Structure of PDB 6dti Chain Q Binding Site BS01

Receptor Information
>6dti Chain Q (length=104) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKY
KLGDVVEIIESRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYQSLSKR
GGKA
Ligand information
>6dti Chain A (length=1507) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uggagaguuugauccuggcucagggugaacgcuggcggcgugccuaagac
augcaagucgugcgggccgcgggguuuuacuccguggucagcggcggacg
ggugaguaacgcgugggugaccuacccggaagagggggacaacccgggga
aacucgggcuaaucccccauguggacccgccccuugggguguguccaaag
ggcuuugcccgcuuccggaugggcccgcgucccaucagcuaguugguggg
guaauggcccaccaaggcgacgacggguagccggucugagaggauggccg
gccacaggggcacugagacacgggccccacuccuacgggaggcagcaguu
aggaaucuuccgcaaugggcgcaagccugacggagcgacgccgcuuggag
gaagaagcccuucgggguguaaacuccugaacccgggacgaaacccccga
cgaggggacugacgguaccgggguaauagcgccggccaacuccgugccag
cagccgcgguaauacggagggcgcgagcguuacccggauucacugggcgu
aaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuca
accgugggggagcgugggauacgcucaggcuagacggugggagagggugg
uggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccg
auggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcg
uggggagcaaaccggauuagauacccggguaguccacgcccuaaacgaug
cgcgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgc
gccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacggg
ggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaaga
accuuaccaggccuugacaugcuaggaacccgggugaaagccuggggugc
cccggggagcccuagcacaggugcugcauggccgucgucagcucgugccg
ugagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguug
ccagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggagg
aaggaggggacgacgucuggucagcauggcccuuacggccugggcgacac
acgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcu
aaucgcaaaaaggugggcccaguucggauuggggucugcaacccgacccc
augaagccggaaucgcuaguaaucgcggaucagcaugccgcggugaauac
guucccgggccuuguacacaccgcccgucacgccaugggagcgggcucua
cccgaagucgccgggagccuacgggcaggcgccgaggguagggcccguga
cuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauc
acuuucu
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<<
.<<<..<<<..<<.<<<<<<<<<<.....>>>>>>>>>>.>>>>>.....
.<<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<<..
..>>>>>>.....>>>>>....<<<<.<<<<<....>>>>>.>>>>...<
<<<...>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<
.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>
>>.>>.<<<<<.<.........>>>>>>.<<<<<..>>>>>...>>>>>>
>........<<<....<<<<....>>>>..>>>..>>.>>>>>>...<..
........<......>........>......<<<<<......<..<....
....>....>.......>>>>>......<<<<<(((...<<<<<.....<
<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<((
.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<....
.>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<
<.<..<<<<<<<.<..<<<......>>>.....>.>>>>>>>...>....
...<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<
<<<...<<...<<<<.<.....>.>>>>...>>>>>>>>..........<
<<<<<..<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>
>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<
<<<<<<.<<.<<<<<<..<<<<<<<<<<......<<........>>....
......<<<<<<<......<<<<<<...<<<<<<<....>>>>>>>...<
<....>>....>>>>>>.<<<.<<<..<<<<<<<......<<<<<<<<<.
...>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<...
<...<<<.....>>>>.....>>>>>>>.....<<<<<....>>>>>...
.....>>>>.......>.>>>...>>>>>>>>>...>>>>>>>...>>.>
>>>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>.
...>>>.....>>>>>>>......<....<<<<<<<........>>>>>>
>....>.....>>>>>>....<<<<<<<.........>>>>>>>......
>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<.<<<
<<<...<.<<<<....<<<<..>>>>.>>>>.>..>>>>>>.>>>>>>..
>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>.....
.......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6dti A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.
Resolution3.54 Å
Binding residue
(original residue number in PDB)		P2 K3 K14 M15 Q16 K17 T18 R25 Q26 L31 Y32 K34 R38 S39 K40 K41 Y42 E61 S62 R63 P64 I65 S66 K67 K69 R70 R72 N94 Y95 L98 S99 K100
Binding residue
(residue number reindexed from 1)		P1 K2 K13 M14 Q15 K16 T17 R24 Q25 L30 Y31 K33 R37 S38 K39 K40 Y41 E60 S61 R62 P63 I64 S65 K66 K68 R69 R71 N93 Y94 L97 S98 K99
Enzymatic activity
Enzyme Commision number ?
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:0022627 cytosolic 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:6dti, PDBe:6dti, PDBj:6dti
PDBsum6dti
PubMed31945376
UniProtP0DOY7|RS17_THET8 Small ribosomal subunit protein uS17 (Gene Name=rpsQ)

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