Structure of PDB 8cd1 Chain X Binding Site BS01

Receptor Information

>8cd1 Chain X (length=77) Species: 208964 (Pseudomonas aeruginosa PAO1)

SRVCQVTGKGPVTGNNISHAHNKTRRRFLPNLQHHRFWVESEKRFVRLRV
SAKGMRIIDKRGIEAVLADLRARGEKF

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): S2 R3 K10 P12 T14 N16 I18 S19 A21 H22 N23 K24 R26 R28 F29 L30 P31 N32 Q34 H36 R37 R48 R50 A53 K54 R57 K61 R62
• Binding residue (residue number reindexed from 1): S1 R2 K9 P11 T13 N15 I17 S18 A20 H21 N22 K23 R25 R27 F28 L29 P30 N31 Q33 H35 R36 R47 R49 A52 K53 R56 K60 R61

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:8cd1, PDBe:8cd1, PDBj:8cd1
• PDBsum: 8cd1
• PubMed: 38443577
• UniProt: Q9HTN8|RL28_PSEAE Large ribosomal subunit protein bL28 (Gene Name=rpmB)