Structure of PDB 4v9r Chain DV Binding Site BS01

Receptor Information

>4v9r Chain DV (length=101) Species: 274 (Thermus thermophilus)

MFAIVKTGGKQYRVEPGLKLRVEKLDAEPGATVELPVLLLGGEKTVVGTP
VVEGASVVAEVLGHGRGKKILVSKFKAKVQYRRKKGHRQPYTELLIKEIR
G

Ligand information

>4v9r 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: 4v9r The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): G8 G9 K10 E23 K24 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90
• Binding residue (residue number reindexed from 1): G8 G9 K10 E23 K24 R66 K69 K74 F75 K76 A77 K78 V79 Q80 Y81 R83 K84 K85 G86 H87 Q89 P90

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v9r, PDBe:4v9r, PDBj:4v9r
• PDBsum: 4v9r
• PubMed: 24412368
• UniProt: P60492|RL21_THET8 Large ribosomal subunit protein bL21 (Gene Name=rplU)