Structure of PDB 4v8x Chain DW Binding Site BS01

Receptor Information
>4v8x Chain DW (length=113) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHGK
Ligand information
>4v8x Chain DA (length=2848) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucgggggcccucggacaccga
auccccagccuagccgaagcuguugggaagcagcgccagagagggugaaa
gccccguaggcgaaagguggggggauaggugaggguacccgaguaccccg
ugguucguggagccaugggggaaucugggcggaccaccgccuaaggcuaa
guacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaa
gaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaagc
agucacggccccgcaagggguuguggcgugccuauugaagcaugagccgg
cgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggga
aaccgaguccgaacagggcgcaagcgggccgcacgcggcccgcaaagucc
gcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagcu
ggggugagacccaguggaggcccgaaccggugggggaugcaaaccccucg
gaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcugg
uucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccug
uagagcacugauagggcuagggggcccaccagccuaccaaacccugucaa
acuccgaagggucccagguggagccugggagugagggcgcgagcgauaac
guccgcguccgagcgcgggaacaaccgagaccgccagcuaaggcccccaa
gucugggcuaagugguaaaggauguggcgccgcgaagacagccagucgag
uggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcugcg
ggucugggggaugaccccaggcgguaggggagcguucccgaugccgauga
aggccgacccgcgagggcggcuggagguaagggaagugcgaaugccggca
ugaguaacgauaaagagggugagaaucccucucgccguaagcccaagggu
uccuacgcaauggucgucagcguaggguuaggcgggaccuaaggugaagc
cgaaaggcguagccgaagggcagccgguuaauauuccggcccuucccgca
ggugcgauggggggacgcucuaggcuagggggaccggagccauggacgag
cccggccagaagcgcagggugggagguaggcaaauccgccucccaacaag
cucugcgugguggggaagcccguacgggugacaaccccccgaagccaggg
agccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaaacc
gacacaggugggcgggugcaagagcacucaggcgcgcgggagaacccucg
ccaaggaacucugcaaguuggccccguaacuucgggagaaggggugcucc
cuggggugaugagccccggggagccgcagugaacaggcucuggcgacugu
uuaccaaaaacacagcucucugcgaacucguaagaggagguauagggagc
gacgcuugcccggugccggaaggucaaggggaggggugcaagccccgaac
cgaagccccggugaacggcggccguaacuauaacgguccuaagguagcga
aauuccuugucggguaaguuccgaccugcacgaaaagcguaacgaccgga
gcgcugucucggcgagggacccggugaaauugaacuggccgugaagaugc
ggccuacccguggcaggacgaaaagaccccguggagcuuuacugcagccu
gguguuggcucuuggucgcgccugcguaggauaggugggagccugugaac
ccccgccuccgggugggggggaggcgccggugaaauaccacccuggcgcg
gcugggggccuaacccucggauggggggacagcgcuuggcgggcaguuug
acuggggcggucgccuccuaaaagguaacggaggcgcccaaagguccccu
caggcgggacggaaauccgccggagagcgcaaggguagaagggggccuga
cugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaaccg
guggucccguguggaagggccaucgaucaacggauaaaaguuaccccggg
gauaacaggcugaucucccccgagcguccacagcggcggggagguuuggc
accucgaugucggcucgucgcauccuggggcugaagaaggucccaagggu
ugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgucgu
gagacaguucggucucuauccgccacgggcgcaggaggcuugaggggggc
ucuuccuaguacgagaggaccggaagggacgcaccucugguuucccagcu
gucccuccaggggcauaagcuggguagccaugugcggaagggauaaccgc
ugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacggcg
ucaagccgguaaggacccgggaagaccacccgguggaugggccgggggug
uaagcgccgcgaggcguugagccgaccggucccaaucguccgaggucu
<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
....>>>>>>.>>....<<<<<.....<<....>>......>>>>>....
.......<<....>>...<<<<<.....<<.....>>....>>>>>...<
<<....<<<<<<<<.....>>>>>>>>.....<<<<<<<<<....<<<..
.<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....
))>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<
<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>...
...>>.>>>>>>.>>...............<<....>>....>>......
...<<<<....>>>>..................>>>>>>>>>>>......
.<<<<<<<<<<<....>>>>>>>>>>>...<............>.<<<<<
<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<..
..>>..<<<<.....>>>>....<..<<<<<....>>>>>>.....>>>>
>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<
<<<......>>>>>>.....>>>...<<<..<<<<........>>>>.>>
>....>>>>>>>>>...<<<.....>>>......>>>>>>......>.>>
..<<<<<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<.
..<<<...<<<<<<<<...<<<<<<......>>>>.>>...>>>>>>>>.
.>>.>...>>>>>>>>>.....>>>>>>>.>>..<<<<<<<.<<......
>>.>>>>>>>.....<<<......>>>...<<<<.<<<...<<<(((...
..<<<<<<...........<<..<<<<<<<<<........<....>....
>>>>>>>>>.>>..........)))......>>>>>>.>>>...>>>>>>
><<<<<<<<.....>>>>>>>>....>>>>>>..<<<<<...<<<.....
.<<<<<.<<<....>>>>>>>>...>>>..>>>>>........>>>>>><
......<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<..
.<<<<<<...<<.....>>.>>>>>>....((<<<<.<<...<<<...<<
<....>>>...>>>...>>...<<<<<........>>>>>))<<<<<<<<
<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>
>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>
>>>>>>>>..>>><...<<<<....>>>>.....>>>>>>...>>>..>>
>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>>.....<<
......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<<<<<
<<.<<.........<.....<<<<<....<....>.....>>>>><<<<<
<<<<<<<.....>>>>>>>>>>>>............<<<<<<<<<..<<<
.........>>>..<<<<<<<.....<<<....>>>.......>>>>>>>
.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>
>...>>>>>>>>..>>>>><<<<<<.......>>>>>>........<...
........<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>
>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>
>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.
<<<<<.<<<<<<<<<<<<<<<<...........<<<<<..<<.......<
<<<<<<<....>>>>>>>>....>>............>>>>>..>>>>>>
>>>>>>>>>>...<<<<<....>>>>>....>>>>>.>>>..>>>>>..<
<<<.....>>>><<<<<<...........>>>>>>..<<...<<<<<<<.
..<<<<<<.......>>>>>>.....<....(((.>....>>>>>>>...
<<<<..<<<......>>>..>>>>.<<<....>>>.>>))).......<<
<<<<<.<<..))))..>>>>>>>>>.............>>>>..>>>>>>
.......<<<<...<<<<<<...<<.......>>...>>>>>>....>>>
.>.......<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.
<<<<<.....>>>>>.....>>>>>..>...>>>.>>....<<<<<<<..
..>>>.>>>>........>>>>>>>>>>>....<<<<<<<...<<<<..<
<<<<<<...............>>>>>>>.<<<<<...<<<<...<<<<<<
<<<<<]]]]>>>>>>...>>>>>...>>>>.>>>>>...<<<....<<<<
<...........>>>>>....>>>.>>>>.......>>>>>>>...<...
......>.....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<.
...<<<<<....>>>>>...>>>..>>>>>.>>>...>>>>....>>>
Receptor-Ligand Complex Structure
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PDB4v8x Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.
Resolution3.35 Å
Binding residue
(original residue number in PDB)		A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 G79 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102
Binding residue
(residue number reindexed from 1)		A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 Y45 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 G79 P80 K83 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
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:4v8x, PDBe:4v8x, PDBj:4v8x
PDBsum4v8x
PubMed23945936
UniProtQ5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)

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