Structure of PDB 8cd1 Chain V Binding Site BS01

Receptor Information

>8cd1 Chain V (length=188) Species: 208964 (Pseudomonas aeruginosa PAO1)

FILNAQVRSDLGKGASRRLRRNAGLVPAVVYGGDKEPQSVTLELREIAKL
LENEAAFSHVIALNVGGAKETVLIKALQRHPAKGFVMHADFLRVVADHKL
TAHVPLHFINEEVAVGVKQAGGEISHTISEVEVSCLPKDLPEFIEVDMAK
VELGQIVHLSDLKAPKGVELVQLAHGNDLAVANIHASR

Ligand information

>8cd1 Chain A (length=2883)

gucaagugaagaagcgcauacgguggaugccuuggcagucagaggcgaug
aaagacgugguagccugcgaaaagcuucggggagucggcaaacagacuuu
gauccggagaucucugaaugggggaacccaccuaggauaaccuagguauc
uuguacugaauccauaggugcaagaggcgaaccaggggaacugaaacauc
uaaguacccugaggaaaagaaaucaaccgagauucccuuaguaguggcga
gcgaacggggauuagcccuuaagcuucauugauuuuagcggaacgcucug
gaaagugcggccauagugggugauagccccguacgcgaaaggaucuuuga
agugaaaucaaguaggacggagcacgagaaacuuugucugaacauggggg
gaccauccuccaaggcuaaauacuacugacugaccgauagugaaccagua
ccgugagggaaaggcgaaaagaaccccggagaggggagugaaauagaacc
ugaaaccguaugcguacaagcagugggagccuacuuguuaggugacugcg
uaccuuuuguauaaugggucagcgacuuauauucaguggcaagcuuaacc
guauaggguaggcguagcgaaagcgagucuuaauagggcguagucgcugg
guauagacccgaaaccgggcgaucuauccaugagcagguugaagguuagg
uaacacugacuggaggaccgaacccacucccguugaaaagguaggggaug
acuuguggaucggagugaaaggcuaaucaagcucggagauagcugguucu
ccucgaaagcuauuuagguagcgccucauguaucacucugggggguagag
cacuguuucggcuagggggucaucccgacuuaccaaaccgaugcaaacuc
cgaauacccagaagugccgagcaugggagacacacggcgggugcuaacgu
ccgucgugaaaagggaaacaacccagaccgccagcuaaggucccaaaguu
gugguuaagugguaaacgaugugggaaggcuuagacagcuaggagguugg
cuuagaagcagccacccuuuaaagaaagcguaauagcucacuagucgagu
cggccugcgcggaagauguaacggggcucaaaccacacaccgaagcugcg
ggugucacguaagugacgcgguagaggagcguucuguaagccugugaagg
ugaguugagaagcuugcuggagguaucagaagugcgaaugcugacaugag
uaacgacaaugggugugaaaaacacccacgccgaaagaccaaggguuccu
gcgcaacguuaaucgacgcaggguuagucgguuccuaaggcgaggcugaa
aagcguagucgaugggaaacagguuaauauuccuguacuucugguuacug
cgauggagggacggagaaggcuaggccagcuuggcguugguuguccaagu
uuaaggugguaggcugaaaucuuagguaaauccgggguuucaaggccgag
agcugaugacgagucgucuagaugacgaagugguugaugccaugcuucca
agaaaagcuucuaagcuucagguaaccaggaaccguaccccaaaccgaca
cagguggucggguagagaauaccaaggcgcuugagagaacucgggugaag
gaacuaggcaaaauggcaccguaacuucgggagaaggugcgccggcuagg
gugaaggauuuacuccguaagcucuggcuggucgaagauaccaggccgcu
gcgacuguuuauuaaaaacacagcacucugcaaacacgaaaguggacgua
uagggugugacgccugcccggugccggaagguuaauugaugggguuagcg
caagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaa
cgguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacga
auggcguaacgauggcggcgcugucuccacccgagacucagugaaauuga
aaucgcugugaagaugcaguguauccgcggcuagacggaaagaccccgug
aaccuuuacuguagcuuugcacuggacuuugagccugcuuguguaggaua
ggugggaggcuuugaagcguggacgccaguucgcguggagccauccuuga
aauaccacccuggcaugcuugagguucuaacucugguccguaauccggau
cgaggacaguguauggugggcaguuugacuggggcggucuccuccuaaag
aguaacggaggaguacgaaggugcgcucagaccggucggaaaucggucgc
agaguauaaaggcaaaagcgcgcuugacugcgagacagacacgucgagca
gguacgaaaguaggucuuagugauccggugguucuguauggaagggccau
cgcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaa
gaguucauaucgacggcgguguuuggcaccucgaugucggcucaucacau
ccuggggcugaagccggucccaaggguauggcuguucgccauuuaaagug
guacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugc
cguggacguuugagauuugagaggggcugcuccuaguacgagaggaccgg
aguggacgaaccucugguguuccgguugucacgccaguggcauugccggg
uagcuauguucggaaaagauaaccgcugaaagcaucuaagcgggaaacuu
gccucaagaugagaucucacugggaacuugauuccccugaagggccgucg
aagacuacgacguugauaggcuggguguguaagcguugugaggcguugag
cuaaccaguacuaauggcccgugaggcuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cd1 70S-PHIKZ014 PHIKZ phage protein occupied ribosome
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R48 I159 H161 L182 N186
• Binding residue (residue number reindexed from 1): R45 I156 H158 L179 N183

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• 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:8cd1, PDBe:8cd1, PDBj:8cd1
• PDBsum: 8cd1
• PubMed: 38443577
• UniProt: Q9HVC4|RL25_PSEAE Large ribosomal subunit protein bL25 (Gene Name=rplY)