Structure of PDB 5fdu Chain 1G Binding Site BS01

Receptor Information

>5fdu Chain 1G (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

Ligand information

>5fdu Chain 1A (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: 5fdu Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K36 V38 N40 G42 L43 E45 T71 A73 K75 N79 F80 I88 S124 D126 R128 N132 G134 L135 G154 M155 D156 A158
• Binding residue (residue number reindexed from 1): K35 V37 N39 G41 L42 E44 T70 A72 K74 N78 F79 I87 S123 D125 R127 N131 G133 L134 G153 M154 D155 A157

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5fdu, PDBe:5fdu, PDBj:5fdu
• PDBsum: 5fdu
• PubMed: 26792896
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)