Structure of PDB 4v6a Chain D2 Binding Site BS01

Receptor Information
>4v6a Chain D2 (length=71) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEVRKQLEEARKLSPVELEKLVREKKRELMELRFQASIGQLSQNHKIR
DLKRQIARLLTVLNEKRRQNA
Ligand information
>4v6a Chain DA (length=2777) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccggggguuguggcgugccuauugaagcaugagccggcg
acucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaa
ccgaguccgaacagggcgcguccgcggccguggacccgaaaccgggcgag
cuagcccuggccagggugaagcuggggugagacccaguggaggcccgaac
cggugggggaugcaaaccccucggaugagcuggggcuaggagugaaaagc
uaaccgagcccggagauagcugguucuccccgaaaugacuuuagggucag
ccucaggcgcugacuggggccuguagagcacugauagggcuagggggccc
accagccuaccaaacccugucaaacuccgaagggucccagguggagccug
ggagugagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccg
agaccgccagcuaaggcccccaagucugggcuaagugguaaaggaugugg
cgccgcgaagacagccggucgaguggcgccgcgccgaaaaugaucggggc
uuaagcccagcgccgaagcugcgggucugggggaugaccccaggcgguag
gggagcguucccgaugccgaugaaggccgacccgcgagggcggcuggagg
uaagggaagugcgaaugccggcaugaguaacgauaaagagggugagaauc
ccucucgccguaagcccaaggguuccuacgcaauggucgucagcguaggg
uuaggcgggaccuaaggugaagccgaaaggcguagccgaagggcagccgg
uuaauauuccggcccuucccgcaggugcgauggggggacgcucuaggcua
gggggaccggagccauggacgagcccggccagaagcgcagggugggaggu
aggcaaauccgccucccaacaagcucugcgugguggggaagcccaacccc
ccgaagccagggagccaagaaaagccucuaagcacaaccugcgggaaccc
guaccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcg
ggagaacccucgccaaggaacucugcaaguuggccccguaacuucgggag
aaggggugcucccuggggugaugagccccggggagccgcagugaacaggc
ucuggcgacuguuuaccaaaaacacagcucucugcgaacucguaagagga
gguauagggagcgacgcuugcccggugccggaaggucaaggggaggggug
caagccccgaaccgaagccccggugaacggcggccguaacuauaacgguc
cuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagc
guaacgaccggagcgcugucucggcgagggacccggugaaauugaacugg
ccgugaagaugcggccuacccguggcaggacgaaaagaccccguggagcu
uuacugcagccugguguuggcucuuggucgcgccugcguaggauaggugg
gagcgccggugaaauaccacccuggcgcggcugggggccuaacccucgga
uggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaa
aagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgcc
ggagagcgcaaggguagaagggggccugacugcgaggccugcaagccgag
caggggcgaaagccgggccuagugaaccgguggucccguguggaagggcc
aucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccccc
gagcguccacagcggcggggagguuuggcaccucgaugucggcucgucgc
auccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaag
cggcacgcgagcuggguucagaacgucgugagacaguucggucucuaucc
gccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggacc
ggaagggacgcaccucugguuucccagcugucccuccaggggcauaagcu
ggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaag
cccgccccaagaugaggccucccacggcgucaagccgguaaggacccggg
aagaccacccgguggaugggccggggguguaagcgccgcgaggcguugag
ccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
....>>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>..
.......<<....>>...<<<<<.....<<.....>>....>>>>>...<
<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<.......<.
..<<<<..<<<<.<<<...<<<<<......>>>>>((......<<<....
.))>>>...>>>...>>>>...>>>>..>...>>>>>.>>>.....<<<<
<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>..
....>>.>>>>>>.>>...............<<....>>....>>.....
....<<<<....>>>>..................>>>>>>>>>>>.....
..<<<<<<<<<<<.>>>>>>>>>>>...<............>.<<<<<<.
...<<<<<<<<<<<<...<<<...<<<.....>>>...>>>...<<....
>>..<<<<.....>>>>...>>>>>>>>>>>>..<<.<...<<<<<<...
..<<<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<
<<..<<<<........>>>>.>>>....>>>>>>>>>...<<<.....>>
>......>>>>>>......>.>>..<<<<<<....<<<<<....>>>>><
<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<...<<<<<...
.....>>>.>>...>>>>>>>>..>>.>...>>>>>>>>>.....>>>>>
>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<......>>>
...<<<<.<<<...<<<(((.....<<<<<<...........<<..<<<<
<<<<....................>>>>>>>>.>>..........)))..
....>>>>>>.>>>...>>>>>>><<<<<<<.......>>>>>>>....>
>>>>>..<<<<<...<<<......<<<<<.<<<....>>>>>>>>...>>
>..>>>>>........>>>>>><......<<.....<<<<<<.......>
>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>.
...((<<<<.<<...<<<...<<<....>>>...>>>...>>...<<<<<
........>>>>>))<<<<<<<<<<<<<...<<<<....<<<<<.<<<..
<<<<<.<<<<.<<..[[[[...>>>>>><<<...<<<<<<<<<<<<<<<<
.<<.....>>>>>>>>>.....>>>>>>>>>..>>><.........>>>>
>>...>>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>
>..>>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<
<<....<<<<<<<<.<<.........<.....<<<<<.............
..>>>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>..
.....>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<.
...>>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>
........<...........<<<<<<.....>>>>>>.....>....>>>
>>..>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<
<<<........>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<
..<<<<<.<<<.<<<<<.<<<<<<<<<<..<<<<...........<<<<<
................>>>>>..>>>>..>>>>>>>>>>...<<<<<...
.>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<...
........>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>
.....<....(((.>....>>>>>>>...<<<<..<<<......>>>..>
>>>.<<<....>>>.>>))).......<<<<<<<.<<..))))..>>>>>
>>>>.............>>>>..>>>>>>.......<<<<...<<<<<<.
..<<.......>>...>>>>>>....>>>.>.......<<<<<.<<<<<<
..<<<<<<<<<......>>>>>>>..>>.<<<<<.....>>>>>.....>
>>>>..>...>>>.>>....<<<<<<<....>>>.>>>>........>>>
>>>>>>>>....<<<<<<<...<<<<..<<<<<<<...............
>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...>>>
>>...>>>>.>>>>>...<<<....<<<<<...........>>>>>....
>>>.>>>>.......>>>>>>>..<<.........>>....<<<<<<<<<
.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...>
>>..>>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
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PDB4v6a Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		K2 L3 R7 L10 Q46 N47 H48 I50 R51 K54 R55 A58 R59 L61 T62 N65 R69
Binding residue
(residue number reindexed from 1)		K1 L2 R6 L9 Q45 N46 H47 I49 R50 K53 R54 A57 R58 L60 T61 N64 R68
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4v6a, PDBe:4v6a, PDBj:4v6a
PDBsum4v6a
PubMed19696344
UniProtQ5SHP6|RL29_THET8 Large ribosomal subunit protein uL29 (Gene Name=rpmC)

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