Structure of PDB 1vy6 Chain D2 Binding Site BS01

Receptor Information
>1vy6 Chain D2 (length=70) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKI
RDLKRQIARLLTVLNEKRRQ
Ligand information
>1vy6 Chain DA (length=2800) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagccc
agcgccgaagcugcgggucuggggccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccgcgggugacaaccccccga
agccagggagccaagaaaagccucuaagcacaaccugcgggaacccguac
cgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggag
aacccucgccaaggaacucugcaaguuggccccguaacuucgggagaagg
ggugcucccuggggugaugagccccggggagccgcagugaacaggcucug
gcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggua
uagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaag
ccccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaa
cgaccggagcgcugucucggcgagggacccggugaaauugaacuggccgu
gaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuuac
ugcagccugguguuggcucuuggucgcgccugcguaggauaggugggagc
cugugaacccccgccuccgggugggggggaggcgccggugaaauaccacc
cuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcgg
gcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaa
gguccccucaggcgggacggaaauccgccggagagcgcaaggguagaagg
gggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccua
gugaaccgguggucccguguggaagggccaucgaucaacggauaaaaguu
accccggggauaacaggcugaucucccccgagcguccacagcggcgggga
gguuuggcaccucgaugucggcucgucgcauccuggggcugaagaagguc
ccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguucag
aacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuug
aggggggcucuuccuaguacgagaggaccggaagggacgcaccucugguu
ucccagcugucccuccaggggcauaagcuggguagccaugugcggaaggg
auaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuc
ccggcagccgguaaggacccgggaagaccacccgguggaugggccggggg
uguaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
.>>>>>>.>>....<<<<<.....<......>......>>>>>.......
....<<....>>...<<<<<.....<<.....>>....>>>>>...<<<.
...<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<<...<
<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))
>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<
<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>.>>...............<<....>>....>>........
.<<<<....>>>>..................>>>>>>>>>>>.......<
<<<<<<<<<<.>>>>>>>>>>>...<............>.<<<<<<....
<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>.
.<<<<.....>>>>....<<..>>...>>>>>>>>>>>>>..<<.<...<
<<<<<....<<<<<<<<<<..<<<....<<<<<<......>>>>>>....
.>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>>..<<
<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<..
..>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<...
<<<<<<......>>>>.>>...>>>>>>>>..>>.>...>>>>>>>>>..
...>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<.
.....>>>...<<<<.<<<...<<<(((.....<<<<<<...........
<<..<<<<<<<<<..>>>>>>>>>.>>..........)))......>>>>
>>.>>>...>>>>>>><<<<<<<<>>>>>>>>....>>>>>><.<<<<<.
..<<<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>..>..
...>>>>>><......<<.....<<<<<<.......>>>>>><<<<....
<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<.
..<<<...<<<....>>>...>>>...>>...<<<<<........>>>>>
))<<<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<
..[[[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>
>>>>.....>>>>>>>>>..>>><...<<<<..>>>>.....>>>>>>..
.>>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>
>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<..
..<<<<<<<<.<<.........<.....<<<<<.....<..>......>>
>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>
>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>....
....<...........<<<<<<.....>>>>>>.....>....>>>>>..
>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<.
.......>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<
<<<.<<<.<<<<<.<<<<<<<<<<<<<<<<...........<<<<<..<.
<......<<<<<<<<....>>>>>>>>...>.>............>>>>>
..>>>>>>>>>>>>>>>>...<<<<<....>>>>>....>>>>>.>>>..
>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<<...
<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>>
>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>))).
......<<<<<<<.<<..))))..>>>>>>>>>.............>>>>
..>>>>>>.......<<<<...<<<<<<...<<.......>>...>>>>>
>....>>>.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>
>>>..>>.<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<
<<<<<<....>>>.>>>>........>>>>>>>>>>>....<<<<<<<..
.<<<<..<<<<<<<...............>>>>>>>.<<<<<...<<<<.
..<<<<<<<<<<<]]]]>>>>>>...>>>>>...>>>>.>>>>>...<<<
....<<<<<...........>>>>>....>>>.>>>>.......>>>>>>
>.<<<.>>>.....<<<<<<<<<.......>>>>>....<<<<<<<<.<<
<....<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
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PDB1vy6 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		M1 K2 L3 R7 R14 K29 S45 Q46 N47 H48 R51 R55 A58 R59 L61 T62 N65 R69
Binding residue
(residue number reindexed from 1)		M1 K2 L3 R7 R14 K29 S45 Q46 N47 H48 R51 R55 A58 R59 L61 T62 N65 R69
Enzymatic activity
Enzyme Commision number ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1vy6, PDBe:1vy6, PDBj:1vy6
PDBsum1vy6
PubMed25132179
UniProtQ5SHP6|RL29_THET8 Large ribosomal subunit protein uL29 (Gene Name=rpmC)

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