Structure of PDB 5ibb Chain D8 Binding Site BS01

Receptor Information

>5ibb Chain D8 (length=100) Species: 300852 (Thermus thermophilus HB8)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR

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): G8 G9 K10 E23 K24 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R82 R83 K84 K85 G86 H87 Q89 P90 E93
• Binding residue (residue number reindexed from 1): G8 G9 K10 E23 K24 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R82 R83 K84 K85 G86 H87 Q89 P90 E93

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)