Structure of PDB 5mmi Chain Y Binding Site BS01

Receptor Information

>5mmi Chain Y (length=77) Species: 3562 (Spinacia oleracea)

RRICPFTGKKSNKANRVSHSNHKTKRLQFVNLQYKRVWWEAGKRFVKLRL
STKALKTIEKNGLDAVAKKAGIDLRKE

Ligand information

>5mmi 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: 5mmi The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): R72 R73 K80 N83 K84 A85 N86 R87 S89 S91 N92 H93 K96 R97 Q99 F100 V101 N102 Y105 K106 R107 K118 R120 T123 K124 K127 K131 N132 K139 R146
• Binding residue (residue number reindexed from 1): R1 R2 K9 N12 K13 A14 N15 R16 S18 S20 N21 H22 K25 R26 Q28 F29 V30 N31 Y34 K35 R36 K47 R49 T52 K53 K56 K60 N61 K68 R75

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:5mmi, PDBe:5mmi, PDBj:5mmi
• PDBsum: 5mmi
• PubMed: 28007896
• UniProt: P82245|RK28_SPIOL Large ribosomal subunit protein bL28c (Gene Name=RPL28)