Structure of PDB 5x8t Chain D Binding Site BS02

Receptor Information

>5x8t Chain D (length=212) Species: 3562 (Spinacia oleracea)

VDAGIGVMGTKLGMMSFFEEDGTVVPVTVIGFKEGNIVTQVKTESTDGYN
AVQVGYERLRDRKLTMPERGHLNKAGVIPMRHLQEFRLVSVDDFTPSQKL
LFEELFKEGDMVDISGTTIGKGFQGGIKRHNFKRGLMTHGSKSHRALGSI
GAGTTPGHVYKGKKMPGRMGGTKTKIRKLKIMKIDTDLRVVMIKGAVPGK
PGNLLRLAPAKI

Ligand information

>5x8t 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: 5x8t Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): M99 M100 P111 Y134 P152 E153 G155 H156 K159 L168 Q169 E170 R172 T203 I204 K206 F208 G210 N216 F217 K218 R219 L221 M222 T223 H224 G225 K227 H229 R230 G233 S234 I235 G236 A237 G238 T239 T240 P241 G242 H243 V244 Y245 K246 G247 K248 M250 P251 R253 K258 T259 K260 I261 R262 K263 L264 K279 V282 G284 K285 K296
• Binding residue (residue number reindexed from 1): M14 M15 P26 Y49 P67 E68 G70 H71 K74 L83 Q84 E85 R87 T118 I119 K121 F123 G125 N131 F132 K133 R134 L136 M137 T138 H139 G140 K142 H144 R145 G148 S149 I150 G151 A152 G153 T154 T155 P156 G157 H158 V159 Y160 K161 G162 K163 M165 P166 R168 K173 T174 K175 I176 R177 K178 L179 K194 V197 G199 K200 K211

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:5x8t, PDBe:5x8t, PDBj:5x8t
• PDBsum: 5x8t
• PubMed: 28582576
• UniProt: P82191|RK3_SPIOL Large ribosomal subunit protein uL3c (Gene Name=RPL3)