Structure of PDB 4v5e Chain D2 Binding Site BS01

Receptor Information

>4v5e Chain D2 (length=71) Species: 300852 (Thermus thermophilus HB8)

KLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIR
DLKRQIARLLTVLNEKRRQNA

Ligand information

>4v5e Chain DA (length=2886)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uugcgcggggggaaccuggggaacugaaacaucucaguacccagaggaga
ggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagcc
uaaaccguccggcuuguccgggcggggucgggggcccucggccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcaagggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguccgcggc
cguggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggu
gagacccaguggaggcccgaaccggugggggaugcaaaccccucggauga
gcuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucuc
cccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagag
cacugauagggcuagggggcccaccagccuaccaaacccugucaaacucc
gaagggucccagguggagccugggagugagggcgcgagcgauaacguccg
cguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucug
ggcuaagugguaaaggauguggcgcggcgaagacagccaggagguuggcu
uagaagcagccauccuuuaaagagugcguaauagcucacuggucgagucg
cgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggu
cugggggaugaccccaggcgguaggggagcguucccgaugccgaugaagg
ccgacccgcgagggcggcuggagguaagggaagugcgaaugccggcauga
guaacgauaaagagggugagaaucccucucgccguaagcccaaggguucc
uacgcaauggucgucagcguaggguuaggcgggaccuaaggugaagccga
aaggcguagccgaagggcagccgguuaauauuccggcccuucccgcaggu
gcgauggggggacgcucuaggcuagggggaccggagccauggacgagccc
ggccagaagcgcagggugggagguaggcaaauccgccucccaacaagcuc
ugcgugguggggaagcccgcaaccccccgaagccagggagccaagaaaag
ccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagguggg
cgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucu
gcaaguuggccccguaacuucgggagaaggggugcucccuggggugauga
gccccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaaca
cagcucucugcgaacucguaagaggagguauagggagcgacgcuugcccg
gugccggaaggucaaggggaggggugcaagccccgaaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucgg
cgagggacccggugaaauugaacuggccgugaagaugcggccuacccgug
gcaggacgaaaagaccccguggagcuuuacugcagccugguguuggcucu
uggucgcgccugcguaggauaggugggagccugugaacccccgccuccgg
gugggggggaggcgccggugaaauaccacccuggcgcggcugggggccua
acccucggauggggggacagcgcuuggcgggcaguuugacuggggcgguc
gccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgg
aaauccgccggagagcgcaaggguagaagggggccugacugcgaggccug
caagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugu
ggaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcug
aucucccccgagcguccacagcggcggggagguuuggcaccucgaugucg
gcucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgc
ccauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucgg
ucucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguac
gagaggaccggaagggacgcaccucugguuucccagcugucccuccaggg
gcauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucua
agcgggaagcccgccccaagaugaggccucccacggcgucaagccgguaa
ggacccgggaagaccacccgguggaugggccggggguguaagcgccgcga
ggcguugagccgaccggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v5e Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): K2 L3 R7 R14 Q46 N47 H48 R51 R55 A58 R59 L61 T62 R69
• Binding residue (residue number reindexed from 1): K1 L2 R6 R13 Q45 N46 H47 R50 R54 A57 R58 L60 T61 R68

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v5e, PDBe:4v5e, PDBj:4v5e
• PDBsum: 4v5e
• PubMed: 18988853
• UniProt: Q5SHP6|RL29_THET8 Large ribosomal subunit protein uL29 (Gene Name=rpmC)