Structure of PDB 8cd1 Chain S Binding Site BS01

Receptor Information
>8cd1 Chain S (length=109) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVAAKLSGARISAQKARLVADQIRGKKVGEALNLLAFSSKKAAEIMKKVL
ESAVANAEHNEGADVDDLKVSTVFVNEGRSLKRIMPRAKGRADRIVKRSC
HITVKVADK
Ligand information
>8cd1 Chain A (length=2883) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
<<<<<<<......<<<<<<<<<<<.....[[..[[<<<<<<<[[<<....
..<<<<<<....(((.>>>.....<<<<<<.<.<<<))).....>>>...
..>>>>>>>...>>>....<<<....>>><<<<<<<....>>>>>>>.<<
<<<<<<<.........>>>>>>>>>.>>...<<<<<<.....<<....>>
......>>>>>.>.........<<....>>...<<<<<.....<<.....
>>....>>>>>...(((.....<<<<<<..<<<<<<.<<<...<<<.<..
....>.>>>((......<<<.....))>>>...>>>...>>>>>>..>>>
>>>...........<<<<<<<<.........>>>>>>>>......<<<<<
..<<<<>>>>>..)))......]].>>>>>>>.]]...............
<<....>>....]].........<<<<.....>>>>..............
....>>>>>>>>>>>.......<<<<..<<<<<.....>>>>>..>>>>.
..<.<........>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<
.....>>...>>>...<<....>>..<<<<.....>>>>...>>>>>>>>
>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<<...<<<<<<.
.....>>>>>>...>.>>>...<<<.<<.<<........>>.>>>>>...
.>>>>>>>>>...<<<.....>>>......>>>>>>......>.>>..<<
<<<<....<<<<<....>>>>>.<<<<<<<<..<<<<<<<<<.....<<<
...<<<.<<<<...<<.<<<.......>>>..>>...>>>>.>>>..>>.
>.....>>>>>.>>>>....>>>>>>>.>...<<<<<<<<<<......>>
>>>>>>>>....<<<......>>>...<<<<.<<<...<<<(((.....<
<<<<<...........<<..<<<<<..<<........<<<<<.<<...<<
<.........>>>...>>........<<<......>>>..>>>>>....>
>..>>>>>.>>...........)))......>>>>>>.>>>...>>>>>>
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<<<<<<....>>>>>>>>...>>>..>>>>>........>>>>>><....
..<<.....<<<<<<.......>>>>>><<<<....<<<<<.<<...<<<
<<<...<<.....>>.>>>>>>....((<<<<<<<...<<<...<<<...
.>>>...>>>...>>>..<<<<<........>>>>>))<<<<<<<<<<<<
<...<<<<....<<<<..<<<..<<<<<<<<<<<....(((...>>>>>>
<<..<<<....<<<.<<<<<<<..<<.....>>.>>>>>>>...>>>...
.>>>...>><..<<<<<<..>>>>>>...>>>>>>...>>>...>>>.>.
.......>>>>...>>....>>>>>>>>>>>>>>>..>>.....<<....
..>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<<
...............<<<<<....<<..>>.....>>>>><<<<<<<<<<
<<...<<<.....>>>....>>>>>>>>>>>>............<<<<<<
<<<..<<<.........>>>..<<<<<<<.....<<<....>>>......
.>>>>>>>.<<<<<.<<<..<<<<<<<..<<<<.......<<<<<<.<<.
...>>..>>>>>>.......>>>>>>>>>..>>>>><<<...........
..>>>........<...........<<<<<<.....>>>>>>.....>..
..>>>>>..>>.>>>>>>>.....>>.>>>>>>>>.>>>>>>.....>..
...<<<<<........>>>>>..<<<<<<<<.(((.[[......<<<<.[
[<<<<..<<<<<.<<<.<<<<<.<<<<<<<<<<<.<.<............
<<<<....<...........<<........>>........>.........
.....>>>>...>.>.>>>>>>>>>>>...<<<.<<<<<<.....>>>>>
>>>>....>>>>>.>>>..>>>>>..<<<<.....>>>><<<<<<.....
......>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>..
...<<.[.(((>>....>>>>>>>...<<<<..<<<......>>>..>>>
>.<<<....>>>.>>)))]......<<<<<<<.((..>>>>..))>>>>>
>>.............>>>>..]]>>>>.......<<<<...<<<<<<...
<<.......>>...>>>>>>....>>>.>.......<<<<<.<<<<<<..
<<<<<<<<<......>>>>>>..>>>.<<<<<.....>>>>>.....>>>
>>..>...>>>.>>....<<<<<<<....>>>.>>>>....]]..)))>>
>>>>>>....<<<<<<<...<<<<..<<<<<<<...............>>
>>>>>.<<<<<...<<<<...<<<<<<<<<<<))).>>>>>>..>>>>>.
..>>>>.>>>>>...<<<....<<<<<...........>>>>>....>>>
.>>>>.......>>>>>>>..<<<<<.....>>>>>.....<<<<<<<<<
.......>>>>>....<<<<<<<<..<<.....<<<<....>>>>....>
>...>>>>>.>>>...>>>>.....>>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8cd1 70S-PHIKZ014 PHIKZ phage protein occupied ribosome
Resolution3.0 Å
Binding residue
(original residue number in PDB)		V3 A4 A5 K6 L7 R11 S13 Q15 K16 R18 R25 K41 K42 K49 S53 A56 N57 H60 N61 F75 N77 E78 R80 K83 R84 P87 R88 A89 K90 G91 R92 D94 I96 V97 K98 R99 H102
Binding residue
(residue number reindexed from 1)		V2 A3 A4 K5 L6 R10 S12 Q14 K15 R17 R24 K40 K41 K48 S52 A55 N56 H59 N60 F74 N76 E77 R79 K82 R83 P86 R87 A88 K89 G90 R91 D93 I95 V96 K97 R98 H101
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0019843 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cd1, PDBe:8cd1, PDBj:8cd1
PDBsum8cd1
PubMed38443577
UniProtQ9HWE0|RL22_PSEAE Large ribosomal subunit protein uL22 (Gene Name=rplV)

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