Structure of PDB 4zer Chain 20 Binding Site BS01

Receptor Information

>4zer Chain 20 (length=77) Species: 300852 (Thermus thermophilus HB8)

GSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDF
TLFALVDGVVEFQDRGRLGRYVHVRPL

Ligand information

>4zer Chain 2A (length=2869)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucggacaccgaau
ccccagccuagccgaagcuguugggaagcagcgccagagagggugaaagc
cccguaggcgaaagguggggggauaggugaggguacccgaguaccccgug
guucguggagccaugggggaaucugggcggaccaccgccuaaggcuaagu
acuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaaaga
accccgggaggggagugaaauagagccugaaaccgugggcuuacaagcag
ucacggccccggggguuguggcgugccuauugaagcaugagccggcgacu
cacggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccg
aguccgaacagggcgcaagcggccgcaaaguccgcggccguggacccgaa
accgggcgagcuagcccuggccagggugaagcuggggugagacccagugg
aggcccgaaccggugggggaugcaaaccccucggaugagcuggggcuagg
agugaaaagcuaaccgagcccggagauagcugguucuccccgaaaugacu
uuagggucagccucaggcgcugacuggggccuguagagcacugauagggc
uagggggcccaccagccuaccaaacccugucaaacuccgaagggucccag
guggagccugggagugagggcgcgagcgauaacguccgcguccgagcgcg
ggaacaaccgagaccgccagcuaaggcccccaagucugggcuaaguggua
aaggauguggcgccgcgaagacagccaggagguggcuuagaagcagccau
ccuuuaaagagugcguaauagcucacuggucgaguggcgccgcgccgaaa
augaucggggcuuaagcccagcgccgaagcugcgggucuggggccccagg
cgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcggc
uggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggug
agaaucccucucgccguaagcccaaggguuccuacgcaauggucgucagc
guaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaagggc
agccgguuaauauuccggcccuucccgcaggugcgauggggggacgcucu
aggcuagggggaccggagccauggacgagcccggccagaagcgcagggug
ggagguaggcaaauccgccucccaacaagcucugcgugguggggaagccc
gcgggugacaaccccccgaagccagggagccaagaaaagccucuaagcac
aaccugcgggaacccguaccgcaaaccgacacaggugggcgggugcaaga
gcacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggcc
ccguaacuucgggagaaggggugcucccuggggugaugagccccggggag
ccgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugc
gaacucguaagaggagguauagggagcgacgcuugcccggugccggaagg
ucaaggggaggggugcaagccccgaaccgaagccccggugaacggcggcc
guaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccg
accugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccg
gugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaa
agaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccu
gcguaggauaggugggagccugugaacccccgccuccgggugggggggag
gcgccggugaaauaccacccuggcgcggcugggggccuaacccucggaug
gggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaa
gguaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgg
agagcgcaaggguagaagggggccugacugcgaggccugcaagccgagca
ggggcgaaagccgggccuagugaaccgguggucccguguggaagggccau
cgaucaacggauaaaaguuaccccggggauaacaggcugaucucccccga
gcguccacagcggcggggagguuuggcaccucgaugucggcucgucgcau
ccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcg
gcacgcgagcuggguucagaacgucgugagacaguucggucucuauccgc
cacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgg
aagggacgcaccucugguuucccagcugucccuccaggggcauaagcugg
guagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagcc
cgccccaagaugaggccucccggcagccgguaaggacccgggaagaccac
ccgguggaugggccggggguguaagcgccgcgaggcguugagccgaccgg
ucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zer The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): T10 R11 N12 R14 D15 S16 A18 K19 R20 K24 R25 Y26 E27 Q29 A33 N35 I36 R39 R41 G42 T43 R44 K46 G54 R55 D56 F57 F60 L62 F69 R74 L75 R77
• Binding residue (residue number reindexed from 1): T3 R4 N5 R7 D8 S9 A11 K12 R13 K17 R18 Y19 E20 Q22 A26 N28 I29 R32 R34 G35 T36 R37 K39 G47 R48 D49 F50 F53 L55 F62 R67 L68 R70

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:4zer, PDBe:4zer, PDBj:4zer
• PDBsum: 4zer
• PubMed: 25984971
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)