Structure of PDB 4v9s Chain B0 Binding Site BS01

Receptor Information

>4v9s Chain B0 (length=83) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL

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): H3 K4 T10 R11 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 G54 R55 D56 F57 F60 L62 F69 R74 R77
• Binding residue (residue number reindexed from 1): H2 K3 T9 R10 N11 R13 D14 S15 Q16 A17 K18 R19 K23 R24 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 G41 T42 G53 R54 D55 F56 F59 L61 F68 R73 R76

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• 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: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)