Structure of PDB 6fkr Chain 2O Binding Site BS01

Receptor Information

>6fkr Chain 2O (length=122) Species: 300852 (Thermus thermophilus HB8)

MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRG
AVKEGDVVKAVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFG
PVARELREKGFMKIVSLAPEVL

Ligand information

>6fkr Chain 2A (length=2872)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucggaccgaauccc
cagccuagccgaagcuguugggaagcagcgccagagagggugaaagcccc
guaggcgaaagguggggggauaggugaggguacccgaguaccccgugguu
cguggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacu
ccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacc
ccgggaggggagugaaauagagccugaaaccgugggcuuacaagcaguca
cggccccgagggguuguggcgugccuauugaagcaugagccggcgacuca
cggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgag
uccgaacagggcgcagcggccgcaaaguccgcggccguggacccgaaacc
gggcgagcuagcccuggccagggugaagcuggggugagacccaguggagg
cccgaaccggugggggaugcaaaccccucggaugagcuggggcuaggagu
gaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuua
gggucagccucaggcgcugacuggggccuguagagcacugauagggcuag
ggggcccaccagccuaccaaacccugucaaacuccgaagggucccaggug
gagccugggagugagggcgcgagcgauaacguccgcguccgagcgcggga
acaaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaag
gauguggcgccgcgaagacagccaggagguuggcuuagaagcagccaucc
uuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaaau
gaucggggcuuaagcccagcgccgaagcugcgggucugggggaugacccc
aggcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggc
ggcuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagg
gugagaaucccucucgccguaagcccaaggguuccuacgcaauggucguc
agcguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaag
ggcagccgguuaauauuccggcccuucccgcaggugcgauggggggacgc
ucuaggcuagggggaccggagccauggacgagcccggccagaagcgcagg
gugggagguaggcaaauccgccucccaacaagcucugcgugguggggaag
cccgggugacaaccccccgaagccagggagccaagaaaagccucuaagca
caaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaag
agcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggc
cccguaacuucgggagaaggggugcucccuggggugaugagccccgggga
gccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucug
cgaacucguaagaggagguauagggagcgacgcuugcccggugccggaag
gucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggc
cguaacuauaacgguccuaagguagcgaaauuccuugucggguaaguucc
gaccugcacgaaaagcguaacgaccggagcgcugucucggcgagggaccc
ggugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaa
aagaccccguggagcuuuacugcagccugguguuggcucuuggucgcgcc
ugcguaggauaggugggagccugugaacccccgccuccggguggggggga
ggcgccggugaaauaccacccuggcgcggcugggggccuaacccucggau
ggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaa
agguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccg
gagagcgcaaggguagaagggggccugacugcgaggccugcaagccgagc
aggggcgaaagccgggccuagugaaccgguggucccguguggaagggcca
ucgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccg
agcguccacagcggcggggagguuuggcaccucgaugucggcucgucgca
uccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagc
ggcacgcgagcuggguucagaacgucgugagacaguucggucucuauccg
ccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccg
gaagggacgcaccucugguuucccagcugucccuccaggggcauaagcug
gguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagc
ccgccccaagaugaggccucccacggcagccgguaaggacccgggaagac
cacccgguggaugggccggggguguaagcgccgcgaggcguugagccgac
cggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fkr The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): M1 Q3 Q5 T6 I22 R23 L25 K26 S28 N29 K31 Y32 S42 G55 K67 E68 K70 R78
• Binding residue (residue number reindexed from 1): M1 Q3 Q5 T6 I22 R23 L25 K26 S28 N29 K31 Y32 S42 G55 K67 E68 K70 R78

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:6fkr, PDBe:6fkr, PDBj:6fkr
• PDBsum: 6fkr
• PubMed: 29526712
• UniProt: Q5SHP8|RL14_THET8 Large ribosomal subunit protein uL14 (Gene Name=rplN)