Structure of PDB 5ibb Chain B8 Binding Site BS02

Receptor Information

>5ibb Chain B8 (length=136) Species: 300852 (Thermus thermophilus HB8)

MNRGALIKLVESRYVRTDLPEFRPGDTVRVSYKVKEGNRTRIQDFEGIVI
RIRRNGFNTTFTVRKVSYGVGVERIFPLHSPLIQKIDIVQRGRARRAKLY
FIRNLSDREIRRKLRADRKRIDQDRAAERAAKEEAQ

Ligand information

>5ibb Chain 1H (length=2841)

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

Structure summary

• PDB: 5ibb The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
• Resolution: 2.96 Å
• Binding residue (original residue number in PDB): R3 R23 R51 R53 R54 N55 N58 T60 I75 R95 R96 A97 K98 Y100 F101 K113 K119
• Binding residue (residue number reindexed from 1): R3 R23 R51 R53 R54 N55 N58 T60 I75 R95 R96 A97 K98 Y100 F101 K113 K119

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:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: P60490|RL19_THET8 Large ribosomal subunit protein bL19 (Gene Name=rplS)