Structure of PDB 4v9q Chain DS Binding Site BS01

Receptor Information
>4v9q Chain DS (length=78) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYN
GKQHVPVYITENMVGHKLGEFAPTRTYR
Ligand information
>4v9q Chain DA (length=1504) [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
ggaggggacugacgguaccgggguaauagcgccggccaacuccgugccag
cagccgcgguaauacggagggcgcgagcguuacccggauucacugggcgu
aaagggcguguaggcggccuggggcgucccaugugaaagaccacggcuca
accgugggggagcgugggauacgcucaggcuagacggugggagagggugg
uggaauucccggaguagcggugaaaugcgcagauaccgggaggaacgccg
auggcgaaggcagccaccugguccacccgugacgcugaggcgcgaaagcg
uggggagcaaaccggauuagauacccggguaguccacgcccuaaacgaug
cgcgcuaggucucugggucuccugggggccgaagcuaacgcguuaagcgc
gccgccuggggaguacggccgcaaggcugaaacucaaaggaauugacggg
ggcccgcacaagcgguggagcaugugguuuaauucgaagcaacgcgaaga
accuuaccaggccuugacaugcuagggaacccgggugaaagccuggggug
ccccgcgaggggagcccuagcacaggugcugcauggccgucgucagcucg
ugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguu
aguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcg
ggaggaaggaggggacgacgucuggucagcauggcccuuacggccugggc
gacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacggg
gagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccg
accccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggu
gaauacguucccgggccuuguacacaccgcccgucacgccaugggagcgg
gcucuacccgaagucgccgggagccuacgggcaggcgccgaggguagggc
ccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcggc
ugga
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<<<
.<<<..<<<..<<.<<<<<<<<<.......>>>>>>>>>.>>>>>.....
.<<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<...
...>>>>>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<
<<<...>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<
.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>
>>.>>.<<<<<.<.........>>>>>>.<<<<<..>>>>>...>>>>>>
>........<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<
......<<<<....>>>>.....>>>>....<<<<<........<<<<..
...>>>>..........>>>>>......<<<<<(((...<<<<<.....<
<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<((
.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<....
.>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<
<....<<<<<<<.<..<<<......>>>.....>.>>>>>>>........
...<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<
<<<...<<...<<<<.<.....>.>>>>...>>>>>>>>..........<
<<<<<..<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>
>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<
<<<<<<.<<.<<<<<<..<<<<<<<<........<<........>>....
......<<<<<<<.......<<<<<<<..<<<<<<<....>>>>>>>...
<<<......>>>..>>>>>>>..<<<.<<<..<<<<<<.......<<<<<
<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<
<<...<...<<<.....>>>>.....>>>>>>>.....<<<<<....>>>
>>........>>>>.........>>>...>>>>>>>>>...>>>>>>>..
....>>>>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>
..>>....>>>.....>>>>>>>......<....<<<<<<<........>
>>>>>>....>.....>>>>>>....<<<<<<<..........>>>>>>>
......>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<
<<<<<<<<<...<.<<<<....<<<<..>>>>.>>>>.>..>>>>>>>>>
>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>
>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4v9q Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		S4 L5 K6 F10 H14 W34 R36 R37 Y52 N53 G54 K55 G72 E73 T77 R78 T79
Binding residue
(residue number reindexed from 1)		S1 L2 K3 F7 H11 W31 R33 R34 Y49 N50 G51 K52 G69 E70 T74 R75 T76
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0015935 small ribosomal subunit

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4v9q, PDBe:4v9q, PDBj:4v9q
PDBsum4v9q
PubMed23824292
UniProtP62660|RS19_THET2 Small ribosomal subunit protein uS19 (Gene Name=rpsS)

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