Structure of PDB 5mmm Chain F Binding Site BS01

Receptor Information

>5mmm Chain F (length=193) Species: 3562 (Spinacia oleracea)

AAGTAVFVDKAEAETINRLKTNYIEKMVPLLKEEFSYSNILEVPKVVKIV
VNCGIGDASQNAKGLDAAINELALITGQRPVKTKAKTSIAGFKVREGMTL
GIAVTLRGNLMYSFLDRLINLALPRTRDFQGVNPNSFDGHGNYSVGFREQ
SVFPEIKPEIVGKARGMDVCITTTAKTDKEAYKLLSLMGMPFR

Ligand information

>5mmm Chain A (length=2798)

ucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagga
agggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagaga
uccggagauucccgaauaggucaaccuuucgaacuucugcugaauccaug
ggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagga
aaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagcag
ccuaaaccgugaaaacgggguugugggagagcaauacaagcgucgugcug
cuaggcgaaucaguggagugcggaacccuagauggugaaaguccaguagc
cgaaagcaucacuagcuuaugcucugacccgaguagcauggggcacgugg
aaucccgugugaaucagcaaggaccaccuugcaaggcuaaauacuccugg
gugaccgauagcgaaguaguaccgugagggaagggugaaaagaaccccca
ucggggagugaaaagaacaugaaaccguaagcucucaagcagugggaggg
ggaccagacccugaccgcgugccuguugaagaaugagccggcgacucaua
ggcaguggcuugguuaagggaacccaccggagccguagcgaaagcgaguc
uucauagggcaauugucacugcuuauggacccgaaccugggugaucuauc
caugaccaggaugaagcuugggugaaacuaaguggagguccgaaccgacu
gauguugaagaaucagcggaugaguugugguuaggggugaaaugccacuc
gaacccagagcuagcugguucuccccgaaaugcguugaggcgcagcaguu
gacuggacaucuagggguaaagcacuguuucggugcgggccgccgguacc
aaaucgaggcaaacucugaauacuagauaugaccuccaaauaacaggggu
caaggucggccagugagacgaugggggauaagcuucaucgucgagaggga
aacagcccggaucaccagcuaaggccccuaaaugaccgcucagugauaaa
ggagguaggggugcagagacagccaggagguuugccuagaagcagccacc
cuugaaagagugcguaauagcucacugaucgagcgcucuugcgccgaaga
ugaacggggcuaagcggucugccgaagcugugggauguaaaaaaacaucg
guaggggagcguuccguguuagggagaaacgcgugcgugagccgcguugg
acgaagcggaagcgagaaugucggcuugaguaacgcaaacauuggugaga
auccaaugccccgaaaaccuaaggguuccuccgcaagguucguccacgga
gggugagucagggccuaagaucaggccgaaaggcguagucgauggacaac
aggugaauauuccuguacuaccccuuguuggucccgagggacggaggagg
cuagguuagccgaaagaugguuaucgguucaaggacgcaaggugacccug
uuuuucaggguaagaagggguagagaaaaugccucgagccaauguucgag
uaccaggcgcuacggcgcugaaguaaccgaugccauacucccaggaaaag
cucgaacgaccuucaacaaaaggguaccuguacccgaaaccgacacaggu
agguagguagagaauaccuaggggcgcgagacaacucucucuaaggaacu
cggcaaaauagccccguaacuucgggagaaggggugcccccucggggguc
gaagugaccaggcccgggcgacuguuuaccaaaaacacaggucuccgcaa
agucguaagaccauguaugggggcugacgccugcccagugccggaagguc
aaggaaguuggugaccugaugacaggggagccggcgaccgaagccccggu
gaacggcggccguaacuauaacgguccuaagguagcgaaauuccuugucg
gguaaguuccgacccgcacgaaaggcguaacgaucugggcacugucucgg
agagaggcucggugaaauagacaugucugugaagaugcggacuaccugca
ccuggacagaaagacccuaugaagcuuuacuguucccugggauuggcuuu
gggcuuuuccugcgcagcuuagguggaaggcgaagaaggcccccuuccgg
gggggcccgagccaucagugagauaccacucuggaagagcuagaauucua
accuugugucaggaccuacgggccaagggacauucucagguagacaguuu
cuauggggcguaggccucccaaaagguaacggaggcgugcaaagguuucc
ucgggccggacggagauuggcccucgagugcaaaggcagaagggagcuug
acugcaagacccacccgucgagcagggacgaaagucggccuuagugaucc
gacggugccgaguggaagggccgucgcucaacggauaaaaguuacucuag
ggauaacaggcugaucuuccccaagaguucacaucgacgggaagguuugg
caccucgaugucggcucuucgccaccuggggcuguaguauguuccaaggg
uugggcuguucgcccauuaaagcgguacgugagcuggguucagaacgucg
ugagacaguucgguccauauccggugugggcguuagagcauugagaggac
cuuucccuaguacgagaggaccgggaaggacgcaccucugguguaccagu
uaucgugcccacgguaaacgcuggguagccaagugcggagcggauaacug
cugaaagcaucuaaguaguaagcccaccccaagaugagugcucuccua

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mmm The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): V88 N90 G92 T121 K124 I127 F130 L138 S174 H178 S182 G184 R186 G204 D206
• Binding residue (residue number reindexed from 1): V50 N52 G54 T83 K86 I89 F92 L100 S136 H140 S144 G146 R148 G166 D168

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mmm, PDBe:5mmm, PDBj:5mmm
• PDBsum: 5mmm
• PubMed: 28007896
• UniProt: P82192|RK5_SPIOL Large ribosomal subunit protein uL5c (Gene Name=RPL5)