Structure of PDB 4ypb Chain R8 Binding Site BS01

Receptor Information
>4ypb Chain R8 (length=64) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPYE
Ligand information
>4ypb Chain RA (length=2891) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggacaccgaauc
cccagccuagccgaagcuguugggaagcagcgccagagagggugaaagcc
ccguaggcgaaagguggggggauaggugaggguacccgaguaccccgugg
uucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagua
cuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaa
ccccgggaggggagugaaauagagccugaaaccgugggcuuacaagcagu
cacggccccgcaagggguuguggcgugccuauugaagcaugagccggcga
cucacggucgugggcgagcuuaagccguugaggcggaggcguagggaaac
cgaguccgaacagggcgcaagcgggccggcccgcaaaguccgcggccgug
gacccgaaaccgggcgagcuagcccuggccagggugaagcuggggugaga
cccaguggaggcccgaaccggugggggaugcaaaccccucggaugagcug
gggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccccg
aaaugacuuuagggucagccucaggcgcugacuggggccuguagagcacu
gauagggcuagggggcccaccagccuaccaaacccugucaaacuccgaag
ggucccagguggagccugggagugagggcgcgagcgauaacguccgcguc
cgagcgcgggaacaaccgagaccgccagcuaaggcccccaagucugggcu
aagugguaaaggauguggcgccgcgaagacagccaggagguuggcuuaga
agcagccauccuuuaaagagugcguaauagcucacuggucgaguggcgcc
gcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucugg
gggaugaccccaggcgguaggggagcguucccgaugccgaugaaggccga
cccgcgagggcggcuggagguaagggaagugcgaaugccggcaugaguaa
cgauaaagagggugagaaucccucucgccguaagcccaaggguuccuacg
caauggucgucagcguaggguuaggcgggaccuaaggugaagccgaaagg
cguagccgaagggcagccgguuaauauuccggcccuucccgcaggugcga
uggggggacgcucuaggcuagggggaccggagccauggacgagcccggcc
agaagcgcagggugggagguaggcaaauccgccucccaacaagcucugcg
ugguggggaagcccguacgggugacaaccccccgaagccagggagccaag
aaaagccucuaagcacaaccugcgggaacccguaccgcaaaccgacacag
gugggcgggugcaagagcacucaggcgcgcgggagaacccucgccaagga
acucugcaaguuggccccguaacuucgggagaaggggugcucccuggggu
gaugagccccggggagccgcagugaacaggcucuggcgacuguuuaccaa
aaacacagcucucugcgaacucguaagaggagguauagggagcgacgcuu
gcccggugccggaaggucaaggggaggggugcaagccccgaaccgaagcc
ccggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccu
ugucggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcugu
cucggcgagggacccggugaaauugaacuggccgugaagaugcggccuac
ccguggcaggacgaaaagaccccguggagcuuuacugcagccugguguug
gcucuuggucgcgccugcguaggauaggugggagccugugaacccccgcc
uccgggugggggggaggcgccggugaaauaccacccuggcgcggcugggg
gccuaacccucggauggggggacagcgcuuggcgggcaguuugacugggg
cggucgccuccuaaaagguaacggaggcgcccaaagguccccucaggcgg
gacggaaauccgccggagagcgcaaggguagaagggggccugacugcgag
gccugcaagccgagcaggggcgaaagccgggccuagugaaccgguggucc
cguguggaagggccaucgaucaacggauaaaaguuaccccggggauaaca
ggcugaucucccccgagcguccacagcggcggggagguuuggcaccucga
ugucggcucgucgcauccuggggcugaagaaggucccaaggguugggcug
uucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacag
uucggucucuauccgccacgggcgcaggaggcuugaggggggcucuuccu
aguacgagaggaccggaagggacgcaccucugguuucccagcugucccuc
caggggcauaagcuggguagccaugugcggaagggauaaccgcugaaagc
aucuaagcgggaagcccgccccaagaugaggccucccacggcgucaagcc
gguaaggacccgggaagaccacccgguggaugggccggggguguaagcgc
cgcgaggcguugagccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<.
.>>>>>.>>...<<<<<<.....<......>......>>>>>.>......
...<<....>>...<<<<<.....<<.....>>....>>>>>...<<<..
..<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<<...<<
<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))>
>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<<
<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>......
>>.>>>>>>.>>...............<<....>>....>>.........
<<<<....>>>>..................>>>>>>>>>>>.......<<
<<<<<<<<<....>>>>>>>>>>>...<............>.<<<<<<..
..<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>
>..<<<<.....>>>>....<<<<<<..>>>>>>...>>>>>>>>>>>>>
..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<......
>>>>>>.....>>>...<<<..<<<<........>>>>.>>>....>>>>
>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<<<.
...<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<
<<<<<<<.<.<<<<<<......>>>>.>>>..>>>>>>>>..>>.>...>
>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>
>.....<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.
..........<<..<<<<<<<<<........<<<<<.<<<..<<<<....
...>>>>..>>>.........<<......>>...>>>>>....>>>>>>>
>>.>>..........)))......>>>>>>.>>>...>>>>>>><<<<<<
<<.....>>>>>>>>....>>>>>>..<<<<<...<<<......<<<<<.
<<<....>>>>>>>>...>>>..>>>>>........>>>>>><......<
<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<
...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>
>...>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<<<..
.<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<
<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>
>..>>><...<<<<....>>>>.....>>>>>>...>>>..>>>>>....
.....>>>>...>>...>>>>>>>>>>>>>>>..>>.....<<......>
>>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<..
.......<.....<<<<<.....<..>......>>>>><<<<<<<<<<<<
.....>>>>>>>>>>>>............<<<<<<<<<..<<<.......
..>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.
<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>
>>>>>..>>>>><<<<<<.......>>>>>>........<..........
.<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..
>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<
<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<
<<<<<<<<<<<<<<<...........<<<<<...<<......<<<<<<<<
....>>>>>>>>...>>.............>>>>>..>>>>>>>>>>>>>
>>>...<<<<<....>>>>>....>>>>>.>>>..>>>>>..<<<<....
.>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<
<.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<
<<......>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<
<..))))..>>>>>>>>>.............>>>>..>>>>>>.......
<<<<...<<<<<<...<<.......>>...>>>>>>....>>>.>.....
..<<<<<.<<<<<<..<<<<<<<<<......>>>>>>..>>>.<<<<<..
...>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>
>>>........>>>>>>>>>>>....<<<<<<<<..<<<<..<<<<<<<.
..............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]
]]>>>>>>...>>>>>...>>>>.>>>>>...<<<....<<<<<......
.....>>>>>....>>>.>>>>>......>>>>>>>..<<<<.....>>>
>....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<
<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>
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]
PDB4ypb Defining the mRNA recognition signature of a bacterial toxin protein.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		P2 K3 M4 K5 T6 K8 K11 K12 R13 T17 A18 S19 K21 T27 K29 R30 H31 L32 N33 W34 K39 I41 R42 Q43 K44 K47 K52 L61 L62 Y64
Binding residue
(residue number reindexed from 1)		P1 K2 M3 K4 T5 K7 K10 K11 R12 T16 A17 S18 K20 T26 K28 R29 H30 L31 N32 W33 K38 I40 R41 Q42 K43 K46 K51 L60 L61 Y63
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:4ypb, PDBe:4ypb, PDBj:4ypb
PDBsum4ypb
PubMed26508639
UniProtQ5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)

[Back to BioLiP]