Structure of PDB 4v8i Chain B5 Binding Site BS01

Receptor Information
>4v8i Chain B5 (length=59) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKHPVPKKKTSKARRDARRSHHALTPPTLVPCPECKAMKPPHTVCPECGY
YAGRKVLEV
Ligand information
>4v8i Chain BA (length=2827) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcagggguuguggcgugccuauugaagcaugagccggcgacuc
acggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccga
guccgaacagggcgcaagcgggccgcggcccgcaaaguccgcggccgugg
acccgaaaccgggcgagcuagcccuggccagggugaagcuggggugagac
ccaguggaggcccgaaccggugggggaugcaaaccccucggaugagcugg
ggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccccga
aaugacuuuagggucagccucaggcgcugacuggggccuguagagcacug
auagggcuagggggcccaccagccuaccaaacccugucaaacuccgaagg
gucccagguggagccugggagugagggcgcgagcgauaacguccgcgucc
gagcgcgggaacaaccgagaccgccagcuaaggcccccaagucugggcua
agugguaaaggauguggcgccgcgaagacagcggucgaguggcgccgcgc
cgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggggga
ugaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccg
cgagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgau
aaagagggugagaaucccucucgccguaagcccaaggguuccuacgcaau
ggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcgua
gccgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggg
gggacgcucuaggcuagggggaccggagccauggacgagcccggccagaa
gcgcagggugggagguaggcaaauccgccucccaacaagcucugcguggu
ggggaagcccgggugacaaccccccgaagccagggagccaagaaaagccu
cuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgg
gugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugca
aguuggccccguaacuucgggagaaggggugcucccuggggugaugagcc
ccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacag
cucucugcgaacucguaagaggagguauagggagcgacgcuugcccggug
ccggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaa
cggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggu
aaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcga
gggacccggugaaauugaacuggccgugaagaugcggccuacccguggca
ggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuugg
ucgcgccugcguaggauaggugggagccugugaacccccgccuccgggug
ggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaacc
cucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgcc
uccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaa
uccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaa
gccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugga
agggccaucgaucaacggauaaaaguuaccccggggauaacaggcugauc
ucccccgagcguccacagcggcggggagguuuggcaccucgaugucggcu
cgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccca
uuaaagcggcacgcgagcuggguucagaacgucgugagacguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcagccgguaaggacccgg
gaagaccacccgguggaugggccggggguguaagcgccgcgaggcguuga
gccgaccggucccaaucguccgagucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.>>>>>.>>...<<<<<<.....<<....>>......>>>>>.>......
...<<....>>...<<<<<.....<<.....>>....>>>>>...<<<..
..<<<<<<<<.....>>>>>>>>......<<<<<<<<<..<<<...<<<<
<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>>>
...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<<.
......>>>>>>>>>......<<<<<..((((>>>>>..>>>......>>
.>>>>>>.>>...............<<....>>....>>.........<<
<<....>>>>..................>>>>>>>>>>>.......<<<<
<<<<<<<...>>>>>>>>>>>...<............>.<<<<<<....<
<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>..
<<<<.....>>>>....<<<<<<<..>>>>>>>...>>>>>>>>>>>>>.
.<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<......>
>>>>>.....>>>...<<<..<<<<........>>>>.>>>....>>>>>
>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<..
..<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<
<<<<<<...<<<<<<......>>>>.>>...>>>>>>>>..>>.>...>>
>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>
.....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<..
.........<<..<<<<<<<<<........<...>....>>>>>>>>>.>
>..........)))......>>>>>>.>>>...>>>>>>><<<<<<<<..
...>>>>>>>>....>>>>>>..<<<<<...<<<......<<<<<.<<<.
...>>>>>>>>...>>>..>>>>>........>>>>>><......<<...
..<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<
<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...
>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<<<...<<<
<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<...
<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>>..>
>><...<<<..>>>.....>>>>>>...>>>..>>>>>.........>>>
>...>>...>>>>>>>>>>>>>>>..>>.....<<......>>>>>>>.<
<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<.........<
.....<<<<<.....<..>......>>>>><<<<<<<<<<<<.....>>>
>>>>>>>>>............<<<<<<<<<..<<<.........>>>..<
<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<<
<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>>>>>>..>
>>>><<<<<<.......>>>>>>........<...........<<<<<<.
....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>>.>>>>>
>>>.>>>>>>.....>.....<<<<<........>>>>>..<<<<<<<<.
<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<
<<<<<<<...........<<<<<..<<<......<<<<<<<......>>>
>>>>...>>>............>>>>>..>>>>>>>>>>>>>>>>...<<
<<<....>>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<
<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......
>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<......
>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..)))).
.>>>>>>>>>.............>>>>..>>>>>>.......<<<<.<.<
<<<<<...<<.......>>...>>>>>>...>>>>.>.......<<<<<.
<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>
.....>>>>>..>...>>>.>>....<<<<<<<....>>>>>>>......
..>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..........
.....>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>.
..>>>>>...>>>>.>>>>>...<<<....<<<<<...........>>>>
>....>>>.>>>>.......>>>>>>>..<<<<.>>>>....<<<<<<<<
<.......>>>>>....<<<<<<<<.<<<....<<<<<....>>>>>...
>>>..>>>>>.>>>...>>>>...>>>
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4v8i How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
Resolution2.7 Å
Binding residue
(original residue number in PDB)
A2 K3 H4 P5 V6 P7 K8 K9 K10 T11 S12 K13 A14 R15 R16 D17 A18 R19 R20 S21 H22 H23 T29 V31 P34 P42 H43 Y52 A53
Binding residue
(residue number reindexed from 1)
A1 K2 H3 P4 V5 P6 K7 K8 K9 T10 S11 K12 A13 R14 R15 D16 A17 R18 R19 S20 H21 H22 T28 V30 P33 P41 H42 Y51 A52
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:0015934 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:4v8i, PDBe:4v8i, PDBj:4v8i
PDBsum4v8i
PubMed22605777
UniProtP80339|RL32_THET8 Large ribosomal subunit protein bL32 (Gene Name=rpmF)

[Back to BioLiP]