Structure of PDB 4v8a Chain AO Binding Site BS01

Receptor Information

>4v8a Chain AO (length=122) Species: 300852 (Thermus thermophilus HB8)

MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRG
AVKEGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFG
PVARELREKGFMKIVSLAPEVL

Ligand information

>4v8a Chain AA (length=2827)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucggggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgcagggguuguggcgugccuauugaagcaugagccggcgacuc
acggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccga
guccgaacagggcgcaagcgggccgcggcccgcaaaguccgcggccgugg
acccgaaaccgggcgagcuagcccuggccagggugaagcuggggugagac
ccaguggaggcccgaaccggugggggaugcaaaccccucggaugagcugg
ggcuaggagugaaaagcuaaccgagcccggagauagcugguucuccccga
aaugacuuuagggucagccucaggcgcugacuggggccuguagagcacug
auagggcuagggggcccaccagccuaccaaacccugucaaacuccgaagg
gucccagguggagccugggagugagggcgcgagcgauaacguccgcgucc
gagcgcgggaacaaccgagaccgccagcuaaggcccccaagucugggcua
agugguaaaggauguggcgccgcgaagacagcagucgaguggcgccgcgc
cgaaaaugaucggggcuuaagcccagcgccgaagcugcgggucuggggga
ugaccccaggcgguaggggagcguucccgaugccgaugaaggccgacccg
cgagggcggcuggagguaagggaagugcgaaugccggcaugaguaacgau
aaagagggugagaaucccucucgccguaagcccaaggguuccuacgcaau
ggucgucagcguaggguuaggcgggaccuaaggugaagccgaaaggcgua
gccgaagggcagccgguuaauauuccggcccuucccgcaggugcgauggg
gggacgcucuaggcuagggggaccggagccauggacgagcccggccagaa
gcgcagggugggagguaggcaaauccgccucccaacaagcucugcguggu
ggggaagcccgggugacaaccccccgaagccagggagccaagaaaagccu
cuaagcacaaccugcgggaacccguaccgcaaaccgacacaggugggcgg
gugcaagagcacucaggcgcgcgggagaacccucgccaaggaacucugca
aguuggccccguaacuucgggagaaggggugcucccuggggugaugagcc
ccggggagccgcagugaacaggcucuggcgacuguuuaccaaaaacacag
cucucugcgaacucguaagaggagguauagggagcgacgcuugcccggug
ccggaaggucaaggggaggggugcaagccccgaaccgaagccccggugaa
cggcggccguaacuauaacgguccuaagguagcgaaauuccuugucgggu
aaguuccgaccugcacgaaaagcguaacgaccggagcgcugucucggcga
gggacccggugaaauugaacuggccgugaagaugcggccuacccguggca
ggacgaaaagaccccguggagcuuuacugcagccugguguuggcucuugg
ucgcgccugcguaggauaggugggagccugugaacccccgccuccgggug
ggggggaggcgccggugaaauaccacccuggcgcggcugggggccuaacc
cucggauggggggacagcgcuuggcgggcaguuugacuggggcggucgcc
uccuaaaagguaacggaggcgcccaaagguccccucaggcgggacggaaa
uccgccggagagcgcaaggguagaagggggccugacugcgaggccugcaa
gccgagcaggggcgaaagccgggccuagugaaccgguggucccgugugga
agggccaucgaucaacggauaaaaguuaccccggggauaacaggcugauc
ucccccgagcguccacagcggcggggagguuuggcaccucgaugucggcu
cgucgcauccuggggcugaagaaggucccaaggguugggcuguucgccca
uuaaagcggcacgcgagcuggguucagaacgucgugagacguucggucuc
uauccgccacgggcgcaggaggcuugaggggggcucuuccuaguacgaga
ggaccggaagggacgcaccucugguuucccagcugucccuccaggggcau
aagcuggguagccaugugcggaagggauaaccgcugaaagcaucuaagcg
ggaagcccgccccaagaugaggccucccacggcagccgguaaggacccgg
gaagaccacccgguggaugggccggggguguaagcgccgcgaggcguuga
gccgaccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8a The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge b2a of the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): M1 Q3 Q5 T6 Y7 I22 R23 K26 S28 N29 A30 K31 Y32 S42 K44 V57 K67 E68 K70 N82
• Binding residue (residue number reindexed from 1): M1 Q3 Q5 T6 Y7 I22 R23 K26 S28 N29 A30 K31 Y32 S42 K44 V57 K67 E68 K70 N82

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0070180 large ribosomal subunit rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8a, PDBe:4v8a, PDBj:4v8a
• PDBsum: 4v8a
• PubMed: 22240456
• UniProt: Q5SHP8|RL14_THET8 Large ribosomal subunit protein uL14 (Gene Name=rplN)