Structure of PDB 5x8p Chain 3 Binding Site BS01

Receptor Information

>5x8p Chain 3 (length=57) Species: 3562 (Spinacia oleracea)

AALCLTKRSRSRKSLARTHGFRLRMSTTSGRALLKRRRAKGRKILCTKTN
PSSGKRA

Ligand information

>5x8p Chain A (length=2809)

ucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagga
agggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagaga
uccggagauucccgaauaggucaaccuuucgaacuucugcugaauccaug
ggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagga
aaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagcag
ccuaaaccgugaaaacgggguugugggagagcaauacaagcgucgugcug
cuaggcgaaucaguggagugcggaacccuagauggugaaaguccaguagc
cgaaagcaucacuagcuuaugcucugacccgaguagcauggggcacgugg
aaucccgugugaaucagcaaggaccaccuugcaaggcuaaauacuccugg
gugaccgauagcgaaguaguaccgugagggaagggugaaaagaaccccca
ucggggagugaaauagaacaugaaaccguaagcucucaagcagugggagg
gggaccagacccugaccgcgugccuguugaagaaugagccggcgacucau
aggcaguggcuugguuaagggaacccaccggagccguagcgaaagcgagu
cuucauagggcaauugucacugcuuauggacccgaaccugggugaucuau
ccaugaccaggaugaagcuugggugaaacuaaguggagguccgaaccgac
ugauguugaagaaucagcggaugaguugugguuaggggugaaaugccacu
cgaacccagagcuagcugguucuccccgaaaugcguugaggcgcagcagu
ugacuggacaucuagggguaaagcacuguuucggugcgggccgcgagagc
gguaccaaaucgaggcaaacucugaauacuagauaugaccuccaaauaac
aggggucaaggucggccagugagacgaugggggauaagcuucaucgucga
gagggaaacagcccggaucaccagcuaaggccccuaaaugaccgcucagu
gauaaaggagguaggggugcagagacagccaggagguuugccuagaagca
gccacccuugaaagagugcguaauagcucacugaucgagcgcucuugcgc
cgaagaugaacggggcuaagcggucugccgaagcugugggauguaaaaaa
acaucgguaggggagcguuccguguuagggagaaacgcgugcgugagccg
cguuggacgaagcggaagcgagaaugucggcuugaguaacgcaaacauug
gugagaauccaaugccccgaaaaccuaaggguuccuccgcaagguucguc
cacggagggugagucagggccuaagaucaggccgaaaggcguagucgaug
gacaacaggugaauauuccuguacuaccccuuguuggucccgagggacgg
aggaggcuagguuagccgaaagaugguuaucgguucaaggacgcaaggug
acccuguuuuucaggguaagaagggguagagaaaaugccucgagccaaug
uucgaguaccaggcgcuacggcgcugaaguaaccgaugccauacucccag
gaaaagcucgaacgaccuucaacaaaaggguaccuguacccgaaaccgac
acagguagguagguagagaauaccuaggggcgcgagacaacucucucuaa
ggaacucggcaaaauagccccguaacuucgggagaaggggugcccccuca
caaagggggucgaagugaccaggcccgggcgacuguuuaccaaaaacaca
ggucuccgcaaagucguaagaccauguaugggggcugacgccugcccagu
gccggaaggucaaggaaguuggugaccugaugacaggggagccggcgacc
gaagccccggugaacggcggccguaacuauaacgguccuaagguagcgaa
auuccuugucggguaaguuccgacccgcacgaaaggcguaacgaucuggg
cacugucucggagagaggcucggugaaauagacaugucugugaagaugcg
gacuaccugcaccuggacagaaagacccuaugaagcuuuacuguucccug
ggauuggcuuugggcuuuuccugcgcagcuuagguggaaggcgaagaagg
cccccuuccgggggggcccgagccaucagugagauaccacucuggaagag
cuagaauucuaaccuugugucaggaccuacgggccaagggacauucucag
guagacaguuucuauggggcguaggccucccaaaagguaacggaggcgug
caaagguuuccucgggccggacggagauuggcccucgagugcaaaggcag
aagggagcuugacugcaagacccacccgucgagcagggacgaaagucggc
cuuagugauccgacggugccgaguggaagggccgucgcucaacggauaaa
aguuacucuagggauaacaggcugaucuuccccaagaguucacaucgacg
ggaagguuuggcaccucgaugucggcucuucgccaccuggggcuguagua
uguuccaaggguugggcuguucgcccauuaaagcgguacgugagcugggu
ucagaacgucgugagacaguucgguccauauccggugugggcguuagagc
auugagaggaccuuucccuaguacgagaggaccgggaaggacgcaccucu
gguguaccaguuaucgugcccacgguaaacgcuggguagccaagugcgga
gcggauaacugcugaaagcaucuaaguaguaagcccaccccaagaugagu
gcucuccua

.............<<<<<<<<<<.....<<..<<<<<<<<<<<.<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<.))......>>.....
>>>>>>>...>>>....<<<....>>>......<<<<<<<<.........
>>>>>..>>>.>....<<<<<<.....<<....>>......>>>>>.>..
.......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<
<<....<<<<....>>>>......<<<<<<<<<....<<<<...<<<.<<
<<.<<<...<<.<<.....>>.>>((......<<<.....))>>>...>>
>...>>>>.>>>..>>>>.>>>>>>..>>>.....<<<<<<<<.......
..>>>>>>>>......<<<<<..<<<<>>>>>..>>>......>>.>>>>
>>>.>>...............<<....>>....>>.........<<<<..
..>>>>..................>>>>>>>>>>........<<<<..<<
<<.......>>>>..>>>>...<.<........>.>.<<<<<<....<<<
<<<<<<<<<...<<<...<<.......>>...>>>...<<....>>..<<
<<.....>>>>.....>>>>>>>>>>>>..<<.<...<<<<<<.....<.
<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<<<.<
<<<<........>>>>>>>>....>>>>>>>.>...<<<.....>>>...
...>>>>>>......>.>>..<<<<<<....<<<<<....>>>>><<.<<
<<<<<....<<<<<<.....<<<...<<<<<<<<...<<<<<........
>>>.>>...>>>>>>>>..>>.>.....>>>>>>..<<<<<<........
.>>>>>>..>>>>>>>..>>..<<<<<<<<<<......>>>>>>>>>>..
..<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.....
......<<..<<<<<<<<<<.........<<<.<<....<<.........
>>....>>.........<<......>>...>>>.....>>>>>>>>>>.>
>..........))).....>>>>>>.>>>...>>>>>>><<<<<......
>>>>>....>>>>>><.<<<<<<...........<<<<<.<<....>>>>
>>.>.......>>>>>>..>.....>>>>>><......<<.....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>
>...<<<<<........>>>>>))<<<<<.<<<<.<<<<.<<<<....<<
<<..<<<..<<<<<<<<<<.....(((..>>>>>....<<<<<...<<<.
<<<<<<.....>>>>>>.....<<<<<<.......>>>>>>..>>>..>>
>>>.....<..<<<<<....>>>>>...>>>>>>...>>>...>>>>...
......>>>>...>>>>....>>>>..>>>>>>>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<.........<.....<<<<<....<....>.....>>>>><<<<<<<..
...>>>>>>>............<<<<<<<<<..<<<.........>>>..
<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<
<<<<<..<<<...<<..<<<<<<..<<<<....>>>>...>>>>>>..>>
...>>>>>>>>..>>>>><<<<<<.......>>>>>>........<....
.......<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>
>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>
>>>..<<<<<<<<.<<<..<......<<<<.<<<<<<..<<<<<..<<<<
<<<..<<.<<<.<<<<<<<<..............<<<..<<<......<<
<<<<.......>.>>>>>...>>>............>>>.....>>>>>>
>>.>>>.>>...<<<<<.<<<..........>>>>>>>>.....>>>>>>
>...>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<
<...<<<<<<<..<<<<<<<.......>>>>>>>....<<...(((>>..
..>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>
))).......<<<<<<<.<<..>>>>..>>>>>>>>>.............
>>>>..>>>>>>.......<<<<.<.<<<<<<...<<.......>>...>
>>>>>...>>>>.>.......<<<<<...<<<<..<<<<<<<<.......
.>>>>>..>>>.<<<<<.....>>>>>.....>>>>.......>>>>>..
...<<<<<<<....>>>.>>>>....>...>>>>>>>>>>>....<<<<<
<<...<.<<..<<<<<<<...............>>>>>>>.<<<<<...<
<<<...<<<<<<<<<<<))).>>>>>>...>>>>>...>>>>.>>>>>..
<.<<...<<<<<<...........>>>>>>...>>>.>>.>.......>>
>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5x8p Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): A91 L93 C94 L95 T96 K97 R98 S99 R100 S101 R102 K103 S104 L105 A106 R107 H109 F111 R112 T118 S119 L123 K125 R126 R127 R128 K130 G131 R132 K133 L135 K138 N140 P141 S142 S143 R146
• Binding residue (residue number reindexed from 1): A1 L3 C4 L5 T6 K7 R8 S9 R10 S11 R12 K13 S14 L15 A16 R17 H19 F21 R22 T28 S29 L33 K35 R36 R37 R38 K40 G41 R42 K43 L45 K48 N50 P51 S52 S53 R56

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:5x8p, PDBe:5x8p, PDBj:5x8p
• PDBsum: 5x8p
• PubMed: 28582576
• UniProt: P82244|RK34_SPIOL Large ribosomal subunit protein bL34c (Gene Name=RPL34)