Structure of PDB 4v83 Chain DG Binding Site BS01

Receptor Information

>4v83 Chain DG (length=159) Species: 262724 (Thermus thermophilus HB27)

PKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRH
KSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSH
PVVVEPPEGITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKG
IYYAGEPVR

Ligand information

>4v83 Chain DA (length=2760)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagg
agaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacca
gccuaaaccguccggcuuguccgggcggggucguggggcccucggacacc
gaauccccagccuagccgaagcuguugggaagcagcgccagagaggguga
aagccccguaggcgaaagguggggggauaggugaggguacccgaguaccc
cgugguucguggagccaugggggaaucugggcggaccaccgccuaaggcu
aaguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaa
aagaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaa
gcagucacggccccgcaagggguuguggcgugccuauugaagcaugagcc
ggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguagg
gaaaccgaguccgaacagggcgucuaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggcuggucgaguggcgccgcgccgaa
aaugaucggggcuuaagcccagcgccgaagcugcgggucugggggaugac
cccaggcgguaggggagcguucccgaugccgaugaaggccgacccgcgag
ggcggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaag
agggugagaaucccucucgccguaagcccaaggguuccuacgcaaugguc
gucagcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccg
aagggcagccgguuaauauuccggcccuucccgcaggugcgaugggggga
cgcucuaggcuagggggaccggagccauggacgagcccggccagaagcgc
agggugggagguaggcaaauccgccucccaaaagcucugcguggugggga
agcccguacgggugacaaccccccgaagccagggagccaagaaaagccuc
uaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcggg
ugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugcaa
guuggccccguaacuucgggagaaggggugcucccuggggugaugagcuc
cggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacagc
ucucugcgaacucguaagaggagguauagggagcgacgcuugcccggugc
cggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaac
ggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggua
aguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcgag
ggacccggugaaauugaacuggccgugaagaugcggccuacccguggcag
gacgaaaagaccccguggagcuuuacugcagccugguguuggcucuuggu
cgcgccggcgcggcugggggccuaacccucggauggggggacagcgcuug
gcgggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcc
caaagguccccucaggcgggacggaaauccgccggagagcgcaaggguag
aagggggccugacugcgaggccugcaagccgagcaggggcgaaagccggg
ccuagugaaccgguggucccguguggaagggccaucgaucaacggauaaa
aguuaccccggggauaacaggcugaucucccccgagcguccacagcggcg
gggagguuuggcaccucgaugucggcucgucgcauccuggggcugaagaa
ggucccaaggguugggcuguucgcccauuaaagcggcacgcgagcugggu
ucagaacgucgugagacaguucggucucuauccgccacgggcgcaggagg
cuugaggggggcucuuccuaguacgagaggaccggaagggacgcaccucu
gguuucccagcugucccuccaggggcauaagcuggguagccaugugcgga
agggauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugagg
ccucccacggcgucaagccgguaaggacccgggaagacuacccgguggau
gggccggggguguaagcgccgcgaggcguugagccgaccggucccaaucg
uccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v83 Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): R59 K62 S63 G66 L67 T70 G108 S110 K138 Q139 G142 Q143 R152 K153 Y157 H158 K160
• Binding residue (residue number reindexed from 1): R48 K51 S52 G55 L56 T59 G97 S99 K127 Q128 G131 Q132 R141 K142 Y146 H147 K149

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:4v83, PDBe:4v83, PDBj:4v83
• PDBsum: 4v83
• PubMed: 21245352
• UniProt: Q72I19|RL6_THET2 Large ribosomal subunit protein uL6 (Gene Name=rplF)