Structure of PDB 4v4r Chain AM Binding Site BS02

Receptor Information

>4v4r Chain AM (length=125) Species: 300852 (Thermus thermophilus HB8)

ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEA
EVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQ
RTRTNARTRKGPRKTVAGKKKAPRK

Ligand information

>4v4r Chain BA (length=2814)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuugcgcggggggaaccuggggaacugaaacaucucaguaccca
gaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaagggg
accagccuaaaccguccggcuuguccgggcggggucguggggcccucgga
caccgaauccccagccuagccgaagcuguugggaagcagcgccagagagg
gugaaagccccguaggcgaaagguggggggauaggugaggguacccgagu
accccgugguucguggagccaugggggaaucugggcggaccaccgccuaa
ggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagg
ugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcuu
acaagcagucacggccccgcaagggguuguggcgugccuauugaagcaug
agccggcgacucacggucgugggcgagcuuaagccguugaggcggaggcg
uagggaaaccgaguccgaacagggcgcaaaguccgcggccguggacccga
aaccgggcgagcuagcccuggccagggugaagcuggggugagacccagug
gaggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuag
gagugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugac
uuuagggucagccucaggcgcugacuggggccuguagagcacugauaggg
cuagggggcccaccagccuaccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccaggagguuggcuuagaagcagcc
auccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccga
aaaugaugcggggcuuaagcccagcgccgaagcugcgggucugggggaug
accccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcg
aggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaa
gagggugagaaucccucucgccguaagcccaaggguuccuacgcaauggu
cgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagcc
gaagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggg
acgcucuaggcuagggggaccggagccauggacgagcccggccagaagcg
cagggugggagguaggcaaauccgccucccaacaagcucugcgugguggg
gaagcccguacgggugacaaccccccgaagccagggagccaagaaaagcc
ucuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcg
ggugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugc
aaguuggccccguaacuucgggagaaggggugcucccuggggugaugagc
cccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacaca
gcucucugcgaacucguaagaggagguauagggagcgacgcuugcccggu
gccggaaggucaaggggaggggugcaagccccgaaccgaagccccgguga
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcg
agggacccggugaaauugaacuggccgugaagaugcggccuacccguggc
aggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuug
gucgcggcgcggcugggggccuaacccucggauggggggacagcgcuugg
cgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgccc
aaagguccccucaggcgggacggaaauccgccggagagcgcaaggguaga
agggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggc
cuagugaaccgguggucccguguggaagggccaucgaucaacggauaaaa
guuaccccggggauaacaggcugaucucccccgagcguccacagcggcgg
ggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaag
gucccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguu
cagaacgucgugagacaguucggucucuauccgccacgggcgcaggaggc
uugaggggggcucuuccuaguacgagaggaccggaagggacgcaccucug
guuucccagcugucccuccaggggcauaagcuggguagccaugugcggaa
gggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggc
cucccacggcgucaagccgguaaggacccgggaagaccacccgguggaug
ggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgu
ccgaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v4r Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.
• Resolution: 5.9 Å
• Binding residue (original residue number in PDB): D83 R93 R94
• Binding residue (residue number reindexed from 1): D82 R92 R93

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v4r, PDBe:4v4r, PDBj:4v4r
• PDBsum: 4v4r
• PubMed: 16377566
• UniProt: P80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)