Structure of PDB 4v9s Chain BN Binding Site BS01

Receptor Information

>4v9s Chain BN (length=140) Species: 300852 (Thermus thermophilus HB8)

MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGD
FVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLE
HAVKGMLPKGPLGRRLFKRLKVYAGPDHPHQAQRPEKLEV

Ligand information

>4v9s Chain BA (length=2731)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcagcggccgcaaaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagcggucgaguggcgccgcgccgaaaaugau
cggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccagg
cgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggc
uggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggug
agaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagc
guaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggc
agccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucu
aggcuagggggaccggagccauggacgagcccggccagaagcgcagggug
ggagguaggcaaauccgccucccaacaagcucugcgugguggggaagccc
gggugacaaccccccgaagccagggagccaagaaaagccucuaagcacaa
ccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagagc
acucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcccc
guaacuucgggagaaggggugcucccuggggugaugagccccggggagcc
gcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcga
acucguaagaggagguauagggagcgacgcuugcccggugccggaagguc
aaggggaggggugcaagccccgaaccgaagccccggugaacggcggccgu
aacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccgac
cugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccggu
gaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaag
accccguggagcuuuacugcagccugguguuggcucuugugggggccuaa
cccucggauggggggacagcgcuuggcgggcaguuugacuggggcggucg
ccuccuaaaagguaacggaggcgcccaaagguccccucaggcgggacgga
aauccgccggagagcgcaaggguagaagggggccugacugcgaggccugc
aagccgagcaggggcgaaagccgggccuagugaaccgguggucccgugug
gaagggccaucgaucaacggauaaaaguuaccccggggauaacaggcuga
ucucccccgagcguccacagcggcggggagguuuggcaccucgaugucgg
cucgucgcauccuggggcugaagaaggucccaaggguugggcuguucgcc
cauuaaagcggcacgcgagcuggguucagaacgucgugagacaguucggu
cucuauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacg
agaggaccggaagggacgcaccucugguuucccagcugucccuccagggg
cauaagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaa
gcgggaagcccgccccaagaugaggccucccacggcagccgguaaggacc
cgggaagaccacccgguggaugggccggggguguaagcgccgcgaggcgu
ugagccgaccggucccaaucguccgaggucu

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

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): T3 V5 W13 T22 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 L82 K89 R97 E100 A102 G105 M106 P111 L112 R114 K118 H130 Q133
• Binding residue (residue number reindexed from 1): T3 V5 W13 T22 G24 R25 T28 R35 K37 N45 F51 T63 G64 K65 K66 Q69 R74 Y75 S76 Y78 P79 G80 L82 K89 R97 E100 A102 G105 M106 P111 L112 R114 K118 H130 Q133

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of 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: P60488|RL13_THET8 Large ribosomal subunit protein uL13 (Gene Name=rplM)