Structure of PDB 4v5e Chain DW Binding Site BS01

Receptor Information

>4v5e Chain DW (length=113) Species: 300852 (Thermus thermophilus HB8)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHGK

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): K4 A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 K49 S53 A56 N57 N60 N61 Y75 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102
• Binding residue (residue number reindexed from 1): K4 A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 K49 S53 A56 N57 N60 N61 Y75 D77 E78 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v5e, PDBe:4v5e, PDBj:4v5e
• PDBsum: 4v5e
• PubMed: 18988853
• UniProt: Q5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)