Structure of PDB 4v9s Chain DS Binding Site BS01

Receptor Information

>4v9s Chain DS (length=110) Species: 300852 (Thermus thermophilus HB8)

RLTAYERRKFRVRNRIKRTGRLRLSVFRSLKHIYAQIIDDEKGVTLVSAS
SLALKLKGNKTEVARQVGRALAEKALALGIKQVAFDRGPYKYHGRVKALA
EGAREGGLEF

Ligand information

>4v9s Chain DA (length=2714)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaac
cgggcgagcuagcccuggccagggugaagcuggggugagacccaguggag
gcccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggag
ugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuu
agggucagccucaggcgcugacuggggccuguagagcacugauagggcua
gggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggu
ggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggg
aacaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaa
ggauguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagccc
agcgccgaagcugcgggucuggggccccaggcgguaggggagcguucccg
augccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcg
aaugccggcaugaguaacgauaaagagggugagaaucccucucgccguaa
gcccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccu
aaggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggc
ccuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagc
cauggacgagcccggccagaagcgcagggugggagguaggcaaauccgcc
ucccaacaagcucugcgugguggggaagcccgcgggugacaaccccccga
agccagggagccaagaaaagccucuaagcacaaccugcgggaacccguac
cgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggag
aacccucgccaaggaacucugcaaguuggccccguaacuucgggagaagg
ggugcucccuggggugaugagccccggggagccgcagugaacaggcucug
gcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggua
uagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaag
ccccgaaccgaagccccggugaacggcggccguaacuauaacgguccuaa
gguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaa
cgaccggagcgcugucucggcgagggacccggugaaauugaacuggccgu
gaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuuac
ugcagccugguguuggcucuuggcugggggccuaacccucggaugggggg
acagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaagguaa
cggaggcgcccaaagguccccucaggcgggacggaaauccgccggagagc
gcaaggguagaagggggccugacugcgaggccugcaagccgagcaggggc
gaaagccgggccuagugaaccgguggucccguguggaagggccaucgauc
aacggauaaaaguuaccccggggauaacaggcugaucucccccgagcguc
cacagcggcggggagguuuggcaccucgaugucggcucgucgcauccugg
ggcugaagaaggucccaaggguugggcuguucgcccauuaaagcggcacg
cgagcuggguucagaacgucgugagacaguucggucucuauccgccacgg
gcgcaggaggcuugaggggggcucuuccuaguacgagaggaccggaaggg
acgcaccucugguuucccagcugucccuccaggggcauaagcuggguagc
caugugcggaagggauaaccgcugaaagcaucuaagcgggaagcccgccc
caagaugaggccucccggcagccgguaaggacccgggaagaccacccggu
ggaugggccggggguguaagcgccgcgaggcguugagccgaccgguccca
aucguccgaggucu

<<<......<<<<<<<<<<<.....<<..<<<<<<<<<<<<......<<<
<<<.((..((.>>>.....<<<<<<<..<<<))..)).>>>.....>>>>
>>>...>>>....<<<....>>><<<<<<<<....>>>>>>>>.<<<<<<
.>>>>>>.>>...<<<<<<.....<......>......>>>>>.>.....
....<<....>>...<<<<<.....<<.....>>....>>>>>...<<<.
...<<<<<<<<.....>>>>>>>>......<<<<<<<<<....<<<...<
<<<<.<<<<.<<<...<<<<<......>>>>>((......<<<.....))
>>>...>>>...>>>>..>>>>>..>>>>>>>>>.>>>.....<<<<<<<
<<.......>>>>>>>>>......<<<<<..((((>>>>>..>>>.....
.>>.>>>>>>.>>...............<<....>>....>>........
.<<<<....>>>>..................>>>>>>>>>>>.......<
<<<<<<<<<<.>>>>>>>>>>>...<............>.<<<<<<....
<<<<<<<<<<<<<..<<<...<<<.....>>>...>>>...<<....>>.
.<<<<.....>>>>....<<..>>...>>>>>>>>>>>>>..<<.<...<
<<<<<....<<<<<<<<<<..<<<....<<<<<<......>>>>>>....
.>>>...<<<..<<<<........>>>>.>>>....>>>>>>>>>>..<<
<.....>>>......>>>>>>......>.>>..<<<<<<....<<<<<..
..>>>>><<<<<<<<<.....<<<<<<<<<...<<<...<<<<<<<<...
<<<<<<......>>>>.>>...>>>>>>>>..>>.>...>>>>>>>>>..
...>>>>>>>.>>..<<<<<<<.<<......>>.>>>>>>>.....<<<.
.....>>>...<<<<.<<<...<<<(((.....<<<<<<...........
<<..<<<<<<<<<..>>>>>>>>>.>>..........)))......>>>>
>>.>>>...>>>>>>><<<<<<<<>>>>>>>>....>>>>>><.<<<<<.
..<<<......<<<<<.<<<....>>>>>>>>...>>>..>>>>>..>..
...>>>>>><......<<.....<<<<<<.......>>>>>><<<<....
<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<.<<.
..<<<...<<<....>>>...>>>...>>...<<<<<........>>>>>
))<<<<<<<<<<<<<...<<<<....<<<<<.<<<..<<<<<.<<<<.<<
..[[[[...>>>>>><<<...<<<<<<<<<<<<<<<<.<<.....>>>>>
>>>>.....>>>>>>>>>..>>><...<<<<..>>>>.....>>>>>>..
.>>>..>>>>>.........>>>>...>>...>>>>>>>>>>>>>>>..>
>.....<<......>>>>>>>.<<<<<....>>>>>..>>>>..<<<<..
..<<<<<<<<.<<.........<.....<<<<<.....<..>......>>
>>><<<<<<<<<<<<.....>>>>>>>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<...<<<<<....>
>>>>...>>...>>>>>>>>..>>>>><<<<<<.......>>>>>>....
....<...........<<<<<<.....>>>>>>.....>....>>>>>..
>>.>>>>>>>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<.
.......>>>>>..<<<<<<<<.<<<.........<<<<.<<<<<<..<<
<<<.<<<.<<<<<.<<<<<<<<..>>>>>>>>...<<<<<....>>>>>.
...>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<..........
.>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<
...(((>>....>>>>>>>...<<<<..<<<......>>>..>>>>.<<<
....>>>.>>))).......<<<<<<<.<<..))))..>>>>>>>>>...
..........>>>>..>>>>>>.......<<<<...<<<<<<...<<...
....>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..<<<<<
<<<<......>>>>>>>..>>.<<<<<.....>>>>>.....>>>>>..>
...>>>.>>....<<<<<<<....>>>.>>>>........>>>>>>>>>>
>....<<<<<<<...<<<<..<<<<<<<...............>>>>>>>
.<<<<<...<<<<...<<<<<<<<<<<]]]]>>>>>>...>>>>>...>>
>>.>>>>>...<<<....<<<<<...........>>>>>....>>>.>>>
>.......>>>>>>>.<<<.>>>.....<<<<<<<<<.......>>>>>.
...<<<<<<<<.<<<....<<<<<....>>>>>...>>>..>>>>>.>>>
...>>>>....>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v9s The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): R3 L4 R9 R10 F12 R13 N16 R17 I18 T21 R23 F87 R89 Y94 R106 F112
• Binding residue (residue number reindexed from 1): R1 L2 R7 R8 F10 R11 N14 R15 I16 T19 R21 F85 R87 Y92 R104 F110

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v9s, PDBe:4v9s, PDBj:4v9s
• PDBsum: 4v9s
• PubMed: 24412368
• UniProt: Q5SHQ4|RL18_THET8 Large ribosomal subunit protein uL18 (Gene Name=rplR)