Structure of PDB 5ib8 Chain 1I Binding Site BS01

Receptor Information
>5ib8 Chain 1I (length=94) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKH
KDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT
Ligand information
>5ib8 Chain 13 (length=1500) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uuguuggagaguuugauccuggcucagggugaacgcuggcggcgugccua
agacaugcaagucgugcgggccgcgcguggucagcggcggacgggugagu
aacgcgugggugaccuacccggaagagggggacaacccggggaaacucgg
gcuaaucccccauguggacccgccccuugggguguguccaaagggcuuug
cccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaugg
cccaccaaggcgacgacggguagccggucugagaggauggccggccacag
gggcacugagacacgggccccacuccuacgggaggcagcaguuaggaauc
uuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaag
cccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggg
acugacgguaccgggguaauagcgccggccaacuccgugccagcagccgc
gguaauacggagggcgcgagcguuacccggauucacugggcguaaagggc
guguaggcggccuggggcgucccaugugaaagaccacggcucaaccgugg
gggagcgugggauacgcucaggcuagacggugggagagggugguggaauu
cccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcga
aggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggag
caaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcua
ggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccu
ggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgc
acaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuac
caggccuugacaugcuagggaacccgggugaaagccuggggugccccgcg
aggggagcccuagcacaggugcugcauggccgucgucagcucgugccgug
agguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugcc
agcgguucggccgggcacucuaacgggacugcccgcgaaagcgggaggaa
ggaggggacgacgucuggucagcauggcccuuacggccugggcgacacac
gugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcuaa
ucgcaaaaaggugggcccaguucggauuggggucugcaacccgaccccau
gaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauacg
uucccgggccuuguacacaccgcccgucacgccaugggagcgggcucuac
ccgaagucgccgggagccuacgggcaggcgccgaggguagggcccgugac
uggggcgaagucguaacaagguagcuguaccggaaggugcggcuggacac
........<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<.
.<<<.<<<..<<<..<<.<<<<<....>>>>>.>>>>>......<<....
...<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<......>>>>
>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<...>
>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<.......
>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>.<
<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>......
..<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<......<
<<<....>>>>.....>>>>....<<<<<........<<<<.....>>>>
..........>>>>>......<<<<<(((...<<<<<.....<<.)))>>
.......>>>>>>>>>>..>>>>>>>>>..........<<<((.....<<
<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>>>
....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....<<
<<<<<.<..<<<......>>>.....>.>>>>>>>...........<<..
..>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<...<
<...<<<<.........>>>>...>>>>>>>>..........<<<<<<..
<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>>.
<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<<.
<<.<<<<<<..<<<<<<<<<<......<<........>>..........<
<<<<<<......<<<<<<<<..<<<<<<<....>>>>>>>..........
.......>>>>>>>>.<<<.<<<..<<<<<<.......<<<<<<<<<...
.>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<..<<<
..<<<.....>>>>>>...>>>>>>>.....<<<<<....>>>>>.....
...>>>>.........>>>...>>>>>>>>>...>>>>>>>...>>.>>>
>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>...
.>>>.....>>>>>>>...........<<<<<<<........>>>>>>>.
.........>>>>>>....<<<<<<<..........>>>>>>>......>
>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<<<
<<...<.<<<<....<<<....>>>.>>>>.>..>>>>>>>>>>>>>..>
>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ib8 The ribosome prohibits the GU wobble geometry at the first position of the codon-anticodon helix.
Resolution3.13 Å
Binding residue
(original residue number in PDB)		K7 R9 H13 G36 P37 I38 P39 L40 P41 T42 R43 V44 R45 T48 R51 G52 P53 F54 K55 H56 K57 S59 R60 H62 H68 R70 D73
Binding residue
(residue number reindexed from 1)		K1 R3 H7 G30 P31 I32 P33 L34 P35 T36 R37 V38 R39 T42 R45 G46 P47 F48 K49 H50 K51 S53 R54 H56 H62 R64 D67
Enzymatic activity
Enzyme Commision number ?
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
Cellular Component
GO:0005840 ribosome
GO:0015935 small 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:5ib8, PDBe:5ib8, PDBj:5ib8
PDBsum5ib8
PubMed27174928
UniProtQ5SHN7|RS10_THET8 Small ribosomal subunit protein uS10 (Gene Name=rpsJ)

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