Structure of PDB 4v5e Chain DH Binding Site BS01

Receptor Information

>4v5e Chain DH (length=159) Species: 300852 (Thermus thermophilus HB8)

PKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRH
KSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSH
PVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKG
IYYAGEPVR

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): R59 R60 K62 S63 L67 T70 F109 S110 K138 Q139 G142 Q143 R152 K160
• Binding residue (residue number reindexed from 1): R48 R49 K51 S52 L56 T59 F98 S99 K127 Q128 G131 Q132 R141 K149

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• 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: P0DOY8|RL6_THET8 Large ribosomal subunit protein uL6 (Gene Name=rplF)