Structure of PDB 5ibb Chain 71 Binding Site BS02

Receptor Information

>5ibb Chain 71 (length=133) Species: 300852 (Thermus thermophilus HB8)

HGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPR
RSDQNVRGTVSLPHGLGFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRA
LEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

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): H3 K5 R6 K36 F37 D38 T40 E42 H44 K46 T168 H172 P174 K205 Y213 T215 T217 G219 P220 S221
• Binding residue (residue number reindexed from 1): H1 K3 R4 K34 F35 D36 T38 E40 H42 K44 T73 H77 P79 K110 Y118 T120 T122 G124 P125 S126

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0006417 regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ibb, PDBe:5ibb, PDBj:5ibb
• PDBsum: 5ibb
• PubMed: 27174928
• UniProt: P27150|RL1_THETH Large ribosomal subunit protein uL1 (Gene Name=rplA)