguaacuucgggagaaggggugcucccuggggugaugagcuccg
gggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcuc
ucugcgaacucguaagaggagguauagggagcgacgcuugcccggugccg
gaaggucaaggggaggggugcaagccccgaaccgaagccccggugaacgg
cggccguaacuauaacgguccuaagguagcgaaauuccuugucggguaag
uuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgaggg
acccggugaaauugaacuggccgugaagaugcggccuacccguggcagga
cgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggucg
cgccugcguaggauaggugggagccugugaacccccgccuccgggugggg
gggaggcgccggugaaauaccacccuggcgcggcugggggccuaacccuc
ggauggggggacagcgcuuggcgggcaguuugacuggggcggucgccucc
uaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaaucc
gccggagagcgcaaggguagaagggggccugacugcgaggccugcaagcc
gagcaggggcgaaagccgggccuagugaaccgguggucccguguggaagg
gccaucgaucaacggauaaaaguuaccccggggauaacaggcugaucucc
cccgagcguccacagcggcggggagguuuggcaccucgaugucggcucgu
cgcauccuggggcugaagaaggucccaaggguugggcuguucgcccauua
aagcggcacgcgagcuggguucagaacgucgugagacaguucggucucua
uccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgagagg
accggaagggacgcaccucugguuucccagcugucccuccaggggcauaa
gcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcggg
aagcccgccccaagaugaggccucccacggcgucaagccgguaaggaccc
gggaagacgacccgguggaugggccggggguguaagcgccgcgaggcguu
gagccgaccggucccaaucguccgaggucu

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

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): R223 F227 R228 S229 S230 G231 A232 G233 G234 Q235 H236 V237 N238 T239 T240 D241 S242 R245 E256 D259 R261 Q263 R277 Q287 R294 R295
• Binding residue (residue number reindexed from 1): R123 F127 R128 S129 S130 G131 A132 G133 G134 Q135 H136 V137 N138 T139 T140 D141 S142 R145 E156 D159 R161 Q163 R177 Q187 R194 R195

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)