Structure of PDB 2f4v Chain J Binding Site BS01

Receptor Information
>2f4v Chain J (length=98) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRG
PFKHKDSREHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT
Ligand information
>2f4v 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
accuuaccaggccuugacaugcuagggaacccgggugaaagccuggggug
ccccgcgaggggagcccuagcacaggugcugcauggccgucgucagcucg
ugccgugagguguuggguuaagucccgcaacgagcgcaacccccgccguu
aguugccagcgguucggccgggcacucuaacgggacugcccgcgaaagcg
ggaggaaggaggggacgacgucuggucagcauggcccuuacggccugggc
gacacacgugcuacaaugcccacuacaaagcgaugccacccggcaacggg
gagcuaaucgcaaaaaggugggcccaguucggauuggggucugcaacccg
accccaugaagccggaaucgcuaguaaucgcggaucagccaugccgcggu
gaauacguucccgggccuuguacacaccgcccgucacgccaugggagcgg
gcucuacccgaagucgccgggagccuacgggcaggcgccgaggguagggc
ccgugacuggggcgaagucguaacaagguagcuguaccggaaggugcggc
uggauca
....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<.....<<<
.<<<..<<<..<<.<<<<<<<<<.......>>>>>>>>>.>>>>>.....
.<<.......<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<...
...>>>>>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<
<<<...>>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<
.......>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>
>>.>>.<<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>
.........<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<
......<<<<....>>>>.....>>>>....<<<<<........<<<<..
...>>>>..........>>>>>......<<<<<(((...<<<<<.....<
<.)))>>.......>>>>>>>>>>..>>>>>>>>>..........<<<((
.....<<<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<....
.>>>>>>....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<
<....<<<<<<<.<..<<<......>>>.....>.>>>>>>>........
...<<....>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<
<<<...<<...<<<<.........>>>>...>>>>>>>>..........<
<<<<<..<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>
>>.>>>.<<<......<<<<....>>>>....>>>..)))).]<<<<<.<
<<<<<<.<<.<<<<<<..<<<<<<<<.<......<<........>>....
......<<<<<<<.......<<...<...<<<<<<<....>>>>>>>...
.<<.......>>...>...>>..<<<.<<<..<<<<<<.......<<<<<
<<<<....>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<
<....<...<<<.....>>>.>.....>>>>>>.....<<<<<....>>>
>>........>>>>.........>>>...>>>>>>>>>...>>>>>>>..
.>..>>>>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>
..>>....>>>.....>>>>>>>......<....<<<<<<<........>
>>>>>>....>.....>>>>>>....<<<<<<<..........>>>>>>>
......>>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<
<<<<<<<<<...<.<<<<....<<<....>>>.>>>>.>..>>>>>>>>>
>>>>..>>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>
>......
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2f4v Interactions of designer antibiotics and the bacterial ribosome aminoacyl-tRNA site
Resolution3.8 Å
Binding residue
(original residue number in PDB)		R5 H13 D17 S35 G36 P37 I38 P39 L40 P41 T42 R43 R45 T48 R51 F54 K55 H56 K57 R60 H62 H68 D73
Binding residue
(residue number reindexed from 1)		R3 H11 D15 S33 G34 P35 I36 P37 L38 P39 T40 R41 R43 T46 R49 F52 K53 H54 K55 R58 H60 H66 D71
Binding affinityPDBbind-CN: Kd=2.2uM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2f4v, PDBe:2f4v, PDBj:2f4v
PDBsum2f4v
PubMed16492561
UniProtQ5SHN7|RS10_THET8 Small ribosomal subunit protein uS10 (Gene Name=rpsJ)

[Back to BioLiP]