Structure of PDB 5ibb Chain L8 Binding Site BS01

Receptor Information
>5ibb Chain L8 (length=58) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRLKVKLVKSPIGYPKDQKAALKALGLRRLQQERVLEDTPAIRGNVEKVA
HLVRVEVV
Ligand information
>5ibb Chain 1H (length=2841) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aagaugguaagggcccacgguggaugccucggcacccgagccgaugaagg
acguggcuaccugcgauaagccagggggagccgguagcgggcguggaucc
cuggauguccgaaugggggaacccggccggcgggaacgccggucaccgcg
cuuuuugcgcggggggaaccuggggaacugaaacaucucaguacccagag
gagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggacc
agccuaaaccguccggcuuguccgggcggggucguggggcccucggacac
cgaauccccagccuagccgaagcuguugggaagcagcgccagagagggug
aaagccccguaggcgaaagguggggggauaggugaggguacccgaguacc
ccgugguucguggagccaugggggaaucugggcggaccaccgccuaaggc
uaaguacuccgggugaccgauagcgcaccaguaccgugagggaaagguga
aaagaaccccgggaggggagugaaauagagccugaaaccgugggcuuaca
agcagucacggccccgcaagggguuguggcgugccuauugaagcaugagc
cggcgacucacggucgugggcgagcuuaagccguugaggcggaggcguag
ggaaaccgaguccgaacagggcgcaaacgggggccgaaaaguccgcggcc
guggacccgaaaccgggcgagcuagcccuggccagggugaagcuggggug
agacccaguggaggcccgaaccggugggggaugcaaaccccucggaugag
cuggggcuaggagugaaaagcuaaccgagcccggagauagcugguucucc
ccgaaaugacuuuagggucagccucaggcgcugacuggggccuguagagc
acugauagggcuaggggccuccaaacccugucaaacuccgaaggguccca
gguggagccugggagugagggcgcgagcgauaacguccgcguccgagcgc
gggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggu
aaaggauguggcgccgcgaagacagccagcucacuggucgaguggcgccg
cgccgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggg
ggaugaccccaggcgguaggggagcguucccgaugccgaugaaggccgac
ccgcgagggcggcuggagguaagggaagugcgaaugccggcaugaguaac
gauaaagagggugagaaucccucucgccguaagcccaaggguuccuacgc
aauggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggc
guagccgaagggcagccgguuaauauuccggcccuucccgcaggugcgau
ggggggacgcucuaggcuagggggaccggagccauggacgagcccggcca
gaagcgcagggugggagguaggcaaauccgccucccaacaagcucugcgu
gguggggaagcccguacgggugacaaccccccgaagccagggagccaaga
aaagccucuaagcacaaccugcgggaacccguaccgcaaaccgacacagg
ugggcgggugcaagagcacucaggcgcgcgggagaacccucgccaaggaa
cucugcaaguuggccccguaacuucgggagaaggggugcucccuggggug
augagccccggggagccgcagugaacaggcucuggcgacuguuuaccaaa
aacacagcucucugcgaacucguaagaggagguauagggagcgacgcuug
cccggugccggaaggucaaggggaggggugcaagccccgaaccgaagccc
cggugaacggcggccguaacuauaacgguccuaagguagcgaaauuccuu
gucggguaaguuccgaccugcacgaaaagcguaacgaccggagcgcuguc
ucggcgagggacccggugaaauugaacuggccgugaagaugcggccuacc
cguggcaggacgaaaagaccccguggagcuuuacugcagccugguguugg
cucuuggucgcgccugcguaggauaggugggagccugugaacccccgccu
ccgggugggggggaggcgccggugaaauaccacccuggcgcggcuggggg
ccuaacccucggauggggggacagcgcuuggcgggcaguuugacuggggc
ggucgccuccuaaaagguaacggaggcgcccaaagguccccucaggcggg
acggaaauccgccggagagcgcaaggguagaagggggccugacugcgagg
ccugcaagccgagcaggggcgaaagccgggccuagugaaccggugguccc
guguggaagggccaucgaucaacggauaaaaguuaccccggggauaacag
gcugaucucccccgagcguccacagcggcggggagguuuggcaccucgau
gucggcucgucgcauccuggggcugaagaaggucccaaggguugggcugu
ucgcccauuaaagcggcacgcgagcuggguucagaacgucgugagacagu
ucggucucuauccgccacgggcgcaggaggcuugaggggggcucuuccua
guacgagaggaccggaagggacgcaccucugguuucccagcugucccucc
aggggcauaagcuggguagccaugugcggaagggauaaccgcugaaagca
ucuaagcgggaagcccgccccaagaugaggccucccacggcgucaagccg
guaaggacccgggaagaccacccgguggaugggccggggguguaagcgcc
gcgaggcguugagccgaccggucccaaucguccgaggucuu
<<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<
<<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>
>>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<
<.....>>>>>>.>>....<<<<<.....<......>......>>>>>..
.........<<....>>...<<<<<.....<<.....>>....>>>>>..
.<<<....<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<
<...<<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<..
...))>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<
<<<<<<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>
......>>.>>>>>>.>>...............<<....>>....>>...
......<<<<....>>>>..................>>>>>>>>>>>...
....<<<<<<<<<<<....>>>>>>>>>>>...<............>.<<
<<<<....<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<
<....>>..<<<<.....>>>>.....<<.....>>....>>>>>>>>>>
>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<...
...>>>>>>.....>>>...<<<<.<<<<........>>>>>>>>....>
>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<<<
<<....<<<<<....>>>>><<<<<<<<<.....<<<<<<<<<...<<<.
..<<<<<<<<...<<.....>>...>>>>>>>>..>>.>...>>>>>>>>
>.....>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<
<<......>>>...<<<<.<<<...<<<(((.....<<<<<<........
...<<..<<<<<<<<<........<<<<......>>>>....>>>>>>>>
>.>>..........)))......>>>>>>.>>>...>>>>>>><<<<<<<
<.....>>>>>>>>....>>>>>><.<<<<<...<<<......<<<<<.<
<<....>>>>>>>>...>>>..>>>>>..>.....>>>>>><......<<
.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<<<<.
..<<.....>>.>>>>>>....((<<<<.<<...<<<...<<<....>>>
...>>>...>>...<<<<<........>>>>>))<<<<<<<<<<<<<...
<<<<....<<<<<.<<<..<<<<<.<<<<.<<..[[[[...>>>>>><<<
...<<<<<<<<<<<<<<<<.<<.....>>>>>>>>>.....>>>>>>>>>
..>>><...<<<<....>>>>.....>>>>>>...>>>..>>>>>.....
....>>>>...>>...>>>>>>>>>>>>>>>..>>.....<<......>>
>>>>>.<<<<<....>>>>>..>>>>..<<<<....<<<<<<<<.<<...
......<.....<<<<<....<....>.....>>>>><<<<<<<<<<<<.
....>>>>>>>>>>>>............<<<<<<<<<..<<<........
.>>>..<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<
<<..<<<<<<<..<<<...<<...<<<<<....>>>>>...>>...>>>>
>>>>..>>>>><<<<<<.......>>>>>>........<...........
<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>>..>..>
>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>>>>..<<
<<<<<<.<<<.........<<<<.<<<<<<..<<<<<.<<<.<<<<<.<<
<<<<<<<<<<<<<<...........<<..<<..<<......<<<<<<<<.
...>>>>>>>>...>>.............>>.>>..>>>>>>>>>>>>>>
>>...<<<<<....>>>>>....>>>>>.>>>..>>>>>..<<<<.....
>>>><<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<
.......>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<
<......>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<
..))))..>>>>>>>>>.............>>>>..>>>>>>.......<
<<<.<.<<<<<<<..<<.......>>>..>>>>>>...>>>>.>......
.<<<<<.<<<<<<..<<<<<<<<<......>>>>>>>..>>.<<<<<...
..>>>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>
>>........>>>>>>>>>>>....<<<<<<<...<<<<..<<<<<<<..
.............>>>>>>>.<<<<<...<<<<...<<<<<<<<<<<]]]
]>>>>>>...>>>>>...>>>>.>>>>>...<<<....<<<<<.......
....>>>>>....>>>.>>>>.......>>>>>>>...............
....<<<<<<<<<.......>>>>>....<<<<<<<<.<<<....<<<<<
....>>>>>...>>>..>>>>>.>>>...>>>>....>>>>
Receptor-Ligand Complex Structure
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PDB5ibb The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
Resolution2.96 Å
Binding residue
(original residue number in PDB)		K10 S11 I13 G14 K17 D18 A21 A22 K24 A25 R29 R30 L31 Q32 P41 A42 G45 N46 K49
Binding residue
(residue number reindexed from 1)		K9 S10 I12 G13 K16 D17 A20 A21 K23 A24 R28 R29 L30 Q31 P40 A41 G44 N45 K48
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: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:5ibb, PDBe:5ibb, PDBj:5ibb
PDBsum5ibb
PubMed27174928
UniProtQ5SHQ6|RL30_THET8 Large ribosomal subunit protein uL30 (Gene Name=rpmD)

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